diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000175.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000175.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0551de4a98574fa7b12985ae8af5e9d08b5172a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000175.fa
@@ -0,0 +1,39 @@
+>GCF_002008305.4_00002
+MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI
+EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL
+PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK
+EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV
+DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD
+DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV
+VSDYRYLVMPVRIA
+>GCF_003691675.1_02007
+MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI
+EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL
+PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK
+EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV
+DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD
+DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV
+VSDYRYLVMPVRIA
+>GCF_005280335.1_00422
+MPVLSGLLITAEAGVVSIASFDYETSARLEIEADVETDGQVLVSGRLLNDIVRALPHAQV
+TVELDGGKVVVTCRSSRFALATMPVGDYPALPELPTPAGTVDGAAFAHAVAQVTVAASKD
+DTLPILTAVKVEIEGDTMTFLATDRYRLAMKEIRWTPADPSISTSLLVKARTLTEVAKSL
+GAGGDLEILLGEGTDLVGFSSGGRRTTSVLVDGEYPKIRSLFPETSPIQAVVDTAALVEA
+SRRVALVAERNTALRMVFTDGQVTLDAGTGDDASANESVPCTLEGEDITVAFNPSYLSEG
+LAVVDQPQVRFAFTSAPKPALLTGVNQEDGVVSDYRYLVMPVRIA
+>GCF_020097155.1_00375
+MKFTVARDILSDAVSWAARSLSPRPPVPVLSGLLVTAEAGLVSIASFDYETSARLQIEAD
+VEDEGQVLVSGRLLNDIVRALPNAPVTLELDGGKVLVTCRSSRFQLATMPVADYPALPEL
+PEPAGTVDGAAFAHAVNQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMTEIR
+WNPADPAISTSLLIKARTLTEVAKSLGGGGRLEIMFGSSHDLVGFSSGGRRTTSVLVDGE
+YPKIRSLFPETSPIQAAVDTEELIAASRRVALVAERNTALRMVFTDGQVTLDAGTGDDAT
+ANESVPCTLEGEEITVAFNPAYLSEGLAVVDQPQVRFSFTAAPKPALLTGVHEEDGTVSD
+HRYLVMPVRLT
+>GCF_023573625.1_00002
+MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI
+EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL
+PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK
+EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV
+DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD
+DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV
+VSDYRYLVMPVRIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000176.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000176.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b4eec98e4ce574b0da47bb81b6297c7334e00b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000176.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_00003
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRAVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLSLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKSSRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAVDMRRTLETQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG
+>GCF_003691675.1_02008
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRAVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLGLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKAGRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAVDMRRTLETQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG
+>GCF_005280335.1_00421
+MHLSHLTVADFRSYRWADLELGPGSTVLLGANGVGKTNLVEAVGYLGSHQSHRVSSDAQL
+VRFGQDRARIAGRVHRGSRTVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLNLVTGEPGGRRRLLDQLMVQLRPALGEAAADFERVLRQRNALLKSARKARRWGPEEEA
+TLEVWDEHLCAAGARLLHGRLHVLRLLAHPLREMYGALTNGSKAATYAYESTVPLARGTH
+AEVPPVAELAADMRRALVAQRDEEQARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRLAAYDVLVADDPDPDGRPVLILDDVFAELDAARRRRLAALVGRAEQVIVTAAALE
+DVPAELAGPRVLIRQDAEGSEAVPAAAPVEGDIRAPRGAGGTEGEAPGARRGRRRRRRHA
+PADPAEDDPDG
+>GCF_020097155.1_00374
+MHLSHLTVQDFRSYRWADLELSPGSTVLLGANGVGKTNLVEAIGYLGSHQSHRVSQDAQL
+VRFGQDRARIAGRVHRGARSVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLGLVTQDPGGRRRFLDQLMVQLRPALGQAAADYERVLRQRNALLKSARKARRWGAEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLAHPLQEDYAALTNGSKTATYSYESTVPAARGTH
+VQAPPVAELAASMHAALVEQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRLAAYDVLVADDSDPEGRPVLILDDVFAELDAARRERLAGLVGRAEQVIVTAAALA
+DIPASLAGHRVLIRQDAEGSEAVAAAEPVEGDIRAPRPGAAPGAAASEAEEPEDGDARA
+>GCF_023573625.1_00003
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRTVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLSLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKSSRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAADMHRTLEAQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000177.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87810aff7f9379fb7a3c362f672e19e8475e821a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000177.fa
@@ -0,0 +1,23 @@
+>GCF_002008305.4_00004
+MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTPSAGRERQD
+RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED
+SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR
+GPRDTYG
+>GCF_003691675.1_02009
+MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTPSAGRERQD
+RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED
+SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR
+GPRDTYG
+>GCF_005280335.1_00420
+MSSVFGRLIRDRGWSTPVAVGSVLTRWDELVGPEIALHCRPESFEDSVVRVRTSSTAWAT
+QLRLMTPVLLQRFDDALGPGVVTRLEVAGPQAPSWRKGPRTVRGGRGPRDTYG
+>GCF_020097155.1_00373
+MRERSPEPDALAELPPDRPDLALVQLRRVRDAARQRGEAPLNRRGTAAGLAQSMAGSEAA
+AAAGGAVARSGHRRPGAPADRDPAVVSSVFGRLIRDRGWSTPVAVGSVLTRWADLVGPEI
+ALHCRPESFEDSVVRVRTSSTAWATQLRLMSPMLLSRFDEALGPGVVTRIDVAGPAAPSW
+RHGPRTVRGGRGPRDTYG
+>GCF_023573625.1_00004
+MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTTSAGRERQD
+RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED
+SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR
+GPRDTYG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000178.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000178.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68e3eb0e305ac0d74087550a972610b3a6c8b900
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000178.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_00005
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEDAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDNVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV
+>GCF_003691675.1_02010
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEEAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDDVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV
+>GCF_005280335.1_00419
+MLAAPSPDAAPETPEAPALAKDRRVPGEYGASAITVLEGLEAVRKRPGMYIGSTGPRGLH
+HLVYEVVDNSVDEALAGYASGIDVTLQADGGVRVADDGRGIPVDLHPTEGKPTVEVVMTI
+LHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSFADGGVPQGELVQ
+GEATDATGTVQTFYPDPEIFDSIEFDWETLRARFQQMAFLNKGLRITLTDERVQEDNEVV
+DDEIAGEAAAEENAEQGLDEAAAQAPQRRQVTYLYENGLLDYVQHLNSAKKVDFVHEDVI
+AFEAEDAEAGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEGFRAALTSLVNRYA
+REKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSEARAFVSKAVTDHL
+GDWLERNPGPAKEVIRKAIMASHARMAARKARDNARRKSPLESFGMPGKLADCSSKDPSR
+CEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGNAEIQSMITAFGTN
+IGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAGHVFLAQPPLYRIK
+WSNAPHDYVFSDAERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQELWDTTMDPEHRT
+LLQVSMEDAAAADAVFSMLMGEDVESRRNFIQQNAKDIRFLDV
+>GCF_020097155.1_00371
+MVDAAPEQPEQPSAPAPDTNPAHQVQEYGASAITVLEGLEAVRKRPGMYIGSTGPRGLHH
+LVYEVVDNSVDEALAGFADGIDVTLQADGGVRVQDNGRGIPVDIHPTEGKPTVEVVMTIL
+HAGGKFGGGGYAVSGGLHGVGISVVNALSTRVETEIRRQGHAWRMSFANGGIPQGELVKG
+EATEETGTVQTFWPDPEIFESVEFDYETLRARFQQMAFLNKGLRITLTDERVQEDNEVQE
+DEIVGEGTAGEDAAAENGLDDEQTPQRRCVTYLYEDGLLDYVKHLNSSKRAELVHEDVIA
+FDAEDAERGMALEVAMQWTTAYSESVHTYANTINTHEGGTHEEGFRSALTALVNRYAREK
+EILKAKDDNLSGEDIREGLTAVVSVKLSEPQFEGQTKTKLGNSEARGFVSKVVTDHLGDW
+LERNPGPAKDIIRKAVQASHARMAARKARDNARRKSPLESFGMPGKLADCSSKDPARCEV
+YIVEGDSAGGSAKQGRNPDTQAILPLRGKILNVERARLDKALGNAEIQSMITAFGTNIGE
+EFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAGHVFLAQPPLYRIKWSN
+APHDYVFSDEERDAAIEAGLARGWRYPKDNGVQRYKGLGEMNYQELWDTTMDPEHRTLLQ
+VTMEDAAAADQVFSMLMGEDVESRRNFIQQNAKDIRFLDI
+>GCF_023573625.1_00005
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEEAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDDVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000179.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000179.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4ebf8ba7891d59e7916c368c735a1988e7ca9d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000179.fa
@@ -0,0 +1,82 @@
+>GCF_002008305.4_00006
+MSDETTPQTPDEPVEGAPTPQPPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDY
+AMAVIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTA
+IYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVD
+MQDNYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEAT
+REELLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVT
+ELPYMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLY
+KHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILR
+GLLKALDMLDEVIATIRRSASAEVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQ
+DEYDDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLI
+PEEEMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFT
+NFGRVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGL
+VKKTPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALR
+PMGRATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRPQNRGGLGIK
+VAKLVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDR
+IVAVTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ
+>GCF_003691675.1_02011
+MSDETTPQTPDEPVEGAPTPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISRKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ
+>GCF_005280335.1_00418
+MSDETTPQTPDESAEVPETPETGQDVAVEQYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRSFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPAVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLTRVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTVFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DELMARIAEYDRILESPQRQREVISEELGEIVAKHGDDRRTEIMAGYDGDMSMEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQGRGGKGVRGATLRGDDIVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLTGYDRAPYLVLATRNGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDALLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEHEMEAQADAEAAEDPVSEGSAAAAGVLPEGEPEALVGAEATAGAAADADVRLDA
+DIDPTDPAAAPEGLFEEDADGEGADGGEQ
+>GCF_020097155.1_00370
+MSDETTPGTAPGTPQDGHDADQTPQIGQDVAVEHYVLPEGAADKVEPVDLESEMKRSYLD
+YAMAVIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRSFNKSARVVGEVMGNYHPHGDT
+AIYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTV
+DMQENYDGKQLEPTVLPARFPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEA
+TREELLAALMQRIKGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVV
+TELPYMTNPDNLAAKIAEMVRDGKIAGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNL
+YKHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIEVIVRRTAFRKKKAEARAHIL
+QGLLKALDMLDEVIATIRRSASAEVAREALKTLLDIDDEQAQAILQMQLRQLAALESQKI
+QDEYDELMARIAEYTAILESPQRQREVVSDELGELVAKHGDERRTEIVAGFDGDMSIEDL
+IPEEEMVVTITRGGYVKRTRIDQYRSQARGGKGVRGAALRGDDVVEHFLTVSTHHWLLFF
+TNLGRVYRIKTYELQEAGRDAKGQHVANLLAFQPDERIAQIQPLAGYDGDAPYLVLATRN
+GLVKKTPLEDYDTNRQAGLIAIKLREGDELVSARVVSAQDDLLLISRQGQSVRFTATDEA
+LRPMGRATSGVTGMKFRGDDALLAMDVIRAGDEDSYVFTVTDGGFAKRTHVDEYRTQGRG
+GLGIKVARLVDDRGELAGGLVVGEDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVVFAKP
+DKRDRIVAVTLNNEDEIEATADERAAAEGAAPEAAGAADGAGVPLDAVNDQTDPAAAAEA
+EAAGEDADGGEQ
+>GCF_023573625.1_00006
+MSDETTPQTPDEPVEGAPTPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000181.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000181.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02bdbad95a053eaf5598cd79950db99d9bc01cb2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000181.fa
@@ -0,0 +1,10 @@
+>GCF_002008305.4_00009
+MGRLARVALVVSAAAAAYGARLWRENSARKDVWATATDDLPEDADGVEPAPED
+>GCF_003691675.1_02014
+MGRLARVALVVSAAAAAYGARLWRENSAGKDVWATATDDLPEDADGVEPAPED
+>GCF_005280335.1_00415
+MGRLARVALVAGAAAAAYGARLWQQNREGKDIWATATDDLPEDAEGVEPAPED
+>GCF_020097155.1_00367
+MRLARIATLVAGAAAAYGVRSWRQQREDKAVWASATDSLEPRKAPAEDGRGEDEETPQG
+>GCF_023573625.1_00009
+MGRLARVALVVSAAAAAYGARLWRENSAGKDVWATATDDLPEDADGVEPAPED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000182.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000182.fa
new file mode 100644
index 0000000000000000000000000000000000000000..285bfc7972d62cd82341290f8442dad914a3a817
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000182.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00011
+MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGVVAFLVGSLLNASIVVRLKERMKERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR
+>GCF_003691675.1_02029
+MNTTTHAPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMKERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR
+>GCF_005280335.1_00386
+MVLDGPVNTTIDTPSPDQPVSGQGTPAYARVPASYYDIFVGVFVALLILSGVTAAKLFYG
+PTVPVFSDVFYGGGPLIFDGGAFLFPFAYIIGDILAEVYGWRRARRAILLGFAMLVLAAL
+TYTVVSWTTPVEGFEVWDQALAPMLRITVAGFVAFLAGSLINATIVVRLKERMRERHVAF
+RLILSTIVGQFFDTLIFCTIAFAGTITLLELANYTFTGFLYKTLVEILIVPITLLVIRRV
+KASEPTYRPASSPARAAADAA
+>GCF_020097155.1_02181
+MNTTPASRSEPTSGQGAAASAAAPHSHYDIFVGVFVALLILSGVTAAKLFYGPTVPGVSD
+VFYGGGPLIFDGGAFLFPLSYVVGDILAEVYGLRRARRAIYIGFAMLVVAALTYRLVALT
+TPVEGFEAWDQALAPTLRITLAGLAGYIVGSLLNATVVARMKARMAERAVAWRLIASTLV
+GEFFDTLIFCLVAFAGTITLADLANYTVTGYVYKCLVEICIVPVTLLVIRWLKRHEPTYR
+AQPTPAPVSAPTA
+>GCF_023573625.1_00011
+MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMRERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000183.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000183.fa
new file mode 100644
index 0000000000000000000000000000000000000000..269b97a53ff369ecbab1d14913cb10d9d32d6e91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000183.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00014
+MARKTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS
+AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE
+EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVQRLRQGAEQYAGAAEK
+DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV
+EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR
+>GCF_003691675.1_02032
+MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKQEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRHRGGRKAKQLRRDGRQAAKGARKDAQRSAALFSDRAGQA
+KDAAAAGGLTLAGLLATGLSALQEQGGKVGPQVQARLADAGDYAQRRKEEVLPVAAARLA
+DGAAHARKTAHDVEVPDALEQALIRLTGDKAIVQRLRKGAEQYAGAAEKDLNRAAGRRTS
+RSGGRAWIVAGMAAAAAGAGYALWRLTKPVQDPWTAPVPGPIAANIPVVEANNPYAQQQK
+VVAEAGSAAAGEGVRVDTAAPDPVAAANAKVLGVQPGQQR
+>GCF_005280335.1_00383
+MARTTLNDEIQHDGGADTFVTRQTENLRHWAAPKLEAARTWGEYGAAFTGVGASVAAEEG
+RRAAHDAKQEYGPRVEKQAKRAGDAVADRYAKLAPAVATGAGVLQDVLHRLQEQAQEAGH
+EAQKQFADARKDAEKAAEKGRKRGAKKAKQVRRAGRGARKDVTKAARGARKDARQAGSFL
+ADRAGQAGSAAAAGGLTLAGALAAAVNALQEQGEKLAPQVQARLSDAGDYAQRRKEEVVP
+LAAARLADGAAHARKTAHDVQVPDAVEQALIALTGDKAIVRKLRKGAEQYAGSAEKDLNR
+AAGRKARSGGRGWILGGMALAAAGAGYALWRLTKPVQDPWTAPVPGPITANIPVVEANNP
+YAQQQKVVAESGSAAAGEGVRVDTAAPVTTAVPAQDPVAEANAKVLGTDR
+>GCF_020097155.1_00364
+MARTTLSNEIEHNGSADTFFARQAENLRHWAAPQLENARAWAEVTTGFGQVGGKVAAAEG
+RRLAEEEVAPRVKDSAERVNAAAKGRYEKAAPVVATGLGAAGTVLQQLLEAAQDKAQQAG
+QQVQDLAEQAQKDAKKSAKRTRKDAKKAGKRVSKKADKAQSLFASKAGDAKGAAAAGGLN
+VAGLLAAAVAAAQDRGQELAPQVKGRVEQAAQYAQDRRAEYAPKAAASLAGVAGRAEKAA
+GDVTVPASVEQLLVKLTGDKNAVKHLRQDVQSRARETQKGLKKQARQESRRGGATGWIIA
+GMAAAAAGAGLAVWKLTKPVQDPWAAPVPGPITANIPVVQADGTVNPYAKQEQAVAEARA
+AQGGMVNVRPQVG
+>GCF_023573625.1_00014
+MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS
+AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE
+EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVKRLRQGAEQYAGAAEK
+DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV
+EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000184.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..492aa1c26872ae26be4b7e8b2abd6584a3ccdd98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000184.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00015
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
+>GCF_003691675.1_02033
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
+>GCF_005280335.1_00382
+MARMANATHIATIKTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGVGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEESQQVVDRLNAVATDPRDRPLEDVVIESVEIAEA
+>GCF_020097155.1_00363
+MTRMTNATQIATIHTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDQLNSVATDPRDRPLEDVVIESVEISEA
+>GCF_023573625.1_00015
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000185.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000185.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6814526f225df60889d9e60548ae115b41fd03b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000185.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00016
+MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTVAPAGAAASVPARRRTGFTASPVTWILLAVTTVVYAAQWMTRDQASGVTEA
+LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY
+VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS
+FLLPGVAWQVHMGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQVAGLVVVAAALAALTV
+LGAARVTVAGLLG
+>GCF_003691675.1_02034
+MSTTPSDPYGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTSPPAAGAAATVPARRRTGFAASPVTWILLAVTTVVYAAQWMTRDQASGVTE
+ALWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLAL
+YVLSAVGGAVFALWASDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVF
+SFLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARLPSVGAQVAGLVVVAAALAALT
+VLGAARVTVAGLLG
+>GCF_005280335.1_00381
+MDCAAQGGAPAGTTTSPAAVGSPGPGGVGMAGAAGRGAPARRRTGLAAAPVTWTLIAVTV
+AAYVAQWATRDTVPGVTEALWYAGLYTSPFGLEPWRMATYALVHDLSGPTHLILNMLALW
+VIGRVLEPALGWWRFAALYVLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLVTRV
+RGGQVRSIAVLIGLNLVISFLLPGISWQVHVGGLITGAVVALVYSLAGGLRPGRASAPSA
+GAQAAGLVLVAAVLAVLTVLGADRIGLDAVLR
+>GCF_020097155.1_00362
+MSTTPSDPHGPDVAEGTPPVCPRHPGRAAYVRCASCADPVCLDCQRPAAGGLTLCPDCAA
+RLAAGVPGPASGTTTSPAPASAGAGRGGVGAALRAAPVTWTLLAVTLLVYAGQWLTRGSR
+TGVTESLWYAGAYTSAIGMEPWRMLTYALVHDVSGPTHVALNMVALWVIGRVLELALGWW
+RFLALYLVSALGGAVFALWTADPLQPVVGASGAVYGLFAALFAVTRFRGGQVTSIAVLIG
+LNLVFSFLMPGISWQVHVGGLLTGAVAGALLVSAGGPPGRSAAADGTARRSSAGVHVAGL
+VLLAAVLAVLTLVGAARLSPAALLG
+>GCF_023573625.1_00016
+MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTVAPAGAAASVPVRRRTGFAASPVTWILLAVTAVVYAAQWMTRDQASGVTEA
+LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY
+VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS
+FLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQAAGLVVVAAALAALTV
+LGAARVTVAGLLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000186.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000186.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4266eac4b16937da1417f44eb8f9614fd10845b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000186.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00017
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLLPIVQIGGWNILVGFGIALVGFLMMSRWSE
+>GCF_003691675.1_02035
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLFPIVQIGGWNILVGFGLALVGFLMMSRWSE
+>GCF_005280335.1_00380
+MAAPSGKRKDSARRKHEELEDARRGARRGSSAVTTDLGDVDPGPKPLSPVYKAVMFGLMI
+VGLLWIVVYYLTQGLFPIVAIGGWNILVGFGIALVGFLMMSRWSE
+>GCF_020097155.1_00361
+MATTSGKRKDSARRKRRELEQARSRRGRTASVSTDLGDVDATPAPLPRWYKAVMFGLLIL
+GLLWIVVYYLSQGLFPIPDAGGWNILIGFGIALVGFLMMSRWSE
+>GCF_023573625.1_00017
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLFPIVQIGGWNILVGFGIALVGFLMMSRWSE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000187.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000187.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c12c83815216a1347cea3bd9d10c000e057f9e72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000187.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00018
+MQSPEVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLATVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLESVGLSGAAERGGRLSPLVRQD
+>GCF_003691675.1_02036
+MQSPQVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLAAVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLESVGLSGAAERGGRLSPLVRQD
+>GCF_005280335.1_00379
+MSGTVPSPEVSVLVVDNYDSFVYTLVGYLEELGARTTVIRNDEVDAARALELAAEHTAVL
+ISPGPGAPADAGVSLDLIRAAADGGRPLYGVCLGHQAIAEAFGATVTHAESLMHGKTSLV
+RHGDHPMFAGLPERFTATRYHSLAAVRSTVDEAVLQITAETEDGVVMGLAHRSAPLWGVQ
+FHPESVLTEGGYRMLGNWLESVGLTGAADRGGRLSPLVRGD
+>GCF_020097155.1_00360
+MSTPPESAPTAVSVLVVDNYDSFVYTLVGYLQELGARTTVIRNDEVSPARALELAAQHDA
+VLISPGPGTPSEAGVSLDLIRSAADGGRPLYGVCLGQQAIAEAFGATVTHAESLMHGKTS
+VLTHTDHPMFAGVPARFTATRYHSLAAVRHTVDESVLEITAQTDDGVVMGLAHRTAPLWG
+VQFHPESVLTEGGYRMLGNWLESVGLVGAAERGGRLSPLVRAAD
+>GCF_023573625.1_00018
+MQSPEVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLAAVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLGSVGLSGAAERGGRLSPLVRQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000188.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000188.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d178f4a994e86088ce20287254225718911e73e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000188.fa
@@ -0,0 +1,66 @@
+>GCF_002008305.4_00019
+MDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGPDRAV
+AWTRGVLEALEHAHEEDIVHRDVKPANVMVTDTGTVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPPAP
+SDVDPDLPPAFDPVVLRALRKDPQDRFPTGAAFLAALEEAAADPHAGPGRHTPPLDAVHP
+ALVGAGGAVLGATPAEHGADVADVPTAAVPLTRPAPSVPAEPDTAQPQAVNHAVAGAGLP
+GAASAAQLAAAAAMDGPRPVTGGQPVTPGAAATPRPEPPPRDTPAPATATPRRVRRRVRR
+RTLLAAGVVLVALALVLAPWLAAALRTTAEVPAVVGLQQDEAVAALEDAGLVAVVSSAYM
+ADAPDGTVTQSDPPTGTEVPRGAEVRIRVSRGEEGIALSDSLHGLSEDAARRELERLGLR
+VSSVQYQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQL
+ALSAPELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTTSSWIAPTAEPSEPAP
+PSSEAPEPTPSASTSPSPPSSESPEPSESPEPSESAEPSPSPSASATPSPEPTTTATPSP
+TQSPSPPSAAPSTSSEPTEQSPSTSPTATPVDPLPTLTPDPEPSIDPPPST
+>GCF_003691675.1_02037
+MSVDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRK
+EARSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDR
+AVAWTRGVLEALEHAHEEGIVHRDVKPANVMVTETGAVKVMDFGIAHALADTSATTSQTQ
+AVVGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPP
+APSDVDPDLPPAFDPVVLRALRKDPEDRFPTGTAFLAALEEAAADPHAGPGRHTPPLDAF
+PPALVGAVLGAAAAEHGADVPTAAVPLTRPTPSVPAEPDAAQPQAANHAVAGAGLPGAAS
+AAQLAAAAAMDGPRPVTVGQPVMPGAAATPWPEPQGDTPAPATATPRRVRRRLRRRTLPA
+AGVVLVALALVLTPWLAAALRTTVEVPAVVGLQQDEAVVALEDAGLLAVVSSAYMADAPD
+GTVTQSDPPTGTEVPRGAEVRIRVSRGKEGIALSDSLHGLSEDAARRELERLGLRVSSVQ
+YQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQLALSAP
+ELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPYSEA
+PEPTPSASASPSPPPSESSEPSESAEPSPSPSASATPSPEPTTTATPSPTQSPSPTSAAP
+SEPTEQPPSTSPTATPVDPLPTLTPDPEPSIDPPPST
+>GCF_005280335.1_00377
+MEEQWTLNGRYRIDALIGRGGMADVFRGTDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSVASLNHPSIVSVYDTGEVSLEDGHHPVDCPYLVMELVTGRSLREVLHAEGAVGTERAV
+AWTREVLEALEHAHQEGIVHRDVKPANVMVTDAGSVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYATGCVLFELLTGRPPFTGDTPLAVAYQHVREAPPAP
+SEVDPDLPRAFDPVLLRALEKDPEDRFPTGAAFREALEAAAADPHAAVDADTAALDLVRA
+GAAGAGGAAVAAGREVRRDGARDSADVPTAAVPLTPAPAPAAPAEPAEPPGGEPRRGRGR
+AARRRLRRPAGGRRLRGRPAPGHRLPTPPSRGPRRPAPRPPPGSALPPPLPPPDGAAAGG
+AACRSPGCCWPASSC
+>GCF_020097155.1_00359
+MQGQRILHERYRVDELIGRGGMADVFRGHDLRLNRTVAVKMMRPDLARDPAFQARFRTEA
+RHAAALNHPNIVSVYDTGDALLDDGPQSVECPYLVMEHVDGRTLRELLDAGEVAWRDAVE
+WTRGLLHALDHSHRQRIVHRDVKPANVMVTRDGGVKVMDFGIARALSDTSAHTGQTQAVV
+GTALYLPPEQAQGARVDARSDLYAAGCVLFELLTGRPPFTGETPLAIAYQHVREEPPAPS
+AVDPSLSTEFDSVVLRALQKDPGLRHQHAREFLSALDFAAARAARAADDDAPTRVVPASG
+AAPLATGSGALAAAVAGSTAAGPTASGSTALGAGGAPEARPATGPPATTPLGAAAGPTEP
+LIAGHAVAGAAVPGAPSASQLAAAEAVETAPAAASTTGGSAGAGATSGAERAGRRHRLSW
+AVLAAVAAVAAVAAILALGAALLIGSRDPGPVTVPALAGRTEAEAVSALTGLGLRSAISP
+DYHSTEPDGRVLKVHPGAGAAVEPGSTVNLSVARGGEGVVLPTSLRGASEARVRQELARL
+GLNVASVEDTPSGELDRGALVQTDPVLGSRVPPGSAVVLHLADGTARVPSLVGMTGADAR
+TTLAALDPEMTVRFQGAAGADPDTGVVVLQDPAAGTVVDNTAMITLITSAEATPTASAVT
+VAPPDPALPSATTTTAPAEPSPGVPAPTTPAAPAVDTPAPAPATTPAPAPESSSTPGAGT
+DPAPTESAPTPDDGPGSTGTPSTEAPTEAPTDPVGTPAPSPSGEPVPQPSPSVEPLPEPT
+APTEAPTADPAG
+>GCF_023573625.1_00019
+MDEQRTLNERYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDRAV
+AWTRGVLEALEHAHEEGIVHRDVKPANVMVTDTGTVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPPAP
+SDVDPDLPPAFDPVVLRALRKNPQDRFPTGAAFLAALEEAAADPHAGPGRHPPPLDAVHP
+ALVGAVLGATPAGHGADVPTAAVPLTRPTPSVPAEPDTTQPQAANHAVAGAGLPGAASAA
+QLAAAAAMDGPRPVTAGQPVTAGQPVTPRPEPPPGDTPAPATATPRRVRRRVRRRTLLAA
+GMVLVALALVLAPWLAAALRNTVEVPAVVGLQQDEAVAALEDAGLVAVVSSAYMADAPDG
+AVTQSDPQTGTEVPRGAEVRIRVSRGEEGIALSDSLHGLSEDAARRELERLGLRVSSVQY
+QDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQLALSAPE
+LRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPSSEAP
+EPTPSASAPPSPPPSESPEPSESAEPSPSPSASATPSPDPTSATPSPTQSPSPPSAAPST
+SPEPTAQSPSTSPTGTPVDPLPTLTPDPEPSIDPPPST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000189.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000189.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f89313d64caa135670d60adeedf9505cfb875117
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000189.fa
@@ -0,0 +1,64 @@
+>GCF_002008305.4_00020
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSSILEKEKVLSPERTLRIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAADALRRKDTRGAVEAVPGLAVFLEEQGVADPSGAE
+TAPLDYDGLRTTHPRTEGIRTDGSPATAALPVTAAQPRTDDAARGPGAAGAAAVGAAGAA
+ASASTRDHEIAAVRDQQTRPGDVVDPGPPAGGGSAPARRRRANPWPLWALLGLVVFALLG
+ALLWPLLTGGRGDGGSAPATSQEESSVNVDPEAYKGRPVSEVRAELEGLGLAVREEDRDA
+QSPQGTVEEINPVGALQRGETVTLAVSTGEGVIPEGLVGQPVDSAIQTLRDRGFTVDRVD
+DPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPVPSASEEP
+SSEPSPSASDEPSPSPTAESPTATADPEPTQEPTEEPTTPTGDPTTESSGESTAPTGEPT
+TDPSADARGAEASSADATPSA
+>GCF_003691675.1_02038
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRNTAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEEGSAYLVMELVPGQPLSSILEKEKVLSPERTLGIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAADALRRKDTCGAVEAVPGLAVFLEEQGVADPSGAE
+TAPLDYDGMRTTHPRAEGTRADGSPATAALPVTAAQPRTDDAARGPGAAGAAAVGAAGAA
+GAAGAVASTRDHEIAAVRDQQTRPGDVVDPAPPAGGGSAPARRRRANRWPLWALLGLVVF
+ALLGALLWPLLTGGRGIGGSAPATSQDESSVRVDPEAYRGRPVSEVRTELEGLGLAVREE
+DRDAQSPQGTVEEINPVGALRRGETVTLAVSTGEGVIPEGLVGQPVESAIQTLRDRGFTV
+DRVDDPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPEPSA
+SEEPSTEPSPSASDEPSPSPTAESPTATADPEPTPEPSEEPTTPTGDPTTESSGESTAPT
+GESTTDPSADARGAEASSADATPSA
+>GCF_005280335.1_00376
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSAILEKEKVLSPERTLRIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDAPPPLPSTVPAPV
+RALIMCMLSKDPKERPTDATAASEAADALRRKDTRAAVEAVPGLAAFLAAEGVADPSGAE
+TAPLDYDGMRTAHPRPEGTRADGTPATAALPVTAAQPRTDDGARGSAATAAGAAGAAGLA
+GAAAAGARPANEEIAAVRDPQTRPSDVVQEAPPAGQGSAPVKRRRANRWPVFALLGLVLF
+ALLGALLWPWITGDRTPGGSTPSGTSQASSVSVDPEAYKGRPAAEVRAELERLGLVVREE
+DRDARNPRGTVEEVNPVGSLQRGETVTLAVSTGEGVVPDGLVGQPVDSAIQLLRDRGFTV
+DRVDDPSADGAEGEVVRVVPGEGQRHRYDTHVQLIVAGGAGGDEPAPTPEPSEPAEPTAE
+PSDEPTTEPTSEPTEEPTTEPTAPSEEPTEEPTEEPTTEPTSDPTGEPTGEPTADPTDDA
+GGSASPTAEESPTA
+>GCF_020097155.1_00358
+MRPTSGITLGGRYALTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSAILEKDRTLSTDRTLSIIRQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDIYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPALPDTISAPV
+RALIMCMLSKNPKDRPANATALSEAAEALRRKDVAGAVAAVPTLAAFLADQGVHSTGGPG
+DAETTALDAAPRTAPQPTVPLGTTTEPAAPATAALPVAAARPDVAATRSPRAAEPARSVP
+AAAPADPAPRTAKPRRRNRWPLFALLALVAFAVLGALLYPLLSGESGAGAGASSSTGTDA
+QVEVDAAAYRGRPADEVRAELEGRGLAVEEEQRDANDPQGTVVEVTPTGTLRRGDTVTLA
+VSTGQGTIPQDLVGQPADTVVGILRDRGFSVDRVDDPNADGATGQVVRVVPGEGQTHRFD
+TPVQVIVAGGTGSSPVTQSVVTAPTAAPASESPAEPAPASSSSGDPAPSSAQPTPSEAST
+EPSPESPAPTSESAAPSTEPSAGTPSTPDASGPSSQGSDAGSPSTDPAG
+>GCF_023573625.1_00020
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEEGSAYLVMELVPGQPLSSILEKEKVLSPERTLGIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAAEALRRKDTCGAVEAVPCLAVFLEEQGVADPSGAE
+TAPLDYDGMRTTHPRAEGIRTDGSPATAALPVTAAQPRTADDARGPGAAGAAAVGAAGAA
+GAAASTRDHEIAAVRDQQTRPGDVVDPGPPAGGGSAPARRRRANRWPLWALLGLVVFALL
+GALLWPLLTGGRGVGGSAPATSQEESSVHVDPEAYRGRPVSEVRTELEGLGLAVREEDRD
+AQSPQGTVEEINPVGALRRGETVTLAVSTGEGVIPEGLVGQPVESAIQTLRDRGFTVDRV
+DDPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPEPSASEE
+PSTGPSPSASDEPSPSPTAESPTATADPEPTPEPSEEPTTPTADPTTESSGESTAPTGEP
+TTDPSADARGAGASSADATPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000190.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebfa3a720a4b0a943561759f0e1f6f172bad835d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000190.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00021
+MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN
+ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA
+ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTIVSGMKAIMEAVVT
+E
+>GCF_003691675.1_02039
+MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN
+ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA
+ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT
+E
+>GCF_005280335.1_00375
+MNEAIRRTWTVMAAMMLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHDPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRVAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN
+ALSSHSATEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWPLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVKLGQDRIREVA
+ERFGFNDSFDYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRPDLTTVEEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGIGHQTIVSGIKAITEAVVT
+E
+>GCF_020097155.1_00357
+MNEAIRRTWTVMVAMFLVLAVAASVIQVVAADSLKENKLNNRQLFLEFGAPRGPILVDGT
+PVAQSVPSGDAYNYQRVYRDSLLYAPLTGHYSLAYGTAGMEKAMNGELAGTSSSQFLDRA
+LEIVTGSTPEGDQVELTLDSELQKLAYESIPDGVKGSVVATDPKTGRVLAMASKPSYDAN
+TISSHTRSEATAAMSAYEGVPGLTVGQNRPTQQRVAPGSTFKLIDLVAMLESGDYAPDQV
+LDVPAAWTLPGTRTQMSNFDGGRCNGVGRATLTWIVANSCNTPFAQAAVALGQDEIRSVA
+ERFGFNQDGSMPLPVTASVFPEDLDDAALAQSAIGQRDVQATALQMNMVAAGIANDGMVM
+EPNLVQAVRRPDLTTVSEFSPREHGRAMDPDVAHQVRDMMVATVEDGTASAAKSSTLQIA
+AKTGTAEKDGTANVNTWVTGFAPAQDPKVAVTIVYEDQNSSSAHTQAVESMQRIMEAVVA
+E
+>GCF_023573625.1_00021
+MNEAIRRTWTVMAAMLLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSGDAYHYQRVYHETELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN
+ALSSHSPAEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREAA
+ERFGFNDSFEYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIEAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT
+E
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000193.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000193.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1145a4e24eb0bcc2e29eaf3138fca61c9e4f0604
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000193.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00024
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGA
+AGAGSSAVDRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRAVPVGPGTAIRIGKT
+VMELEA
+>GCF_003691675.1_02042
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGA
+AGAGSSAVDRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
+>GCF_005280335.1_00372
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGV
+AGAGSSAVDRPAPASTPAPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
+>GCF_020097155.1_00354
+MNELAVAVLRLGLLLALWILIISIVLSQGRDLVVGRRNKLRLEQARRDAGLVTAVPAAGA
+HAASADRPAPAATPAAERPAPVPPAPAPRLARTLRITEGPLAGQTVDLGGRPLLIGRAQD
+ADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTFVDGDPVTRTLPVGTSSTIRIGKTV
+MGLED
+>GCF_023573625.1_00024
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGV
+AGAGSSAADRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000200.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000200.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e45d61a57228e9ca24423623fbdffe41dfab793b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000200.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00042
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAATTIGGTGAALGGILV
+TGLLLTVIGVIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVAFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVREAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMAAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEQFEASEAGRLG
+>GCF_003691675.1_02055
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIGGTGAALGGILV
+TGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEQFEASEAGRLG
+>GCF_005280335.1_00358
+MSSSPSRPAPGFGWRLHGDGRTITSGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGVGTLLFLLLTGNRLPSYLGSSFAFIAPITAATTAGGVGAALGGVLV
+TGVLLAVIGLIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPLTTFGTAL
+AIVLTAVLFRGLLGRLSILVGIVVGYLLALAQGQVDFTAVGEAGWLGLPPFHAPELHWNL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTTLSGLGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGVMG
+VRIWVQNRVDFSSTINLMTAGAGLIIAIADPQLVLGGLVFGGITLGTIAALVVYHLMTAI
+ARVRGTEPVSEDDEAYEASEAGRLG
+>GCF_020097155.1_00300
+MSSSPTPSAPRAGHVPGPGPAVRSWRLHGDGRTITPGTVVAPDERLSWGRTVGIGVQHVM
+AMFGATVLVPAITGMPATTALLFSGLGTLLFLLITGNRLPSYLGSSFAFIAPLTAASASH
+GVGAALGGIAATGVLLMVIGVVVGWAGTGWIHALMPPAVMGTIVALIGLNLAGATTQAMQ
+EVPLTTFGTALAVVLTAVLFKGLLGRLSILVGIVVGYLLALAQGQVDFTAVGQAAWVGLP
+PFHTPELHWSLLPLFLPVVLVLIAENIGHVRTVGLMTKRDLDPLTGRALLADGLATTLSG
+LGGGVGTTTYAENIGVMASSKVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG
+IILYGMIGVMGVRIWVQNRVDFSNTINLMTAGAGLIVAIANPELVVGGLVFGGITLGTLT
+ALVVYHLMTLVARVRGTEPVDEDTEDPASYRAAEAGRLG
+>GCF_023573625.1_00037
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIGGTGAALGGILV
+TGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEEFEASEAGRLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000204.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000204.fa
new file mode 100644
index 0000000000000000000000000000000000000000..528cc4cc26dd5f99bda1bc5d01c0b6df196cb223
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000204.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00046
+MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID
+GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVVLVSHDADFAPQLT
+DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPYE
+FL
+>GCF_003691675.1_02059
+MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID
+GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVVLVSHDADFAPQLT
+DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPYE
+FL
+>GCF_005280335.1_00349
+MGRRADAPAGPGRAVVVPTTTSSPAPASAPVHTPAPAPATSSAPAGSLGQVSESTTYLLV
+DGENIDATLGTSILQRRPQPDERPRWNRLLSFMGEHWDQPVKGLFFLAIDGDIPVPFVQA
+LTAIGYKPIMLRGAGKVVDIGIQKTMEALQEREDDVVLVSHDADFAPQLTDLAATPDRRT
+AIIGFEEFLSHELRRIPDVEFFDLEYGVGAFDTPLRRLRVIDIDEFDPLEFL
+>GCF_020097155.1_00294
+MSRRADLPTGPATAVPAAPAAPVSPTAEDRSAATPADTLDTMSARTTYLLVDGENLDATL
+GMSVLNRRPNPEERPRWNRVLRHVERAWGQEVRPLFFLAVDEDGDIPFGFVQALTTMGYQ
+PILLRGAGKVVDIGIQRMAEALIGRDADVVLASHDADFAPQMLDLAAHGHKIAVMGFDEF
+MSAELRAVNGMEVWDLEHDVAAFDVPLPRLRVIDIDDFDPRDFL
+>GCF_023573625.1_00041
+MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID
+GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVILVSHDADFAPQLT
+DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPNE
+FL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000205.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000205.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2eec9f34f2f6d37a1969dd2adabf174a4bd66a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000205.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00047
+MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA
+ALVGVGARLEAEWLGRGRAVPRALVRAAALCGAAWLTGHFGAAVVNVLAHLAVLTVIMAL
+LAALPLAAHLVLAVLAGGGGLLLAATPTADVVDRLVPLAQALGLSRATLTPYVSAFLTDG
+PYRLPLFLTWALLGAVLVRTVHGTTTAAPARSARLTGLAWAAGGIALAGVVLALSRTQTG
+AAPVPYTATPAEALLDTGLVLTVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR
+RLGPGPWRSATGTDDTWFNLAVLVAGALLLPLLWRAVVRIGPFRAGPLEGVVRLLTAPFD
+RAR
+>GCF_003691675.1_02060
+MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA
+ALVGVGARLEAEWLGRGRAVPRALVRAAALCGAAWLTGLFGAAVVNVLAHLAVLTVLMAL
+LAALPLAAHLVLAVLAGGGGLLLAATSTADVVDRLVPLAQALGLSRATLTPWVSAFLTDG
+PYRLPLFLAWALLGAVLVATVHGTTTAAPARRARLTGLAWAAGGIALAGVVLALSRTQTG
+AAPVPYTATPAEALLDTGLVLAVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR
+RLGPGPWRSATGADDTWFNLAVLVVGALLLPLLWRAVVRVGPFRAGPLEGVVRLLTAPFD
+RAR
+>GCF_005280335.1_00348
+MPRVSSRPHTGRDRLVWVDVARGVALVSMFVAHVAPSGGPAGVLNLSEHLTAALFAALVG
+VSARLEVQGLGVGRALVRAMVRAAALLGAAWLTSLFDAAVVDVLTHLAVITVLMALLAAL
+PLAVHLVLALLAGGGGILLTASGTLAVADALAPAARALGLDPAELVPAVAGFLTAGPYRL
+TAFLGWALLGAVLVRTVHGTTTALPRSGRLVGLGWGVGGVVLAGLVILLSRVQTGAAPVP
+YTGTAAEILVDTGLVLGVLGLCAAVVPSRPSPATDLLAVPGSMTLSVYVAHQAYLGWVLT
+AGPGPWVDGRGADDTWFNLAVLLAGGILLPLLWRGLVRVRPFRAGPLEGVVRLVTDPIGR
+RSRGEH
+>GCF_020097155.1_00295
+MTLAAGHRLTWVDVARGLALVSMFVAHTAPTGGPGGVLNLSEHLTAALFAALVGVSAHLE
+QRRHGFWRAFLRAVVRAAALCGAAWLTSHFGAAVVDVLTHLAVLTVLMSVLALLPGLVQL
+LLVPAAAWAGVRVGALTADDVAARLEPARALVPAQVRPGPAVVAEQAAAFFTVGPYFLLF
+FTAWALLGAVVVRSVQGGGLRAALRLGGHPGPGLGGRAAGGVWAGVGLLVGGAGVALARQ
+RTEDSPVPYEATWDYALLAAGLVLIVLGACAAVVPSHVPWLTAVLAVPGSMTLSVYVAHQ
+AYLGWVLRAGPGPWLSELGTDDTWFNVGALCAAGLLLPLLWRALVRAEPWRRGPLEGPVA
+LVTHGLARR
+>GCF_023573625.1_00042
+MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA
+ALVGVGARLEVEWLGRGRAVPRALVRAAALFGAAWLTGLFGAAVVNVLAHLAVLTVLMAL
+LAALPLAAHLVLAVLAGGGGLLLAATPTADVVDRLLPAAQALGLSRATLTPWVSAFLTDG
+PYRLPLFLAWALLGAVLVATVHGTTTAAPARRARLTGLAWAAGGIALAGVVLALSRTQTG
+AAPVPYTATPAEALLDTGLVLIVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR
+RLGPGPWRSATGADDTWFTLAVLVAGALLLPLLWRAVVRIGPFRAGPLEGVVRLLTAPFD
+RAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000206.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000206.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b3d6d09196a63b30d375f0bb43428011c70fe09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000206.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00050
+MAALTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPLAGLGAETATLDLTD
+ETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEADYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKATRDAETPLRS
+AAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGT
+>GCF_003691675.1_02063
+MAALTDRAVLIAGATSASGRAATRTLLDAGAHVVPTGRDAAKLAPLAALGAETAALDLTD
+EAAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLTGQTEDDYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKAARDAEAPLRS
+AAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD
+>GCF_005280335.1_00353
+MGTLTGRTVLISGATSASGLAAARALLAAGADVVATGRSPERLAPLAALGADTAALDLSD
+EAAVRGLVEDLHARGVRVDGLLHLVGGWRGGGGLAGQSEEDYRALESSLTALRHVSRALD
+DDLRASSAGRLAIVSSTAVARPLAGGAAYAAVKAASEAWTRAVAQGWDKAARDAGTELRG
+AAVVLRVKSLAGLEDRLAEQFVRLWSADAAQLNDSILAVQEKETA
+>GCF_020097155.1_01218
+MSAPAAPDLTGALVLVTGASSGIGSALARGLAAAGADLVLVARRAGRLAALADELRAAHR
+TEVTVLPRDLAAPDAGPALRAELSSRGPRVTGLVNNAGFGSGLPFGREDPARLEAMPAEE
+ERGRERVLCVSPSSTGTEFFDVAGTPGAGGGFARRAAPDDVAAAVLRVLARRGGPAEVVP
+HDRAVTVAARLLPRTVLRGMGAMHRRGAARR
+>GCF_023573625.1_00045
+MAALTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPLAELGAETAALDLTD
+ETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEEDYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKAARDAEAPLRS
+AAVVFRVRSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000208.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000208.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4054b463cd025dfbff8923cc6f28eadc03d3da7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000208.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00055
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGRDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGHAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHRQQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLKQVQAEAQKLVDAVIG
+>GCF_003691675.1_02068
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYRTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGQAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLTQVQAEAQRLVDAVIG
+>GCF_005280335.1_00342
+MTEHTAAPPASERPGTPALPQDLIDVDALLTAYRTGRPDVSDPAQKVVFGTSGHRGSALK
+TSFNDDHIAAITQAVVEYRAEHGITGAVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRDLTPAGFSADGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANALLAAGLEGVRRVAAADVDGHAKLGGFDFLDRYVTDLPDVID
+VEAIREAGVRIGADPMGGASVAYWGEIARRHGLDLTVVNPDADPRFGFMTLDWDGKIRMD
+CSSPHAMASLIERMTPDADGQAPYDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHRERWPADAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVKLDGGPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGSPAYARIDAPA
+TAEQKARLKTLSPDDVTVTELAGETILATLTNAPGNDAPIGGLKVVTQNAWFAARPSGTE
+DVYKIYAESFRGPEHLKQVQEEAQRLVDAVIG
+>GCF_020097155.1_00281
+MSTPAAGRAGTPALPEDLIDVEALLAAYRDLHPDPADPAQKVVFGTSGHRGSALKSSFND
+DHIAAITQAVVEYRAEHGITGAILVGKDTHALSGPAQDTAVQVLLANDVEVLVDSRGGFT
+PTPAVSHAILHLNAGRDLTAAGFSADGDNAGLVDGLVITPSHNPPADGGFKYNPPHGGPA
+DTDATSWIAARANDLLAARLDGVTRLAPEDVEGHAKLGSFDFLDRYVTDLPQVIDLDAIR
+EAGVRIGADPMGGASVAYWGEIGRRHGLDLTVVNPDVDPQFGFMTLDWDGKIRMDCSSPN
+AMASLIERMTPDADGHAPFDVATGNDADSDRHGIVTPDGGLMNPNHFLAVSIDYLYRNRS
+QWPQNAGVGKTLVSSSMIDRVATDLGRELVEVPVGFKWFVPGLLSGTGVFGGEESAGASF
+VKFDGGAWSTDKDGLLLCLLAAEIQAVTGQSPSERYRDLVALHGDPAYARIDAPATAEQK
+AALKALSPDDVTATELAGETILAALTNAPGNDAPIGGLKVVTKNAWFAARPSGTEDVYKI
+YAESFLGEEHLKQVQQEAQAIVDAVIS
+>GCF_023573625.1_00050
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGQAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLTQVQAEAQKLVDAVIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000209.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000209.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30f1d369fb4f16658116cfa43fa65285da20fcd1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000209.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00056
+METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLAAVRRALPGTSHQAVY
+DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE
+GHGFAVDEAEVYYWGLCAGCRE
+>GCF_003691675.1_02069
+METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLTAVRRALPGTSHQAVY
+DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE
+GHGFAVDEAEVYYWGLCAGCRE
+>GCF_005280335.1_00339
+MVSTDMDTTTQTPDERTLLRAAGLRVTRPRVAVLTALGECPHADAATVLAAVRRELPAVS
+HQAVYDSLHTLTDVGLVRSIQPAGSTARYEIRRNDNHHHLVCRDCGTVVDVPCHTGQAPC
+LEARTDHGFLIDEAEVYYWGLCPSCRADPGAAAS
+>GCF_020097155.1_00279
+MSTVTVEQPEESALLRSVGLRVTRPRVAVLQGLRRHPHADAGSLLSAVREDLPQVSHQAV
+YDCLHVLTDAGLVRSLQPAGSPARYELAAHDNHHHLVCRGCGDLVDVPCQTGVAPCLHAP
+EDHGFLIEEAEVYYWGLCPDCRSGGYTTTSDGTPAPAPPAP
+>GCF_023573625.1_00051
+METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLAAVRRALPGTSHQAVY
+DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE
+GHGFAVDEAEVYYWGLCAGCRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000211.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000211.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb0ff86a3310a1294382b6a575ba7b9bc427b39f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000211.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_00058
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RDGARVHVLVATAGEASHPHSPTHTPEDLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLPLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTADVAARADRVVGLEASSTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALAAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGHDEVLVLGT
+VDVHQGPLRQAWLRGYRHEEGHPHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGDGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG
+>GCF_003691675.1_02071
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RGGARVHVLVATAGEASHPHSPTHTPADLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLPLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTAAVAARAGRVVGLEASPTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALTAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGRDEALVLGT
+VDVRQGPLRQAWLRGYRHEEGHAHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGEGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG
+>GCF_005280335.1_00337
+MVSFSHTDAGTSEEAWAAAGVGALPVLESPAWDADTLLLVAVAHPDDETLGATGLIRSAL
+RGGARVHVLVATAGEASHPDSPTHAPEDLVRLRRAEMEHALDALAADLPGPGEDRRSALT
+WESLGLPDSGVAGREDAVRAAVVAALAAHPGPAVLASHDPGDGHADHEAVGRAVGELAGE
+RDLPLCAFPIWFWHWADPAELPARRYRRLALTDDDRAARRAALDAHASQVRPLSDAPGDE
+AVLGPQVLAHHDRPFEAHRLSGPDDADAHRAAAVFDRLYREHEDPWRYLSSPYEARKRAL
+TLAVLPRPRYGTVVEAGASIGVLTGEVAARADRVVGLEASPTAVERAAARLADTPHAEVR
+RAVLPGHWPDDVAGADLVIASEIGYFLQPEELDALVDDADAALAPGGELLLCHWRHPIEG
+WPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVIVPAKDEQERLPAAL
+AALGAALDRWEEHHAQGSAAVVVAADRCDDATVAAAVAARHADPRVHVLELGEPGPGEAG
+VGRARAEAARRARALFPDVPAQRLWLASTDADSRVPADWLLAQTTAAGPDGALVLGTVDV
+REGALRRAWVRDYRHEEGHPHVHGANLGLPWSLYEAAGGFPPVAEHEDVRLVEAVRALAE
+ARVRATDTTRVLTSSRLTGRTPGGFAGHLQEVGGEAVPRRGAQARP
+>GCF_020097155.1_00277
+MVSFDHRDDGTAEAVWMAAGVGELPALPARAWTRADTLLVAVAHPDDETLGAAGLIRAAL
+RGGAAVHVAVATAGEASHPDSPTHTPADLVRLRRAEMDHALAALADGLGPDAGALTWESL
+ALPDGGLTDRPDEVRAALERVLAGRTPAEEGGGAVVLVSHDPDDGHGDHDAVGAAAAALA
+ADHDLELYAFPLWLWHWGAPEDLAPRRYRRLELAAGDDAARLAALDAHASQTRPLSAAPG
+DEAILPERMIAHFTRGFETYRRTAPDDADASRASAVFDRLYREHEDPWRYLTSPYEARKR
+ALTLAVLPRPRYGTVVEAGASIGVLTAALAERAERVVGLEASQVAVERAAAHLAEIPHAE
+VRRAVLPADWPADVGPAEEGAGAPADLVVASEIGYFLQPEELDALVDAADASLGAGGELL
+LCHWRQPITGWPLDGDAVHDRVAADPRWRLLSEHVEADLRLSVHARAAAATHAVAVVPAM
+DEAEHLPAGLDALSAALDLWEAQHTQGSAAVVTVVPADDAPTLEAAHAARARDPRIRVLE
+LAPGAGGVGRARAAAARHARGLFPDVPAEALWLASTDADTRVPADWLVGQPALAARRRAD
+GQVLVLGTVDLPAHADDDLAHRWRADYEHREDHPHVHGANLGLPWGLYERAGGFAEVAEH
+EDVRLAEAVRALGEDRVLATDRVRVHTSSRLEGRTPGGFAGFLRGLLEEGAAEG
+>GCF_023573625.1_00053
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RGGARVHVLVATAGEASHPHSPTHTPEDLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLRLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTADVAARADRVVGLEASPTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALTAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGRDEALVLGT
+VDVRQGPLRQAWLRGYRHEEGHAHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGDGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000213.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000213.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71ef966a747c6c1a600a218875c19180a73291e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000213.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00061
+MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC
+RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK
+>GCF_003691675.1_02074
+MSAFETVDVNEIPADATILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC
+RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK
+>GCF_005280335.1_00334
+MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHLPLGQLPDRLEELDPDTDYYVIC
+RTGGRSARAAEFMVGRGYTAINVAGGSGAWLEAGKPMEADGGAEPTVK
+>GCF_020097155.1_00275
+MSHFETVTVDQIPADAAILDVREDDEWALGRAAGAQHLPLGQLPERIEELDPDTDYYVIC
+RTGGRSARAAEYMVGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK
+>GCF_023573625.1_00056
+MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC
+RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000214.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000214.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63f36a902c640cb02a0bea7863dcac61224ebb0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000214.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00062
+MTGTDSADATPSRLRYAFLGPAGTFTEAALRKVADPAEAEFVPAGSVLSAVAALRRGEVD
+RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVAISFVLVGRPGVAIEDVRRVTTHPH
+AWAQVRGWAETALPGVEFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED
+VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR
+PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD
+AAYRSGRAWVESLRSR
+>GCF_003691675.1_02075
+MTGTGSADATPSRLRYAFLGPAGTFTEAALRKVADPAEAEFVSAGSVLSAVAALRRGEVD
+RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVPISFVLVGRPGVAMEDVRRVTTHPH
+AWAQVRGWAETALPGVDFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED
+VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR
+PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD
+AAYRSGRAWVESLRSR
+>GCF_005280335.1_00333
+MTRDDAAPLGRCTFLGPAGTFTEAALRAVPGAEQAELIPATSVPAALAAVRAGEADHAMV
+PIENSVEGGVSATLDDIASGDDLQILREELVQISFVLVGRPGVELADVRRVSTHTHAWAQ
+VRGWVEANLPGVEYTPSGSTAAAARALADAEPGSEPFDAAVCAPLVAEQTGLPVLARAIE
+DVTGAVTRFVLVGRPGPLPAHTGSDKTTLTVPLPDDHPGALREILDQFATRGINLSRIES
+RPTGEGMGKYFFSIDLEGHLAEERVAAAMGALHRIFPGVRFLGSYPRAEHRPVAVRRHTS
+DDAYRAGRAWVDGLLAR
+>GCF_020097155.1_00274
+MSPAPRYAFLGPAGTFTEAALRQVASPEDVDLLPASSVLAALAAVRVGEAERAVVPIENS
+VEGGVTATLDDIGADEPLQILAEVLVPISFVLVGRPGVALEDVRRVTTHTHAWAQVRGWM
+EAHLPGVEFTPAGSTAAGARALLPSAGGDGAVASFDAAVCAPLVAEQTGLPVLAEAIEDV
+TGAVTRFVLVSRPGPVPEPTGADKTTLTVPLPDDHPGALREILDQFATRGINLSRIESRP
+TGEGMGRYFFSIDLEGHVAEERVGAALAALHRTFPGVRFLGSYPRAEGRPPTVPEHVTDA
+AYRRGTAWVRGLRSR
+>GCF_023573625.1_00057
+MTGTDSADATPSRLRYAFLGPAGTFTEAALRKVADPAKAEFVSAGSVLSAVAALRRGEVD
+RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVPISFVLVGRPGVAIEDVRRVTTHPH
+AWAQVRGWAETALPGVEFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED
+VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR
+PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD
+AAYRSGRAWVESLRSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000215.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000215.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d1a3bcc77c7ddf6f5c63739414f47313777c5fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000215.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00065
+MIDVKDLIEQPEKYRASQEARGEDASLVDRLVEADASRRSSIAGFEQLRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV
+LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLKGVGARLELALMQL
+GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGFHA
+GEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEEAEAEHERL
+LAWEERMLAAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR
+RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNADGSVTVPAALRPYLGG
+MERFELV
+>GCF_003691675.1_02078
+MIDVKDLIEQPEKYRASQEARGEDASLVDRVVEADASRRSSIAGFEQLRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV
+LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLTGVGARLELALMQL
+GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGYHA
+DEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEDAEAEHARL
+LAWEERMLGAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR
+RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNVDGSVTVPAALRPYLGG
+MERFELV
+>GCF_005280335.1_00330
+MVPISGAQLTYRLRPAARLKPVIDVKDLIEQPEKYRASQEARGEDASLVDRMVEADASRR
+ASITAFEELRAEQKAFGKKVAKAQGEEKQALLAEVKDLAARVKEAEAAAGAAEGRVAELQ
+RAFPNLVLDGVPTGGEDDFVVLREVGAPRDFAAEGFEPRDHLELGELLGAIDMERGAKVS
+GARFSFLKGVGARLELAIMQMGMDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYR
+LERDDLYLVGTSEVALAGYHADEIIDVDAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQF
+NKLEMFVYATQEDAEAEHARLLEWEERMLAAIEVPYRVIDIAAGDLGLSAARKFDCEAWV
+PTQGTYRELTSTSNCTTFQARRLNIRERVRQEDGDGGARRGGTRMVATLNGTLATTRWIV
+AILENHQNADGSVTVPVALRPYLGGMERFELV
+>GCF_020097155.1_00272
+MIDVKDLIDQPEKYRVSQEARGADVSLVDQVVAADAARRAAISRFEELRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAASVKEAEAASNEAEAELLRLQRLFPNLVIEGVPQGGEDDFVV
+VKEVGTPRDFAAEGFEPRDHLELGELIGGIDMERGAKVSGARFSFLKGAAARLELALMQM
+GLDLAVENGFVPVIPPTLVRPETMQGTGFDVAHDDEIYRLERDDLYLVGTSEVALAGYHA
+DEIIDVADAPIRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFVYTTVERAEEEHAR
+LLAWEEQMLARIEVPYRVIDTAAGDLGMSAARKFDCEAWVPTQGTYRELTSTSNCTTFQA
+RRLNIRERQVKEDGTGSNAKKGGTRTVATLNGTLATTRWIVAILENHQNADGSVTVPEAL
+RPYLGGLERFELV
+>GCF_023573625.1_00059
+MIDVKDLIEQPEKYRVSQEARGEDASLVDRVVEADAARRSSIAGFEQLRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV
+LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLKGVGARLELALMQL
+GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGYHA
+DEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEDAEAEHERL
+LAWEERMLGAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR
+RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNADGSVTVPAALRPYLGG
+MERFELV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000218.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000218.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d4570c2b70b318b276a3ca344a38f21149c3e51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000218.fa
@@ -0,0 +1,46 @@
+>GCF_002008305.4_00069
+MGQVDTGRTGRRDRRTERPRSRSLHAVLLAALAAVLVACGPVTAPPAPSSAPASSTTAAP
+TSSSPSAGPTAAEVAAAVEPGLETSPGTASAEFRDLATGEVLYARDADEPVAPASSLKVL
+AAAAIVSALGPETTLQTTVVAQPTADDAATELVLVGGGDVLLGTGASDSTHVSGRAGLRT
+LAQRTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPESGNIAPVQPLATYGGRE
+APGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTLPATEVPRATVLAAAPVA
+AVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATRLLTATVEDLGVDTAG
+MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRPGEDSTLGDRFPDAPARQ
+AVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL
+>GCF_003691675.1_02082
+MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACGPVTAPTAPSSASASTSTAAP
+TSSSPSAGPTAAEVAAAVEPGLETSPGTVSAEFRDLATGEVLYARDADEPVAPASSLKVL
+AAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLGTGASDSKAVSGRAGLRT
+LAERTVAGLVEDGVTGRVVVSTDLRLFADRTALNPRWTSDIPESGNIAPVQPLATYGGRE
+APGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTFPATEVPRATVLAAAPVA
+AVESAPVGQQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATQLLTATAEDLGVDTAG
+MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALGTVLEGLPRPGEDSTLGDRFPDAPARQ
+AVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL
+>GCF_005280335.1_00323
+MTPGSPFASLLAALAAALLSAAPVLTPLAGPAALAPGNPVTAEAVAAPSPDARALASAVD
+AALDASPGRVAAQVRDAATGEVLHARDADFLAAPASSLKVLTAAAALRTLGPERTLRTRV
+VAVPAADDGATELVLVGGGDVLLGDGASDPDAVAGRAGLRTLAERTVAGLAEAGVSGDVV
+VSVDLRLFDGAAVNPAWTPDLLEDGHVSAVQPLATWGGREVPGVDEERIEDPAGHAALVF
+QRLLDEEIERTGADLDLGLRDSIPATTAVRDDVVAAEPTAQVESAPVAEVAAYMLAHSEN
+QVAEALGHLSAYAVGRPATHEGAADLLEDVAADLGADTAGMAVLDASGLAEGSLVSPAQL
+AAVVSAASRVPWLAPVLDGLPRPGEDSTLDERFRGTAAEGAVAAKTGTLDHTVSLTGTVT
+TQDGRVLAFSIVASDLDWRLDEAREAVDAAVTAMAGL
+>GCF_020097155.1_00265
+MTPSNRAARVAAVTRVLLALAICALLGLLAHDVLLPRLPTPAAPAASAPSAPVPAASPSG
+GATAPSSTALASVAPVDPADVAAAVAPALAQAPGTASAEVRDAATGEVLYARSADQAVAP
+ASALKILTAVTAVDVLGADRALTTSVVALPGGGATELVLVGGGDALLGAGASDPGRVDGR
+AGLRTLARRTVAGLRERGVTGPVAVSTDLRLFTDASPLNPAWSAGLVESGNITAVQPLAT
+YGGRTAPGTGEDRIADPAAFAALAFQRELTAAVADSGADLSVRARDVVPATSAPRGDVLA
+TEPVARVESAPVGQQVAYLLAHSENQVAEVLARVAAAADGRPATHAAVPGLLRDRAAAHG
+VDTAGMRLVDASGLSPQNRVTAHQLAGLVEAVQADPALAPVRDGLPRPGEDSTLAERFPG
+SPAREAVAAKTGTLDQTVSLTGTVTTGSGRVLAFSIVCSGVDWRIAPARAAIDEAVSALA
+AL
+>GCF_023573625.1_00063
+MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACGPVTAPPAPSSAPAASTTAAP
+TSTSPSAGPTAAEVAAAVEPGLATSPGTVSAEFRDLATGEVLYARDADEPVAPASSLKVL
+AAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLGTGASDSTHVSGRAGLRT
+LAERTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPESGNIAPVQPLATYGGRE
+APGTGEDRIEAPAQFAALTFQAALDDAVAASGADLEVGLRDTLPATEVPRATVLAAAPVA
+AVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATRLLTATAEDLGVDTAG
+MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRPGEDSTLGDRFPDAPARQ
+AVAAKTGTLDQTVSLTGTVTATSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000221.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03c29b5532656f5141e0dcc09734d9bcca3de521
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000221.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00072
+MDAQDVQNDLTHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL
+HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
+>GCF_003691675.1_02085
+MDAQDVQNDLTHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL
+HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
+>GCF_005280335.1_00320
+MDAQDVQNDLTHVLMRREEVQETVKDLAAQIDRDYEGKDLLIVAVLKGAIMVVADLTRAL
+HSHVQIDFMAVSSYGSGTKSSGVVRILKDLDADLTGRDVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPDAMKVEIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
+>GCF_020097155.1_00262
+MDAQDVQNDLTHVLMSKEEVQDTIRDLAAQIDRDYEGKDLLIVAVLKGAVMVVADLTRAL
+HSHVEMDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+TRGPASVEICTFLRKPDAMKVDIDVKYVGKDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
+>GCF_023573625.1_00066
+MDAQDVQNDLSHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL
+HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000222.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000222.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9bb254529d0f3cc1a73d8b81b729fd5313eec72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000222.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_00074
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAAGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGEQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF
+>GCF_003691675.1_02087
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAAGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGQQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF
+>GCF_005280335.1_00319
+MKKLFNKPYIWILLGLLVLAVAIPLATSQTGRTMVDTNVGMAMLQDDKAAQARVVDGDQR
+VDLTLREPYSQDGRDLGKEVYFHFATARASDVVTAVDDSALDGYTDEPVRSNWLLSLLGF
+MIPFLLIALLFWFLLSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVEAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYALGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGNSEPFVG
+GGGGGSSREYSEELAYLVDAEVRGLLDGAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAEIFRDVRKRPERDVWLASDERLPQDIPPVLSPSERRSRHEGGEQTPVGVEGTTVPVH
+PEGAPPSSLGGDAPTPGLPPHGGPSSSPGAGEGPTY
+>GCF_020097155.1_00260
+MKKQFNKPYIWILLGLLVLGLVIPLTTAQSGRGMVDTNVGMALLRDDKVAQARVVDGEQR
+VDLTLREPLSQDGRDLGRDVYFQFSAARAQDVVRTVQDSSVDGYQDEPVRDSWLLSLLGL
+MIPFLLISLLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELHE
+IKEFLTEPERFHAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKANAPAIIFVDEIDAVGRSRGVGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVEAPDLDGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSRNNVIDNAALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPENDKYSVTRNELLDQL
+AYAMGGRVAEEVVFKDPSSGAANDIQKATETARKMVTDYGMSSKVGAVKLGSANTDPFLG
+GGGAASREYSEELAYLVDAEVRALLDGAHAEAHWVLTENRDVLDRLAAELLEKETLTQEQ
+IAEIFKDVRKRPERPLWLAADDRPPHDVPPVLTARERASRLEGEQPEAVGVEGTTVPDAP
+EGAPPTALGGAGGSAGGPGDLPGQHSPTPGPTY
+>GCF_023573625.1_00068
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFASARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRARILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAPGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGEQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000223.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000223.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42e5deee0a874a2271dfeee960d8ec4bb0ebe032
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000223.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00075
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG
+>GCF_003691675.1_02088
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG
+>GCF_005280335.1_00318
+MTEQTHHDDAARGPVPAADGSAAAPTASTPAAAGVPGTFDPDSTAIDRPRIEAAVREILL
+AIGEDPDREGLQDTPKRVAKAYAEFFAGLHQGPEQVLGTTFDIAHEELVLVKDIPFYSTC
+EHHLVPVHGTAHIGYIPSAAGRVTGLSKLARLVELYARRPQVQERLTTQVVEALMEHLAP
+RGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG
+>GCF_020097155.1_00259
+MTEQHRDAALADAHLHRPHEAAADVAPTTGAGAALAGAVPGVPGTFDPDQDTVDRPRIEA
+AVREILLAIGEDPDREGLQDTPKRVAKAYAEFFAGLHQRPEQVLGTTFDLSHEELVLVKD
+IPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVVEA
+LMEHLQPKGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRAEAMSLIMHG
+>GCF_023573625.1_00069
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000224.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000224.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00126b3588d2ef43f633f357dd58177e4fed5d20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000224.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00077
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARAVLAEQPVVTAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA
+>GCF_003691675.1_02090
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAADDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARAVLAEQPVVAAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA
+>GCF_005280335.1_00316
+MSARDRIRLTGLSAVGHHGVFDHERRDGQPFVTDVVLHLNAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLAERIARAVLAEQPVVEAVEVTVHKPQAPIPHDFADAAVTVHR
+TRRDAS
+>GCF_020097155.1_00257
+MSDVIRLTGLTATGRHGVFEHERRDGQPFTTDVALTLDAGPAAARDDLARTANYAEVAET
+VVRLVTGEPFDLIETLAVRIAEAVLAEQPVVTAVEVTVHKPQAPIPHDFTDVSVTVARRR
+GA
+>GCF_023573625.1_00071
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARTVLAEQPVVAAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000225.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000225.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b8724520769bde6cbbc8b005a30e614f38c89a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000225.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00078
+MSTVDWSHLAEGPAPVPALGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTAPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVVPLRPACPDALGREDT
+>GCF_003691675.1_02091
+MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVAPLRPARPDALGREAT
+>GCF_005280335.1_00315
+MSGVDWRHPAEDPAPTPALGARPAEPVAAVLALGANLREPAQTLDAAVAALSALPHVTDV
+QASPRAVTAPVGGPPGQPDYLNQVLTLRTTLSAWELLAVAHRLEQEHHRRREVRWGARTL
+DVDVIAYGDLVSDHPDLTLPHPRAAERGFVLLPWLWLDPDAVLAGRPVAELAALAADAPG
+VRRAEPERHRLLAGRDDVVPVRPRAVRAPGRDAIDGSGP
+>GCF_020097155.1_00256
+MSRPEAAHPAEGPAPTPELAARPSSPVTAVLALGANLGDPSETLDASVAVLTVTPGIEAV
+AASPRALTAPVGGPPGQPDYLNQVVRIRTALSPWELLGVAHRLEQDHHRRRTVRWGARTL
+DVDLIVYGDLTSDHPDLVLPHPRAAERGFVLLPWAWLDPEAELAGESVAELGARAADAPH
+VRREPARTAHLDGPRPDVLRPDSTPGLPSAPLPDGAAIARPWSDPT
+>GCF_023573625.1_00072
+MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVAPLRPARPDALGREAT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000226.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000226.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd53a6447cf7281be977a553d94c27b225cce872
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000226.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00079
+MIALRSGWTLLVVLAAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCIGLGWRVR
+RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVGAPTVREAAL
+QAAGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRGRPVRPETEGGYARARH
+>GCF_003691675.1_02092
+MIALRSGWTLLVVLVAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCLALGWRVR
+RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVEAPTVREAAL
+QAVGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRPARPETEGGYARARH
+>GCF_005280335.1_00314
+MIALRSWWTVVAVAVAVLLGWLAGLAAPSLGWGAPVVGRSGLITVTAVSVLCLVLGWRVR
+RDREKPPAARMDPIAAARTLVLGQAAGFAGAALAGWHAGVALQVAARAGAGAPTVREAAL
+QAAGGLVLLAVGLVVERWCRIPPEGDAAEGGRGEDGTAGRGRAPRPETEGGYARARD
+>GCF_020097155.1_00255
+MISLVSGRTALLAFAAAVLGWLAALTAPSLGLAAPVMHLAALVTVVAVGVLCLVLGWRVR
+RDRDRPLAQRMDPLAAARTLVLGQASGLTGAGLAGWHAGVGLEVASRAGIEAPAVLTAGL
+LALGGAALLTVGVVVERWCRIPPEGDGAEPGAGQDGGGSGGHGARRPEAEGGFARARD
+>GCF_023573625.1_00073
+MIALRSGWTLLVVLVAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCLALGWRVR
+RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVEAPTVREAAL
+QAVGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRPARPETEGGYARARH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000228.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000228.fa
new file mode 100644
index 0000000000000000000000000000000000000000..afa38f59a79edfbad6d2a1a1af8ed4820f1edbd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000228.fa
@@ -0,0 +1,56 @@
+>GCF_002008305.4_00081
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGMLGGAGADAS
+APERAAEPGLPDADAADAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVAL
+LPEAVLDEGETLTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETT
+HQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVLRVLT
+VVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRTGFTT
+TRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDED
+VAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVVGGA
+VVGEESGAHVPAVRGEEER
+>GCF_003691675.1_02094
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGVLGGAGADAS
+APERAAEPGLADADPDAVDADAGELLLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLAL
+VVALLPEAVLDEGETLTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGL
+TETTHQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVL
+RVLTVVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRT
+GFTTTRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRD
+LDEDVAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGV
+VGGAVVGEESGAHVPAVRGEEER
+>GCF_005280335.1_00312
+MSAAAPVPATRPADDDGWARVHPASPWVRGWTFLLLILFFLGRNAVEDFAAGRFGAGAGG
+GSGEGEGSLLVAGGILLGVTLLVSLAFFFSWWFTRFRIGEDQIELRQGWLFRTRRQMKYD
+RIQAVDLQHPLVARLLGLAVVKVEAADGGESALELSFLPKARAEQVRREILDRASGVLVG
+PASAPRIAEGADAAAGVIPGVMPGVMPGAEAGPGVAPPGADADPTTPRADAPEGAAPSSS
+DPGLARRADDEGELMLRVPSGRLIGSVLLSGGVAGTVAVYLVVVLGTSLFFALAPGTWLE
+GEDTPLTGIVVAWGLPLAFAVVGQAWSGLNGGWGFQVRRSADGLRLRHGLTETTHQTVPP
+GRVQGVTVSQPLFWRPFGWHRVKVSVAGYGEDAAGKRSTALPVGPWEDVLRVLTVVAPDP
+GLDGDPREAEGLTPARLMHLGLHGSGTEGGFHHIPHRGRWWFNWFAWRRRGFTTTRALLV
+VRSGRWNRVLQTLQHERVQTAALDQGPVQRRLRLATVHVRTAGGRAVLPDLDEAVALELF
+AEEARHAAVSRRLADRDRWMRPEELARFEQRTREVAATEVGREELARAGVARPAAPAGGV
+AGTDPEPRTSHEERP
+>GCF_020097155.1_00253
+MSAPAPRPEGLASGPSPEDGRIAPAPAADDAGWVRVHPASPWIRGWVMVATFLFFALRDV
+VERWIGGLFGADAGGGPGVDGRGLLIGGGIALGVLLLVGLAFFFSWWFTRFRIGAEEIEL
+KQGWLFRSRRQMHYDRLQAVDLQHPLPARLIGLAVVKVEAADGGGDSALELAYLPKAQAA
+AVRRQILDRASGAAAARPVPSAAPEAAGGPAAAGPVRGLLVDPEEQGPVLLRVPAGRLIG
+SVLLSSTVMGLLGAVVAVPAVLSLLLLLFPDANAGEEAGVWAVTLGSTFPLLFSLAGAVW
+SGLNKGWGFTVRDSSDGLRLRYGFTETVSQTVPPGRVQGVEISQPLFWRPFGWHRVKVSV
+AGYGGLEAEGRRRDVALPVGPWEDVLRVLQVVAPDPGLGGDARAAGELMRTAMTGSGEEG
+GFRHVPRRAAWWWHWLTWRRHGYALTPTLLVVRHGRLSRSVQTVQHERLQAVALTQGPVQ
+RRLRVATLRVHMAGGAARLRGLDEDVLAELFEVESRHAAVSRRLTDRNRWMLPEELERFE
+RRTAEVARTEVGRAEMAAAGVVPMETGPRPGDTPPVATTEHRGEETA
+>GCF_023573625.1_00075
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGMLGGAGADAS
+APERAAEPGLPDADAADAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVAL
+LPEAVLDEGETLTGIGAAAALPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETT
+HQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVLRVLT
+VVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRTGFTT
+TRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDED
+VAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVVGGA
+VVGEESGAHVPAVRGEEER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000229.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000229.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3424bdac13bb12a9e0e655b0aed20ea5dc8d3a5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000229.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00082
+MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA
+EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG
+VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV
+VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD
+GALTGPVARGDVDTLRTHRETLGELEAGGLPPDVRAVWETLARATTDRAETRGTLRADTA
+ARLREVLDDSDDPHDD
+>GCF_003691675.1_02095
+MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA
+EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG
+VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV
+VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD
+GALTGPVARGDVDTLRTHRETLGELEAGGLSADVRAVWETLARATTDRAETRGALRADTA
+ARLREVLDDSDDPHDD
+>GCF_005280335.1_00311
+MTGGLDLTLDPTDPTQRPGRLGVGVVGAGRVGAVLGAALRNAGHTITGVHAVSEASRTRA
+EALLPEAPVLEIPEILRRSEMVLFAVPDDVLPELVAGLAAAGHVQTGHLVVHTSGRHGVG
+ALNPVRAHGAIPIALHPAMTFTGLSLDLARLQDCVFGVTADPVVLPVAQALAVEMGGEPV
+VIKEADRGVYHAALSHGSNHLVTLTAQAAQLLRSIGVQDTERLLRPLMHASLENALADGD
+GALTGPVARGDVETVRGHRETLRELVAEGMPADVLAVWETLARATADRAEARGALRPDVA
+ARLREALAPDA
+>GCF_020097155.1_00252
+MSRMDMSPELTGADPADRPGRLGVGVIGAGRVGAVLGAALRGAGHTITGVHAVSEASRTR
+AEALLPGVPVLELPEILRRSEMVLFAVPDDALPELIAGLAAAGHIQTGHLLVHTSGRHGV
+RVMDPVRAHGAIPLAVHPAMTFTGLSLDLARLQDCVFGVTADPVVLPVAQALVVEMGGDP
+VVVKEADRAAYHLALSHGSNHLVTVTAQARQILEEIGVAEPERMLRPLMQASLENALTDG
+DGALTGPVARGDVETVRGHRDTLRELVDGGMPADVLAVWESLARATAQRAARRGALRADA
+AERILAVLDGADDGPDATG
+>GCF_023573625.1_00076
+MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA
+EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG
+VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV
+VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD
+GALTGPVARGDVDTLRTHRETLGELEAGGLSADVRAVWETLARATTDRAETRGALRADTA
+ARLREVLDDSDDPHDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000231.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000231.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7aec217cce3399acb8f710d4949ba323fc3666e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000231.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_00086
+MTSVRRHAARGLVALAAAVAVSAPLAAPAAAAPAAPTTPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARYGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEYGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDGLRDYDFYETAAGMREVRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDPNARGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDTWMQGKKEHPGRGVGKTAQRGLKVR
+>GCF_003691675.1_02099
+MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDVWMQGKKEHPGRGVGKTAQRGLQGR
+>GCF_005280335.1_00305
+MISVRRHAARGLVALAAAVAVSAPLAAPAVAAPAAPTAPAAAQSATGKPVVRPEVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYNGRYQVPTFEEVLELRER
+LSDRYGRQIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGTPYDSVAAGDTVRDYDFYETAAGMREVRAAGVDTLGPAFAQ
+VITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSADSNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDTWMQGKKEHPGRGVGKSAQRGLQVR
+>GCF_020097155.1_00250
+MTALRTTARGLAALTAAVAVAAPLAVPASAAIPAKEPITQAERPDVVAHRGASAYRPEHT
+LAAYELAVAQGADVIEPDLVSTKDGVLVDRHENDITGTTDVSERPEFADRKTTKTVDGVE
+ITGWFTEDFTLAELKTLRAKERLPEARPGSAAYDGMYQVPTFEEDLKLREELSAKYGREI
+GIIPEIKHPSYFDGIGLSQEEEVIELLEEHGLNHADGRAVVQSFEFSNLAEMNTRLGLQA
+DTAYLLWYEGSGYDAVLSGDTARDYAYFSTPAGAAEAAFNGIDIYGPELRQVIALNQDGS
+LGAPTGLVEVAHDAGLTVVPYTFRAENQSLPLQFRSSENPVEHGDLAAYITEVLDAGVDG
+FFTDFPDVGVAARDAWLAEKPAEQPSEQPSDGSHAVPGKVQTGDAAAWLPAGLAAAAAGV
+LVALRRRLTAAR
+>GCF_023573625.1_00081
+MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDVWMQGKKEHPGRGVGKTAQRGLKGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000232.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000232.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78b88381f11bda9982fc86bbd26d05d7013c1455
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000232.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00087
+MTTNTPKNAHGSSAEGRDAKDQAKDKAQQAAGEAQGQAKAVAQDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERFAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+VQPDSAASTSPRRHTTRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDTPYGTQAPVQQGLTAERPFDQTRPGGDA
+>GCF_003691675.1_02100
+MTTNTPKNAHGSSAEGRDAKDQAKGKAQQAAGEAQGQAKAVAHDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDSTASTSPRRHETRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDVPYGTQAPVQQGLTAERPFDQTRPGGDA
+>GCF_005280335.1_00304
+MTTNTPKNAHGSSAEGRDAKDQAKDKAQQAAGEAQGQAKAVANDAKDKVQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEEVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDAAAPTAPRRRDTRPEAVHADVTPHHLDSQAPAYSSDSLSQADGRVASGAGPRRAAG
+VGDTPYGVEAPEQHGLTAERPFDRSQPGGRA
+>GCF_020097155.1_00249
+MAKNHSARAADPQQSETRQKAEAAAGAAQDQAAGVAQDAKAHAQDLAQSAQQEAVAVKDE
+AVQHAKSLAGSLQDQAAQQASTQQGRLAEQSRGITDDLHRLLSGEQPQGDAVRQAVAAVA
+DRAETLTQRLETAQPMDLVDDVRRFAARRPGTFLAIALGAGVLAGRMTRGVRDASQDGPA
+SLSSAPRTPQHRRELEPQGVQADVTPHHLDSQIPAHTGDDAPRPVSDTAAGLPYGTEPLP
+TIDPLTGEPVAEDPYDQTRDGGRA
+>GCF_023573625.1_00082
+MTTNTPKNAHGSSAEGRDAKDQAKGKAQQAAGEAQGQAKAVAHDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDSTASTAPRRHETRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDVPYGTQAPVQQGLTAERPFDQTRPGGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000233.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000233.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ca95d0ccb8a2277c22c0643b01fbe6673b0f4b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000233.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00088
+MSTAHEPFRDATPHSGAHTPPPTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA
+TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL
+AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR
+>GCF_003691675.1_02101
+MSTAHEPFRDATPHSGAHTPPSTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA
+TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL
+AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR
+>GCF_005280335.1_00303
+MSTPYEPIRDATPHAGAHTPPPTQAEFRAEHESLGEMFKSLSSRLSTLVSQEIALAKAEA
+TESAKKAGTGAGLLAGAAVGGFFLLMFLSLALMWALGSAMHLGWAALIVAVLWGVCAAVL
+ALMGKKHLEKIKGLPQTQETLQEIPETLNPAKETR
+>GCF_020097155.1_00248
+MSHATPNGGAPRHADPAAHQSTPAAGAHTPPPTQAEFRAEHESLGEMFSSATEKVSLLMR
+QEIALAKAEATDSAKKAGKGAGMFAGAAVGGFFLLMFLSLALMYALGSLMPLGWAALIVA
+VLWGVVAAVLALQGKKNIEKIKGLPQTQETLQEIPETLNPAKETR
+>GCF_023573625.1_00083
+MSTAHEPFRDATPHSGAHTPPSTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA
+TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL
+AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000235.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000235.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7356fb21c0e6b26d43369f7cd8d8935fc8a2686
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000235.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00090
+MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA
+TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR
+TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT
+VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS
+RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT
+FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP
+>GCF_003691675.1_02103
+MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA
+TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR
+TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT
+VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS
+RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT
+FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP
+>GCF_005280335.1_00301
+MTPLDRVPDRTPVPPRTGLTLEDQVPEAGGTRPRLTTTKADFRAAVAELVGRAAAEDPGE
+EVSVGLVPTMGALHGGHAALARQARSENDVVAASIFVNPLQFGDRADLEHYPRTLEADLD
+LLGAVGVDVVFAPSVDEMYPGHPDAPIVSVSAGRMGEVLEGASRPGHFDGVCTVVAKLWN
+LSMPPAPAVLRSYFGQKDAQQLAVLRRLAHDLDVAVDVRAVPIVRSPEGLALSSRNTRLD
+EAGLHAALVLNRALTRLEEAAVAGRVLDVQAAREEVAAEPGVTLDHLVVVDRETLEELGA
+ELLCQPLRRDALALVAAHVPPVRLIDNRVLPAAGPLP
+>GCF_020097155.1_00246
+MTPLDRTPDRRPVPAGTGLTLEDALPVADGARRPRLARTVAEARAALRELTAAAGQERGG
+APVVVGMVPTMGALHGGHAALIRQARAENDVVVASIFVNPLQFGDPADLENYPRTLEADL
+DLLGAAGADLVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGVSRPGHFDGVVTVVAKLW
+NIVRPAVPALRSYFGQKDAQQLAILRRLAHDLDVDVEVRAVPIVRSPEGLALSSRNTRLD
+ADGLEHALVLSRALRALVDAAEAGEPIDVRAARQMVSDEPGVTLDHLVVVDRETLEELGP
+ELLCQPLRREALALVAAHVPPVRLIDNMVLPAAGPLP
+>GCF_023573625.1_00085
+MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA
+TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR
+TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT
+VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS
+RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT
+FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000238.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000238.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fa433253e3e388ae354e064c31520582cd446cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000238.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_00093
+MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGTGFDPAQARVQATAAAGAHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+LDAFHEAFGTREGDPMWLAPEERVTIW
+>GCF_003691675.1_02106
+MTATAEPRVPSPREDLYRHVNTGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEGAVR
+EVGAGFDPAQARVQATAAAGAHRDAPLAPLDAEDTEGMEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVTTPAELLTLSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLTLAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHMTPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPVEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTREGDPMWLAPEERVTIW
+>GCF_005280335.1_00298
+MTATAEPRVPAPREDLYRHVNAAWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGAGFDPAQARVDATAAAGAEHHTPLEPLDAEETEGMELPEVKRRIAALYASFMDDETV
+EARGLEPVATDMAAVASVQTPAELLELSGRLQRQGVSGLVNTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHAGRLLGLAGIGADSAEAAEAGVRVVELEKRIAAL
+HWDVVRSRDAVARYNLMTHEQLVELFPLAEAWLEGVDAAGERSREVVVWQPDFLSGVQAL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRHRWKRAVAF
+VNGAAGEDVARLYVDRHFPEGHVAAMDELVNLLQEAYRRSIDELEWMSEETRQRALEKLS
+MFRPMVGRPVRWVDYSSLEVHAGDLLGNARAASEFEWERDLRKIEDGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEKSMAANLGAIGAVIGHEIGHGFDDQGSRYDGSGR
+LEDWWTQEDRAAFTELTSRLVAQYNVLSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFSAWAAVWRQLTRPETMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTQEGDPMWLAPEERVTIW
+>GCF_020097155.1_00243
+MTATAEPRVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRRIAEDAAR
+DAAMAAPAPEVEAPAQDEASQDPAAAERAARERIAVLWSAFMDEEAVEAAGILPLAADLE
+AVDAVASPAELLALSGRLQREGVSGLIGTGALNDAGDPERMLLHLIQSGLGLPDESYYRE
+EAYAEILAQYTEHVGRLFALAGVGGDEAGAAALGERVVALEKRIAAHHWDVVRSRDAVAR
+YNLLTRDQLLELLPLAPGWLEGIGAADARADEVVVWQPDFLTGVQALLEGPDAADLADWK
+AWLTLQVLRSRAGFLPDAFVQENFSFYGRRLAGTQEVRPRWKRAVAFVNGGVGEDVGRLY
+VARHFPEGHVAAMDQLVGLLLEAYRRSIDALDWMGEQTRQSALEKLAMFRPMVGFPETWR
+DYSALELTPGDLVGCARAVDRFEWDRDLAKIETGPDPREWHMTPQTVNAYYTPLENAIVF
+PAALLQPPFFDPERSMAANLGGIGAVIGHEIGHGFDDQGSRYDGSGRLHDWWTEQDREAF
+AERTGRLVAQYSALSPAEAPDRQVNGEFTLGENIGDLGGLGIAHQALEIWREEQDGSTED
+ESSGDREFFQAWAAVWRQLTRPETMVTRIASDPHSPNQFRCNQVVKNLDAFHTAYGTREG
+DPMWLAPEERVTIW
+>GCF_023573625.1_00088
+MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGTGFDPAQARVQATAAAGAHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTREGDPMWLAPEERVTIW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000239.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000239.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d110392d90028155daac6a1738d43ef5b006907a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000239.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_00094
+MADGAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSPALSVGAMKAFMM
+LANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE
+>GCF_003691675.1_02107
+MVDGAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMARYAEALSPTLSVGAMKAFMM
+LANEGTMTPSAVAEGMLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE
+>GCF_005280335.1_00297
+MAERGHGDDRGLDGVGAERGDAGGEIDGFEAAVRGLEDAFARMVRQHRQVVTRQAAALKP
+GLSAGAMKAFITLCNAGTMTPSTLAEHLLLDRAQVSRMVRDLEDEGLITREPDPVDRRSA
+LLTATEEGRARLDAVRGGPAGEGLRADLAHWDRADIHTLVRLLGRLVEEQQARVDRTPDA
+G
+>GCF_020097155.1_00242
+MADPADHGSDGRGTGADAFAPEAFDAAVRELEGSFNRLVRQYRATLARQAEAVHPGLPLG
+AMKAFVAICHRGPLTPSDLAEHLMLDRTQISRVLKDLEGDGLIHREPDPRDRRSALLTAT
+DEARARLDAVRQGPAGGGTRARLQRWDLEDVRALSALLRRFVDEREDPAADDACRP
+>GCF_023573625.1_00089
+MADGAPDPGRGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSPALSVGAMKAFMM
+LANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000240.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000240.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b54243583c574373ff1ab8ba73d8018cfb3d999
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000240.fa
@@ -0,0 +1,61 @@
+>GCF_002008305.4_00095
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTSAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDSLRVIFEDVYAQGIALAFLVAVPLAIVALIAILFLPNLPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRSVSAERPATAVADRPVVPAA
+LAVAGTALLAAVVTALVRARRG
+>GCF_003691675.1_02108
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTTAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDGLRSIFEDVYATGISHAFLVGVPLAIVALIAILFLPNIPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRSVSAERPATAVADRPVVPAA
+LAVAGTALLAAVVTALVRARRG
+>GCF_005280335.1_00296
+MIDHRQSLTAVNHSDDPAEGPHEPHLPAVAGTAPAGAPSLERAAADAARHRAVLQALTGL
+LLGMFVSMIANTVVSTSMPVIISDIGGNQNDYTWVITAALLATAVSTPVWGKLADLMDRK
+MLFQVALVIFVGASAAAGFTNDPTFLIVCRVVQGLGGGGLAALSQVIMADIISPRERGRY
+MGLFGAVMAVATVGGPLAGGVITDLWGWRWNFFVAVPFALVALVMVQRTLHLPAREPRKV
+SIDYLGIVLLGVATSLLLIWVTTAGQQFPWASWTTAWMVGGAVLAAALFVVVELKVTEPL
+IPLTLFRNRTFTLATIASIATGLAMFGAGVYLAQYMQLARGATPTQAGLMTIPMIAGLLI
+TSTVIGRVITRTGVWKRWLIVGAVLLTAGMALLATLHYDTPFVLVSLHMLLLGAGVGMTM
+QNLVLVVQNTTDPRQMGVASSGVTFFRSLGGSVGVAAMGAVVANVVPSRFEARGADLAAA
+LQSLGADGPVWAQRLQSGTLPRVAEMPEPLRVVVEDVYATGISQAFLVGVPLAVVAVVAI
+VFLPNIPLGRMTTSERLDASRADLATVTAPAAMQKVPATGEIPVVAPAAGGAGGTDDACT
+AEDADGTEGVPAAQGPTTAPAEPTAERAERPAVQPAAESVPARVVAPAAAAPSTAAASGR
+SGGARPGARAAAAVALLTAIAVLMRQARRG
+>GCF_020097155.1_00241
+MSTTTAPPATAGPAAVGNSPAVPSLERAADDAARHRTVLRALTGLLLGMFVSMIANTVVS
+TSMPVIISDIGGDQTAYTWVITAALLATAIATPIWGKLADLVDRKVLFQVALVLFVAASA
+AAGFTTDPTFLIVCRVIQGLGGGGLAALSQVIMADIISPRERGRYAGLFGAVMAVATVGG
+PLAGGIITDLWGWRWNFFVSLPFALVALVMVQRTLHLPARESRKVSIDYLGIVLLSTATA
+LLLIWVTNAGHQFDWASATTAWMLGGAALAAVLFVVVELTVAEPLIPLTLFRDRTFTLGT
+IASIATGLAMFGASVYLSQYMQLARGATPTQAGLMTIPMIVGLLVSSTVIGGVITRTGVW
+KRWLVIGAVLLIAGAAMLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQ
+MGVASSGVTFFRSLGGTIGVAVMGAVVANVVPDQVEQRRTDIGAALASLGPAGAEWAQRL
+QSGSLPRVAEMPDALRVIFEDVYATGISQAFLVGVPLAVVALAAILFLPNIPLGHMTTTE
+RIDAERADLATVSVPQAMQTLPATGSTPVVAQAQVQEAAPASTTTTPAPAARALRVPAGL
+RERRIAPAGTGRSTAWRATASALAAGAAAAAFVPLLRRSRRG
+>GCF_023573625.1_00090
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTTAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDGLRSIFEDVYATGISHAFLVGVPLAIVALIAILFLPNIPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRAVAAERPATASPVAGRPVAP
+AALAVAGTALLAAVVTALVRARRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000241.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000241.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd4890b0c773b8d61d531f1e903cc9e9d606a46d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000241.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00096
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMEVVFAPRPPAH
+REVAAAELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDADVIAKMKDDAVLVN
+TARGPVVDEAALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEAPALVNPEVRG
+>GCF_003691675.1_02109
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN
+TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEVPALVNPEVRG
+>GCF_005280335.1_00295
+MSPRFLLMTEIPEPGLGMLREAGEVTLGSEVGGNDALPALAASGDYDVVVCALAQKFDAD
+VLAQARLKGIANYAVGYNNVDVAAATEAGIAVGNTPDVLTDATADIALLLILGVSRRAHE
+GEAMMRAGEFTGWRADLLVGKDVKGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAPEELGELAGRVEQVRWEELVERSDFLSLHVPLTADTEHLVDADVLARMKDDAVLIN
+TARGPVVDEAALVEALRAGRLFGAGLDVYEDEPAMAPGLAELDNVMLLPHLGSATRDTRA
+AMAELTARNAIAMATGGEVPALVNPDVRR
+>GCF_020097155.1_00240
+MSPRFLLMADLPEPGLGMLREAGEVVRGGDVGGNAALADLCASGEYDVVVGALDQRYDAD
+LLARARVKGIANYAVGFDNVDVPAATEHGILVGNTPDVLTAATADIALLLILGVTRRAVE
+GERMMREGRFEGWRADMLVGKDVVGATLGLAGFGRIGRAVAERALAFGMEVVFAPRPPAH
+REVPAEELGDLAGRVRQVRWEELVETADVLSLHVPLTEDTRHLVDEDVIARMKDDAVLVN
+TARGPVVDEAALVTALREGRLFGAGFDVYEDEPAMAEGLAELPNVMLLPHLGSATRDARA
+AMAELTARNAIGMATDGEAPALVNPEARG
+>GCF_023573625.1_00091
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN
+TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEVPALVNPGVRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000243.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000243.fa
new file mode 100644
index 0000000000000000000000000000000000000000..677ef7b4637431b081fec3252cb19abad842b0f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000243.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00098
+MAAFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR
+>GCF_003691675.1_02111
+MADFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR
+>GCF_005280335.1_00293
+MATFWEYFSVLAPSIGLGLIFWLVMRSLLRSDTAERESMGRRSTGEDARAAREEADAREW
+ARRRGGDDVPRRGDDSR
+>GCF_020097155.1_00238
+MAAFWEYFSVLAPSVGIGLVFWLVMRSLLRSDTAEREARQRRGEDARAAREEAEAREWAA
+RRRGDAPAGPGGAERP
+>GCF_023573625.1_00093
+MAAFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000244.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000244.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b174a8b478a7a59e9a6e349f752f84fd70305fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000244.fa
@@ -0,0 +1,80 @@
+>GCF_002008305.4_00100
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFSGGREALEGADLAELESG
+AGDPVDADRSV
+>GCF_003691675.1_02113
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVQIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDTTGEGEGAELTFAFSGGREALEGADLAELEPG
+AGDPVDADRSA
+>GCF_005280335.1_00291
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVKLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLKDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVPEPSVEDAT
+EILRGLRDRYEAHHRVSITDGALKAAATLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLEDERRQKEEAWRTGADSDV
+ATVDEELIAEVLSKSTGIPVFKLTAEETDRLRTMEDELHKRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQAAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFGFSGGREALEGAELPELEPG
+SGETVEAGRSA
+>GCF_020097155.1_00237
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLAAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGSEGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAQEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIERG
+DVPETLKGKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVPEPSVEDAT
+QILRGLRDRYEAHHKVSITDGALSAAASLADRYISDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEVKAYEERIAEVKAQKEAAIDGQDFEGAARLRDQEKQLEEEREQKEQAWRAGQDAAV
+ATVDEDLIAEVLSLSTGIPVFKLTEEETDRLRNMEAELHQRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHADLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSSTDTSTGYERMKGKVREELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLAKRLAEQDLSIELTPAAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFAGGRAALEGDDAAEPAAL
+PAAADAPVEGREAPGADVPRGDDAGQDGPEAGGALGARLD
+>GCF_023573625.1_00095
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFSGGREALEGADLAELEPG
+AGDPVDADRSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000245.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000245.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a54721030bee96251ac7ed566faa6f0c6e61f7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000245.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_00101
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVNKGVDGAQEKFLSGDEGEQQA
+>GCF_003691675.1_02114
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHADTVNKGVDGAQEKFLSGDEGEQQA
+>GCF_005280335.1_00289
+MGIGDLNNLANQHSDKINEAVDGAQEQHGDKLGEHADTVNKGVDGAQEKFLSGEKNEGEQ
+QA
+>GCF_020097155.1_00235
+MVGFDDVKNLANENSDKINEQVDAAQAQHSDKLGQHADLADKGIDGAQDKFLNGQSAENE
+GEQQA
+>GCF_023573625.1_00096
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVDKGVDGAQEKFLSGDEGEQQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000247.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000247.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d029ce3d71784f92479aedaf1ffc04107be9e27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000247.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00103
+MPAPAPLVPPTVDVPHLHDAMLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAVVGRHDGRVPADPA
+ALRALPGIGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR
+DDDGGLTFPA
+>GCF_003691675.1_02116
+MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA
+ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR
+DDDGGLTFPD
+>GCF_005280335.1_00287
+MPAHETAVPPSVDVPRLHDAVLDWFAVHARDLPWRSPDCPPWGVLVSEIMLQQTPVARVL
+PRWHAWLERWPTAADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHSGEVPADPA
+ALRALPGIGEYTAAAVSSFAFGLPETVVDTNVRRVIARAVGGQALPGRSLTRAEMRRAHA
+LMPEDPDRAQAWNAGVMELGALVCTARSPACERCPLADACAWVAAGSPPPEQAPRGQAWA
+GTDRQVRGAVMAAVREHGRVAGDGLRAVVVAGGRLGAHRPGDAQWERCVAGLLADGLLAR
+DDDGALAFPS
+>GCF_020097155.1_00233
+MPAHDDAAPRPDLTALQDEVLDWFAAHGRDLPWRDPDCPPWGVLVSEIMLQQTPVVRVLP
+RWRAWMERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHGGEVPADPAA
+LRALPGIGEYTAAAVSSFAFGIPETVVDTNVRRVLARALRGEGLPGRTLTRAEMAAAHAA
+LPADEHRANRWNAAVMELGALVCTARSPACDRCPIRARCAWVAAGSPAPEVARRGQAWVG
+TDRQVRGAVMAAVREHGRVPRGGLREAVDGTGRLGAHTPDDAQWERAVAGLLGDGLLVAH
+DDGALAFPA
+>GCF_023573625.1_00098
+MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA
+ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPTRANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGWLGSHRPEDAQWARCVAGLVSDGLLAR
+DADGGLTFPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000248.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000248.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d97bcd9739c13c91d0e8e8ed95948629bdaeb5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000248.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00104
+MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVALVRAGIGAFSSEDADPSAA
+PTPVHSPSPAPATDAESSSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI
+TNLSSTPCRTDVGTARQEFTIRTAEGDDVFSTRICQADPAEAQRVLYPHEELTAVYRWSG
+RASSQDCGRLGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDSSSSAAPSSATPS
+SATPSSSGSASPSGSASDPASASTTDPSPSSSR
+>GCF_003691675.1_02117
+MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVSLVRAGIDAFSSEDADPSAA
+PTPVHSPSPAPATDAESGSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI
+TNLSSTPCRKDVGTARQEFTIRTAEGDDVFSTRICQADPAEAPRVLYPHEELTAVYRWSG
+RASSQDCGRPGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDSSSSAAPSSATPS
+SATPSSSGSASPSGSASDPASASTTDPSPSSSR
+>GCF_005280335.1_00286
+MPSRPSSPGPKPSAAVYRRRRLVAALLALILLLLVGWGLWSLIRLGMGALSGDDAEPSVS
+APPTPVHSPSPAPPSGATPGSAAPTVALEDAAECQPSDLRLVASADKAQYLRGEEAVLRL
+GVTNLSSSPCRADVGTARQEFTVRTAEGDDVFSTRVCQADPTSSERVLTPHEELTAVYRW
+SGHASNEDCGTPGALAAAGPHLLTVTLGEQTSRPVALRIQEEAAPGAWDGASSGAPASGS
+PAPSTPASPSASPSATGSAPAASSPAPASGSPAASTPATPSASPSR
+>GCF_020097155.1_00232
+MPSASPAPRPRPSAAVLRRRRVVAGCLAAAFLLLVGWGIGALVNALLPSGRPDAEPSAAP
+TPVSSPTPAAARSLDAQAGQTQDPASVESCAPMDLRLVAAADRERYAPGEEAVLRLEVTN
+LSGRPCRTDVGTAQQEFRVTDASEQQVMSTRVCQADPTHEDVVLEPRDQKAAVYRWNGRA
+SSADCARLGPAVEPGEYRLTVTLGEVTSRPVALTVTDGTKSAAPASSPAASSAAPGPSAT
+TAPASAETSSASPSASSSSAQPSSPAPRASEPTSSAPTSSPAGSGRASSSPAAPSSSAAS
+PTR
+>GCF_023573625.1_00099
+MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVSLVRAGIDAFSSEDADPSAA
+PTPVHSPSPAPATDAESGSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI
+TNLSSTPCRTDVGTARQEFTIRTAEGDDVFSTRICQADPAEAPRVLYPHEELTAVYRWSG
+RASSQDCGRLGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDGGSSATPSSATPS
+SSGSASPSASASAPASASASASASASASASPSAAPATTTDPSPSPSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000249.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00d6eaa77234ce1809f7d3b4a34e80ab2c4d324a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000249.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00106
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+EAVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPTGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALRENDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSVLDEGVFDDDDRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARGYLPRV
+>GCF_003691675.1_02119
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+ETVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPIGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALREDDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSALDEGVLDDDVRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARAYLPRV
+>GCF_005280335.1_00284
+MSDRFATATGTVPMVAPESRGARLRRFLRRRSRAGWSRVRSSVAHAALMAVCAVGAYWFA
+ETVLGHHQPLFSSTALLIALGFQREPTLRKVAEVAVGCTVGILIGDLLLAALGRGLWQAT
+VVVFVSVMVARFLDSGATFTMQMSLQSVLVVLLPAAQGGPFARSADALVGGLLALVVTFL
+SPQDVRRGTARHLEGLYDSMATVLRDLSRALRQEDSRTAWMALVACRGTQGTLESIRAEL
+KMAQEQATFNPLQRGSRSFVSDAANAADRSDLAVRSLRIVARRVVSVLDEGAFDDDHRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASRLDPRELGGGSLHGEAL
+VMLLRPMMVDLLEATGAPHDEARAYLPRV
+>GCF_020097155.1_00225
+MTDRHATATGTLPAVPAAAGPSGVGRFLRRRARAGWSRLRSSVGHAALMAVCAVGAYWFA
+ETVLGHAQPLFAATALLIALGFQREPRVRKVAEVAFGCTLGILIGDLMMAALGRGLWQAV
+LVVFVSVLAARFLDSGATFTMQMSLQSVLVVLLPLNADGPFARSADALVGGLLALLVTLL
+SPRDPTRLPARQLRGLYESMASVLRELSAALRAEESRTAWMALVECRRTQSTLEDVRKEL
+KVTREQTVLNPLQRPARDAADVMAVAADRSDLAVRSLRIVARRVVSILDHGAVDGDHRER
+LAAWFDDAADAVEILHRSLAEPQAEGRHRSLDVARDALGASASWLDPHELAGGTVHGEAL
+VMLLRPMMVDLIEATGASHAEALTYLPRV
+>GCF_023573625.1_00101
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+EAVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPTGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALRENDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSALDEGVLDDDVRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARGYLPRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000250.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000250.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4342b735ebc95e4d4e19997af1d8650c35372716
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000250.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00107
+MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS
+QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKEN
+CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL
+PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS
+QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES
+GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM
+ERIEAISVKG
+>GCF_003691675.1_02120
+MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS
+QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKKN
+CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL
+PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS
+QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES
+GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM
+ERIEAISVKG
+>GCF_005280335.1_00283
+MKALRFGRSAALLSVAALALTACGGNGGGDASSSAPAGGSSSAAAEGSGAAAASGTLIGG
+GASSQEAAMTAWSEGVKATSPELTVQYSPDGSGAGREGFLGGAFSFAGSDAALKEDEAEQ
+AKQICGDNGAFHVPAYISPIAIAYNLEGVDEVKMDAETIAKVFSKEITTWNDPAIAEQNE
+GVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWKYDEVETWPSEITAESAQGTRGVV
+GQAAQTDGAITYADASAVGELGTVAVKVGEEYVPYSSDAAAKTVSASVQNEDGSIELDRA
+TTEAGVYPIVLVSYHIYCNQYQNQETADQVKAFASYVVSEDGQKAAEEAAGNAPIGAETR
+DAAVERIEAITAG
+>GCF_020097155.1_00224
+MKALRFGRSAALLSVAALALTACGGGNDSASSSSSAASSSAAGSSSASSSAAGSSSASSS
+AAESSSASGSSSAAQGGYAIDVPTASGTLMGSGASSQEAAMTAWTEGVKATSPELQVQYS
+PDGSGAGRKAFLSGAATFAGSDAALKDEEKTQAQEVCGPDGAFHVPAYVSPIAVAYNLEG
+VDSLNLDADTIAKIFSKKITKWNAPEIAALNEGVELPDTAITVVHRADESGTTENFTAYL
+DQVAPEAWTYGKVKEWPGDITAESAQGTKGVVSQAAATNGAITYADESGVGSLKTAKVGK
+DGKFAEISPEAAAKIVADGKKQDDGSIELDRANAGEGVYPIVLVSYHIFCNQYGDQETVD
+QVKAFASYVISEDGQKAAQEASKSAPLDAELAKEAKTRIDAIKVG
+>GCF_023573625.1_00102
+MKAHRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEHASGSAGGEQGTTSEVQG
+NLVGAGASSQEAAMTAWTQGVTEIAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKE
+EEAESAKENCGDEGAFHVPAYISPIAVAYNLPGVDEVKMDAETIAKVFSGEIKNWNDEAI
+AAQNEGVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQG
+TKGVVGLASQTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSI
+ELDRATDESGVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPI
+SEDTRKKAMERIEAISVKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000251.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000251.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af8cfb9feb446329c437e3ea6ce4b13cfbd82d36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000251.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00108
+MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP
+GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID
+LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM
+VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIISSIMLGLGRALG
+ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV
+NMIARAIVNKHKEFSGAN
+>GCF_003691675.1_02121
+MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP
+GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID
+LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM
+VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIISSIMLGLGRALG
+ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV
+NMIARAIVNKHKEFSGAN
+>GCF_005280335.1_00282
+MTSPATEAPPRATTLKSSRGGAAGDKVFSGLSLAAGVLILLTLAFVAIFLVVRSLPALFP
+DAYGTQLKSADTFFQYVWPLMAGTIMAAVIALLLATPVAVGVALFISHYAPPKIAQPVGY
+VIDLLAAIPSVIYGIWGWLTLAPVMVPIYQWLNEYLGFIPFFGGPVTGTGRVIMTSGVVL
+AVMILPIITALCREIFRQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSVMLGLGR
+ALGETMAVTLVLSAGGFSLSLIEEGRNATIPSEIALNFPEAYGIRLNELIAAGLMLFVIT
+LVVNMTARWIVNKHKEFSGAN
+>GCF_020097155.1_00223
+MSHTATEAAPSSSALKSSRAGAAGDKVFSGLALAAGVLILLILAFVAIFLVSEAWPALFP
+AEGANLESGDSFWGYVWPLMAGTVMAAIIALLLATPVAVGVALFISHYAPPKIAQPVGYV
+IDLLAAIPSVVYGIWGWLTLAPLMVPIYEWLNEYLGWLPFFGGSVTSTGRVLMTSGIVLA
+VMVVPIITALCREIFSQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSIMLGLGRA
+LGETMAVTMVLSPGKFSPSVIEEGRNATIPSEIALNFPEAYGIRLNELIAAGLMLFVITL
+VVNMVARWIVNKHKEFSGAN
+>GCF_023573625.1_00103
+MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP
+GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID
+LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM
+VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSIMLGLGRALG
+ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV
+NMIARAIVNKHKEFSGAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000252.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000252.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1a8c22ebd202312d10653aded93c0c3889fbd97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000252.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00109
+MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV
+IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI
+ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT
+SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM
+GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS
+GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA
+RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR
+>GCF_003691675.1_02122
+MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV
+IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI
+ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT
+SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM
+GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS
+GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA
+RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR
+>GCF_005280335.1_00281
+MSTAIDDVSTRQDTPPSKHRQNSLTAGQKPGWVWMAIAAAAVLLGLGIEALLSGAAPFSE
+DFSLARFVVLAGVLYIAGMYLVTRVMENRRRASDGLWKNLVWTAFLIALVPLVSVIWTVL
+EGGGPTLLSNPQVLWNDMDGVTGATDAAYDQAGSPAGGLPGGFAHALIGTLVITIIATLI
+AVPIGLLASIYLVEYGRDGWLSRAITFFVDVMTGIPSIVAGLFAYAAMTVLLELIMGPGP
+AALQAVKMGFTAAVALTVLMIPVVVRSTEEMLRVVPNELREGSYALGVRKWRTIFKVVLP
+TAISGIASGVTLAIARVTGETAPILVTAGYAMTTNWNAFDNWMTALPVYIYRQIVSPTSP
+TAADPSMARAWSAALVLIFIVMALNLLARVIAKAFAPKTGR
+>GCF_020097155.1_00222
+MSTALNDTPTRENTPASKHTQNSLTAGQKPRWTWMAVAAGAVVLGLGLEALLAGGFADFS
+IARFIILAAILFVAGMYVATRVLENRRQATDGLWRNLVWAAFLIALVPLISVLWSVVADG
+GATLFGNPQLLVNDMQGVTGVTDAQYVQAGEPMGDLPGGFAHALVGTFLITVIATVIAVP
+IGLLTSIYLVEFGRDGWLSRAIIFFVDVMTGIPSIVAGLFAFAAMSVVLEMVMGSGPKAL
+QSVKMGLTAAIALTVLMIPVVVRSTEEMLRVVPNELREGSYALGVRKWRTIFKVVLPTAI
+SGIASGITLAIARVTGETAPILVTAGFASAVNWNPFDNWMTALPVYIYRQLVAPTSPTAM
+DASTSRAWAAALVLIIIVMVLNLLARIVAKAFAPKTGR
+>GCF_023573625.1_00104
+MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV
+IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI
+ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT
+SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM
+GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS
+GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA
+RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000255.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000255.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ffc27dafdde39e54b35488329f88248c478b8153
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000255.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00112
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES
+>GCF_003691675.1_02125
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES
+>GCF_005280335.1_00278
+MSPRMPWPVTRDTPALRHIVDLAEALRRSVHLVAQVAGARGPEADRTARELEDLDAASTA
+SLMSFLTALRSAYVTPLPRQDLYRLAGGVHAATQRVVSAGVLIQRADLEHLPAHALDVLE
+TVGRQAELLGRSTTELRDLDALEATWMQLLRASRRTERIMVQWLADLGMDLLQRDFNRQR
+EVAWALQSALEALGRVNTDLGMVLVRES
+>GCF_020097155.1_00219
+MTPRPAWLVTRDSPALGHLTDLCDTLGRAVRAVAQAVAADGSERDRVERDLSALDAAATA
+ALMAFLTALRSAYVTPVPRPDLYRLADGVKTAAHRVVGAGVLVHRADLDALPRNAVELLE
+TLGRQAELLAHGTRQLRDLDALEDTWMQLERGIRRMERLMVDWLAALGTDLLQRDYNRQR
+EIASALRDAVLALDRVNTDLGVVLVRES
+>GCF_023573625.1_00107
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000256.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000256.fa
new file mode 100644
index 0000000000000000000000000000000000000000..674684856751fd2c6af96e84ef718c7d6a234c41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000256.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00113
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD
+>GCF_003691675.1_02126
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD
+>GCF_005280335.1_00277
+MARHRQTTGRGASSSASGLVRPHRPRLSEPDELAHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPEVVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATARDGERWAAW
+YRAGHAAHAARAVAGAVEPPGPDELRRLTDTILTGAYRSEIDVAFERAGAYGRVVALGQV
+EHAEAAEAADPALAAGLTRRAARLVSTSEALEEAARAFRNGSLD
+>GCF_020097155.1_00218
+MAHHRAPAGRGASSTASGLVRPHRPRLTDPGLIADLADGEDPQEIAAAASRLAHALVAGG
+RAEEDPDVVARLVGLVREVGVETLAGLWADAPAVSLAGALWRLYALQEATARDGERWAAW
+YRAGHAAHAARAVAGAVEPPGPEELRRLTDTILTGAYRSELDVALERAGAYARVVALGQA
+EHAAAAEHADPAHAARLTLRAARMISTAEALEAAARSWRDGSLD
+>GCF_023573625.1_00108
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000258.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000258.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0a54c8a3b8f8696ee01f61fc7354d392343e67c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000258.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00116
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMLLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGVAQGRAGGESAGAKDDGGVLGAIRRALPGGKDEKDDRQKKGKPAA
+>GCF_003691675.1_02129
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMLLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGAAQGRAAGESEGTKDYGGVFGAIRRALPGGKDEKDKPAA
+>GCF_005280335.1_00271
+MAKNSMIGRYTSGKVKDFALKSALDENGEPTEGFEKVVSKVLGIQRPLVLKHIQNVAAKN
+PELTAEQIAERLGQQYLNTVTGAGAAVGGTAIVPGVGTVAALGLSAAATVGFMEATALYA
+QSLAELHGITMEDPQRAETLVMALMLGDDAKELLREAAAKAGRPFDPNASLNALAGSAAG
+TGGGAGISAFVMDRLKRTFMKKMLVRQGAGFLGRAVPFGVGAVIGGVGNRAMGKAVMENA
+QELFGPLPTVIPGEIREGAARQAQEDDGEGGVFAAIRRALPGGDDKKDAAKA
+>GCF_020097155.1_00203
+MAKNSIIGRYASGKAKDFAMKSAFDENGNPTEGFEKLVFTTLDIQRPLVLKNIQRLHESH
+PGETPEQLAERLADQYVTASTGAGAAVGGTAIVPGIGTVAALGLSAAATVAFLEATALYA
+QSLAELHGLTTKDPARSKALVMAVMLGDDTKELLKDISRKSGVKNTGTPDSAAGLAAMMN
+GGAAGQAAGGAGLGAVAIEQLKKQFVKKVLVRQGAGFLGRAVPFGVGAVIGGVGNRAMAK
+AVVKNSRDLFGPLPAQIPGEIVAASAKGQDVGQSAEDGKGGLVSGLIKALPLGKKDEKKA
+>GCF_023573625.1_00121
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMRLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGAAQGRADGTKDDGGVFGAIRRALPGGKDEKDDRQKKGKPAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000259.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000259.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d81741ff86b7b27b93c491b53b0179e8d7c292d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000259.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00117
+MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE
+KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD
+WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL
+AERLHAETLKYLAGIRRDREHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER
+LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA
+AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSVVGALAGLAIHGV
+ATLFL
+>GCF_003691675.1_02130
+MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE
+KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD
+WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL
+AERLHAETLKYLAGIRRDRQHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER
+LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA
+AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSIVGALAGLAIHGV
+ATLFL
+>GCF_005280335.1_00270
+MSLSPDPARQLLSAGTLERERGLRRMKAVALGLLVALAVVFAVAFPLQDVHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGIPVPHTALIPRKKDQLGAALTEFVQENFLDSDVARE
+KVEGLEVAAAAGGWLRRPENAERAAREVATAARGAMAAADDDAVQELLRQLMQRHMVEPE
+WSPTLAGVLQDVVTGRHHERVVDLVVEHTGDWVAAHPEMFVETVRRRSPEWSPDLVDRLL
+AERLHAEALKYLAGIRDDRDHEARRAVDDWLTRLSAEMRDDPHTRASVERFKHSLFADER
+LRAWAGRAWTSLRDSLLDALEDPASDLHRALVAALRDLGARLQEDPVLRDRVDGHARAAA
+AYALSTYGPAVTGVIEETVARWDGDQTARTLELFVGRDLQYIRINGSIVGALAGLTIHAV
+ATLFL
+>GCF_020097155.1_00201
+MAPSPVPADSPFPLTPAALERAAGLRRMKAVALGLLIVLAVVFAVAFPLQRVHPAWGFVR
+AAAEGGMVGALADWFAVTALFRRPLGLPIPHTALIPEKKDQLGAALTEFVQENFLDSDVA
+REKVAGLQVARAAGGWLRERPHAVHAAGEIAMAARGAVAATDDDAVQDLLQQLMQRHMVE
+PDWSPTLAGVLEDVLAGRHHEKVVDLVVEHTGDWVATHPEMFLETVRRRSPEWSPDLVDR
+LLAERLHAETLKYLAGVRADRDHEARRSVDDWLARLAGNMRDDPATRASAERFKADLFAD
+EQLRAWAGRAWITLRDSLLAALEDQDSDLHRALVDALVDLGVRLQEDPALQASVDGRARA
+AASYALSSYGPALTGVIEETVARWDGRQTADTLENLVGRDLQFIRINGSVVGALAGLAIH
+TLASLVF
+>GCF_023573625.1_00122
+MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE
+KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD
+WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL
+AERLHAETLKYLAGIRRDRQHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER
+LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA
+AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSIVGALAGLAIHGV
+ATLFL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000260.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000260.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e50774add8749ed98e4ab32d3dcbcf4bfef7c7c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000260.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00122
+MATRADRGRPVHNPDIIGFTDAELNETPIRPKWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVILGVIFKIVLVEGVGRWYLSTGKTIFQGWRSLGSWTSWYFGPYILIWGFV
+YGATAMSSAALPLAALFPGVDMKVYAIGLGLVGLGLVWLNRYGLIEKLMAVLIGVMFLTV
+LLSAALTAPNVGDILAGLVPRIPSGDPDVMFYVLGLAGGVGGTITLGAYAYWLREKGWNV
+PKYMRVMKFDNATSYILTGIFVIATMIMGVELLHSAGLAISSGDRGLLDVGNVLAERYGQ
+AYSVVFLVGFFAASFSSLLGVWHGVSLMFADFWTNFRRPADELDQDDAPSLASKPGRFFL
+LWLTFPPMTLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNKKEVPAQFRNGWIRNTL
+LGLTAAVFVAIGVNELWKALQPLIGG
+>GCF_003691675.1_02136
+MAHAVDPGRPVHNPDIVGFTDAELNETPIRPRWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRYYLSTGKTIFQGWRTLGAWTSWYFGPYILIWGIV
+YGATAMSSTALPLAALFPGVDSKVFAIASGLIGLGLVWLDRYRLIEWLMTVLIGVMFVTV
+LLSAALTVPNLGAILAGLVPRLPSGDPQAMFYVLGLAGGVGGTITLAAYGYWLREKGWNV
+PKYLKVMRFDNATSYILTGIFVIATMVMGVELLHSAGLAISSGDKGLLDVGDVLAERYGS
+AWSTVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPAEELDQDDAPSLSSKPGRFFL
+LWLTLPPMALLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNTKDVPRQFRNGWVRNTL
+LGLTAAVFVAIGVNELIKALQPVLGG
+>GCF_005280335.1_00263
+MPHTADRGHPVHNPDIVGFTEAELNETPIKPRWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRWYLSTGKTIFQGWRQLGSWTSWYFGPYILIWGFV
+YGATAMSSTAIPLAALFPAVDAKVFAIAAGLIGLALVWLNKYGLIEKLMTALIGVMFVTV
+LISAALTAPNVGEILSGLVPRIPSGDPQVMFYVLGLAGGVGGTITLGAYAYWLREKGWNV
+PKYMKVMKFDNATSYVLTGIFVIATMIMGVELLHSAGLAISSGDKGLLDVGNVLAERYGQ
+VWSYVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPADELDQDDAPSLASKPARFYL
+LWLTILPMSLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNRKDVPVQHRNGWIRNIL
+LGLTAAVFVAIGVNELIKALQSVLGG
+>GCF_020097155.1_00197
+MSHTTPPGHGLVDRHHPVHDPDIVGFTEAELNETPIKPKWNSLGPGIVAAATGVGAADLV
+ATLTAGSRYGYMLLWAVVLGVVFKIVLVEGVGRYYLSTGKTIFQGWRGLGSWTSWYFGPY
+ILIWGFVYGATAMSSTALPLAALFPGVDSKVFAIASGLVGLGLVWLNRYGLVEKVMTVLI
+GVMFVTVLISAALTVPNLGDILGGLVPRIPSGDPDVMFYVLGLAGGVGGTITLGAYGYWL
+REKGWNTPKYMRVMRFDNTVSYVLTGVFVIATMIMGVELLHSAGIAISSGDKGLLDVGDV
+LAQRYGDVWATVFLIGFFAASFSSVIGVWHGVSLMFADFWTNFRRPADELDQDDAPSLAS
+KPGRFYLLWLTFPPMVLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNSRRVPGKFRN
+GWVRNVLLALTTAVFLVIGGNELLKALKPLIGG
+>GCF_023573625.1_00130
+MATRADRGRPVHNPDIIGFTDAELNETPIRPKWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRYYLSTGKTIFQGWRTLGAWTSWYFGPYILIWGIV
+YGATAMSSTALPLAALFPGVDSKVFAIAAGLIGLGLVWLDKYRLIEWLMTVLIGVMFVTV
+LLSAALTAPNLGEILAGLVPRLPSGDPQAMFYVLGLAGGVGGTITLAAYGYWLREKGWNV
+PKYLKVMRFDNATSYILTGIFVIATMVMGVELLHSAGLAISSGDKGLLDVGDVLAERYGS
+AWSTVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPAEELDQDDAPSLSSKPGRFFL
+LWLTLPPMALLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNTKDVPRQFRNGWVRNTL
+LGLTAAVFVAIGVNELIKALQPVLGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000261.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..559da924c0de944ea5af40aae45a0ba4a595014f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000261.fa
@@ -0,0 +1,18 @@
+>GCF_002008305.4_00123
+MIVAFSVAPSGQPADSAHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDWD
+EVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHSGELDGKLERLEAALAEDGNGDAADAR
+>GCF_003691675.1_02137
+MIVAFSVAPSGQPADSAHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDWD
+EVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHTGELDGKLERLESALAEDEGRRAAPAPH
+DGDAG
+>GCF_005280335.1_00262
+MIVAFSVAPSGTPADAAHQPGDEDSASVHRAVAAAVAVVRESGLPHRTSSMFTEIEGDWD
+EVMDVVRGAVDAVAPYGSRVSLVLKADIRPGHTGELDGKLARLEAALASDDVS
+>GCF_020097155.1_00196
+MIVAFSVSPSGAPADAAYAPSSDGDSASVHRAVAAAVAVVRASGLPHRTSSMFTEVEGEW
+DEVMGVVKRAVEAVEPYGSRVSLVLKADIRRGRTGELDGKLERLEAALTDGTPATPDRFR
+A
+>GCF_023573625.1_00131
+MIVAFSVAPSGQPADAEHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGEWD
+EVMEVVRAAVDAVSPYGTRVSLVLKADIRPGRTGELDGKLERLESALAEDEGRRAAPAPR
+DGDAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000262.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000262.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73a103ac3cd0e9eac7a33ae9b6ad7cd0b4b886d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000262.fa
@@ -0,0 +1,23 @@
+>GCF_002008305.4_00124
+MAVTVRPATSDDVEPLLRVKAQAWREAYGGLLPAAHLDAVDAGVPEQVPGWAALVGSDRE
+LWVADDGGRLLGMALAGPRRSQGGGLPDLELMALYVLAEAYGTGLGALLLDAVVGKRPAV
+LRVLAENPRAVAFYAKHGFAPEGGPEPMTGPWAGLHEQLMVRRG
+>GCF_003691675.1_02138
+MPESVTVRPAAPGDVEALLRVKARSWREAYGALLPSAYLDAIEARIPEDVPAWTALIGPD
+RDLWVADDGGRLLGVALAGPRRSAAETGRTGADDAAASPADLPDVELMVLYVLAEAYGTG
+LGARLLDAVVGERPAMLRVLAENPRAVAFYAKHGFAAVGAPEPMTGPWAGLHEQLMVRRR
+PHDGGAA
+>GCF_005280335.1_00261
+MAVVVRPARREDAEALLRVKAQSWREAYGAHLPAEVFDRADARVPQDAPAWAALVGSDRD
+LWVAEDDDGGRLVGVALAGPSRIEDEGLPPRELMVLYVLAEAHGTGVGARLLDAVVGDGP
+AVLDVLAENPRARAFYAKHGFEDHGAPAPMDGAWAGLHEQRMVRRG
+>GCF_020097155.1_00195
+MRETDGASDAVVRDVNPPSAPAPTVRPAGADDLPAVLAMKNAAWRETYAHLLEPGFLAAQ
+EAELPRAVEAWTRLLGEPGMEVWLAEGAGVVVGMAAAGPADDPALGPEGRELIALYVRAR
+LHGAGLGAALLRAAVGGRPARLDVLVGNERAIAFYERHGFVAVGEPAVLGGPWGDAREQR
+MVRR
+>GCF_023573625.1_00132
+MPESVTVRPAAPGDVEALLRVKARSWREAYGALLPSAYLDAIEDRIPEDVPVWTALIGSD
+RDLWVADDGGRLLGVALAGPRRSAAETGRTGADDAAASPADLPDVELMVLYVLAEAYGTG
+LGARLLDAVVGDRPAVLRVLAENPRAVAFYAKHGFASVGAPEPMTGPWAGLHEQLMVRRL
+PHDGGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000263.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000263.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eafb3d5d88cc72494a8838b2754ce39f8c13ae0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000263.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00125
+MSRRSGRSSGRSSAASSSSRGSAARRGRAAEPEGIVPGVHEISHGTAEIREDPYEPGAFV
+LYVNGVESSPLDPDHPERMGFEYMRWAVAAVRAHWPEPTPLRALHLGGAGCALARWVDHA
+HPGSHQTAVEIDAGLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAP
+DPTDLTGARHITPPGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFE
+HVEVIADPPMLKGRRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAE
+DPRGFPAGVAPGITGLVPGPEA
+>GCF_003691675.1_02139
+MSRRSSARRGRAAGGSAGPAGIEPGVHAITHGTAEIREDAFEPDAFILYVNGVESSPLDP
+ERPERMAFEYMRWAAAAVRAHWPEPTPLRALHLGGAGCALARWVDHAYPGSHQTAVEIDA
+GLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAPDPTDLTGARHITP
+PGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFEHVEVIADPPMLKG
+RRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAEDPRGFPAGVAPGI
+TGLVPGPEA
+>GCF_005280335.1_00260
+MITPGVFAISSGTAEILPDPWTDGVYLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLAH
+RFAPDAERLRVLHLGGAGCTFARWVTHTWPQAHQLAVELDAGLAELARTHFDLPRAPQLK
+IRVGEAGQVLAGLREATREVVFRDVFAPADPLSLAPDSPHVTPAHLTGADAAAHAARVLV
+PGGVYVLNIGGGPDLASVRREVAALRTAFAHVEVMADPAMLKGRRRGNVIAAASSVPLAA
+EELGGRAALARALRSDALPAQLVDDVARFAGGLAPDPTPLVQASDGTSEGASTQASPGPA
+Q
+>GCF_020097155.1_00194
+MITPGTFPISSGTAEIVPDPWTDGVFLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLTH
+RFAPDARLRVLHLGGAGCTFARWVTHTYPASHQLAVELDAGLAAVAREHFDLPRAPQLKI
+RVGEAGEVLAGLRDATREVVFRDVFAPDPADPTGALHVTPAHLTGLDAAAHAARVLTPGG
+VYLLNIGGGPDLTSVRREVAALTETFAHVEVMADPAMLKGRRRGNVIAAASSAPLSADGL
+GGRSALARALRSDALPAQLLDDVVAFTAGLTPDATPLVTPAEG
+>GCF_023573625.1_00133
+MSRRSSARRGRAAGGAAGPAGIEPGVHAITHGTAEIRENAFEPGAFILYVNGVESSPLDP
+ERPERMAFEYMRWAAAAVRAHWPEPTPLRALHLGGAGCALARWVDHAYPGSHQTAVEIDA
+GLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAPDPTDLTGARHITP
+PGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFEHVEVIADPPMLKG
+RRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAEDPRGFPAGVAPGI
+TGLVPGPEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000266.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000266.fa
new file mode 100644
index 0000000000000000000000000000000000000000..365bf0d943a72067d2bccb510a8ceac77a93cdc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000266.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00131
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAQQAELTAAVVELLRTAREAGRPVFLVR
+TEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRDE
+MRQPLLGQDEALTLLRTGLVPDRG
+>GCF_003691675.1_02145
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAQQAELTAAVVELLRTAREAGRPVFLVR
+TEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRAE
+MRQPLLGQDEALTLLRTGLVPDRG
+>GCF_005280335.1_00254
+MPDSAPAPEPIAGERPSGGETALVVVDMQYSYFEHPDLAARQAELTEAVVELVRTAVEAG
+RPVVLVRTEHERDRSTWTLNMLEDGEGFAFPGTRQAAVLDEVARAARGAVEVVKTRDSAF
+HRTDLDAQLRRRGVGRLLLCGVSTHSCVFQTATDAFARDFHAATAVDAIASEDPRLSAAM
+LEFLRDEMRQPLLGREDALALLRTGLVPDQG
+>GCF_020097155.1_00651
+MNTLQNPALIVVDVQRGFDDVEYWGSRDNPDCETNISSLLTHWRDRSWPIVFVRHDSTNP
+ESTLAVGTPGNEFKEVITGDPDLLVSKTVNSSFHGTPDLDDWLRAEGIEQVVICGITTNH
+CCETTARIAGNLGYDTYFAIDATHTFDRPALDGTVLPAATVSAMTAANLHGEFATVVSTR
+TLIDGNSYAPRYEQEK
+>GCF_023573625.1_00139
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAHQSELTAAVVELLRAAHEAGRPVFLVR
+TEHARDRSTWTLNMLADDEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRDE
+MRQPLLGQDEALTLLRTGLVPDRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000267.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000267.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab42debec2ea2a66e38ac36388157f150bed21bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000267.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_00133
+MSDPTPPSTEPMIPEQPGNHPSSATAPDAGVAPATSAAAGRDRVLLPWVFWPSAVIVLSF
+VGATLLAPAQMTVGIGLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK
+PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTQAEAAQSALATTFL
+HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYVMIGAVTCVVLYTVVSGVERGMKWLSN
+TNLILAAGLLLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS
+AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR
+PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA
+TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS
+LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA
+AGVPASEGPRRPRLRRHEH
+>GCF_003691675.1_02147
+MSDPTPPSTEPMIPEQPGNHPSSATAPDAGVAPATSAAADRDRVLLPWVFWPSAVIVLSF
+VVATLLAPEQMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK
+PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTQAEAAQSALATTFL
+HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSN
+TNLILAAGLLLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS
+AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR
+PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA
+TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS
+LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA
+AGVPASEGPRRPRLRRHEH
+>GCF_005280335.1_00252
+MSESIPPSHPSAPPGPASAHPAAPAAGAADAREASGAVAPASSDAATGARVLLPWVFWPS
+TIVVLLFVGATLLFPEPMTAAIGTVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGAIT
+LGKPDEKPEFSTLSWFALLFAAGMGIGLVFFGMTEPLMHFVSPRPDLAATDPNPAQAAQA
+ALATTFLHWGLQPWAIYAVVGVAVGLAIHRRGRPLALRWAFEPLLGERRVRGGWGHLIDN
+IALIGTVFGVATSLGLGVTQMSAGLRSLGVVPEESAWVEYAMIGLVTLVVLYTVVSGVER
+GMKWLSNVNLVLAAGLLLFIAIVGPTAFLFKEMVQSFGAYLQTFFGASLNVSAFQGAEGD
+AWQAGWSAYYWGWWMSWTPFVGIFIARISRGRTVRQFLAGVLLVPTLIGVVWFGVLGGTA
+IYLETVRPDGYTSVVGADGSIDSNTALFQVVEQLPAGALLVIGAIMLSAIFFVTSADSGA
+LVMGMLATGGDVNPKVPVKIFFAIATALMSAALLAAGGLSAIQTLAITIGLPFSVLMLVM
+CLATFRSLGYSVARVEAVRRQAMLASIKDRFGLDTDDDEVVDGGPVAASQWWASLSRDRQ
+RTIAQAASAGPDDEIRLAGSSAEEPAGSPDARR
+>GCF_020097155.1_00188
+MTPAPAGRDADAPAANRPHRTGPDPDVKHPAPATADQADRGHAGLLPWVFWPSTLIVLLF
+VVATLAFPAQMTDVIGDVQAAIIRNFSWWYAIVAFAFVVFCAYLVFSRKGSITLGKPDEK
+PEFSTMSWFALLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTEAQAAQSALATTFL
+HWGLQPWAIYAVVGVAVGLAIHRRGRPLSLRWAFEPLLGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMAAGLRSLGIVPADSPWLEYAMIAAVTCVVMYTVVSGVERGMKWLSN
+INLVLAAGLLLFIALVGPTPFLLKETVQSFGAYLQNFFADSLNVSAFYGAEGDAWQAGWT
+AYYWGWWMSWTPFVGIFIARISRGRTVREFLMGVLLVPTLVCVVWFGILGGTAIWLETVR
+PAGYTSVVGADGAIDSNSALFQVLEQLPAGLLLVIGAIILSGIFFVTSADSGALVMGMLA
+TGGDVNPKTAVKIFFAIATAFMAAALLAAGGLSAIQTLAITIGLPFSVLMLVMCVATFRS
+LGYSAARVEAVRRQAMLASIQDRLGKDTDDDEVVEGGPVAASQWWASLSRDHQRTIARLA
+SPGPDDEIRLHEDATATSARPDTTRGGSTAR
+>GCF_023573625.1_00141
+MSDPTPPLKNPLDPERADTRPSSAPTADGAVAPATSAAAARDRVLLPWVFWPSAVIVLSF
+VGATLLAPEQMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK
+PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDVAAANPTQAEAAQSALATTFL
+HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSN
+TNLILAAGLLLFIAIVGPTAFLLKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS
+AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR
+PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA
+TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS
+LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA
+AGVPASEGPRRTRLRRHGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000268.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9530497d7d68bd88fd6f2d23734db308f7bd397c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000268.fa
@@ -0,0 +1,59 @@
+>GCF_002008305.4_00135
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPTRGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
+>GCF_003691675.1_02149
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPTRGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
+>GCF_005280335.1_00250
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPDSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFLDQDRVHEVYRDWRRVLDSYGHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPARGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTDPVDLPTGHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
+>GCF_020097155.1_00185
+MTTQRLTTPPSEARNRPETPWWVDAVVYQVYPRSFADGDGNGMGDLPGVTAKIPYLSRLG
+VDAIWLSPFYLSPQHDAGYDVADYRTVDPRFGTLADADALIDAAHAADIRVIVDLVPNHT
+SSEHPWFQAAMAAGPGSRERARYHFTEGRGEHGELPPSNWESTFGGGAWSRVTEADGTPG
+QWYLHLFDTTQPDLNWENPEVREEFESILRFWLDRGVDGFRVDVAHGLVKKPGYPDADHT
+RMGMVTDAGEDQDPDFDVDAFEPAMPFLDQDGVHEVYRQWRRVLDSYPHEPMMVAEAWVS
+PLPRTFRYVRPGEMHQAFNFTYLMAGWDAESLTSAIDRSFTEAEKVGAPNTWVLSNHDTV
+RHTSRYGLSDPTAYPAGITAEDEQPDEALGRRRARAAAMIELALPGSAYIYQGDELGLPE
+HTTLPAELREDPYFFRTGGAEPGRDGCRIPLPWAADEPALGFSGPDADAAPWLPQPDSFR
+VLAADRQVGVEGSHFELYRHLLQIRAELDLGTGTFAWSAEHHRPEQGVLAFTVSSGGGRH
+LGSGVPIPARTVLVMANIGDTPVALPGDHVRAQFSLPESEAVVDDRLAPDAAAWLLLR
+>GCF_023573625.1_00143
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPARGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTDPVDLPAGHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000269.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000269.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f96620a7770d332edd3a70ccc5b3bef6d06110f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000269.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00136
+MTHDDGGPPPGVARGTAHLRVFQPLAAFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA
+RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHSAAIPPA
+ARAMNRGRALVALEDEWGLSPDPDAAVEDPQDEDGAPEHHRVQTRTATWGVPHGWLTVFD
+PEEPVQRLVDGERTAYRRAPIVAARERAGHAAAVLARHAPDAELIGELTVMVEWLGAFHP
+DSWVELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWATVGMLARLT
+>GCF_003691675.1_02150
+MTHDDGGPPPGVARGTAHLRVFQPLATFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA
+RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHEAAIPPA
+ARAMNRGRALVALEDEWGLSPDPDAAGQDPQDEGGAPEHHRVQTRTATWGVPHGWLTVFD
+PEEPVKRLVDGERTAYRRAPIVAARERAGHAAAVLARHALDAELIGELTVMVEWLGAFHP
+DSWIELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWAAVGMLARLT
+>GCF_005280335.1_00248
+MVHDDGADGPAPGGGRVPGGAPPPGIAHGTAHLRVFQPLAAYPDAVQARLIAGAHRTRAE
+VEAEAAERARRRLARPVTDPFPEPGEDDLVRVLQDEQGSAFYCPDEFGLRAEMAAAQLEE
+TMLPLAYEAAVPTAARAMNRGRVLVALEEEWGLSPDPDADRAHPDEEDGPGRDEDGPSGR
+HRVQTRTATWGVPHGWLAVFDPEEPVRRLVDGERTAYRRAPALAALERAGHAAAVLSRHA
+PDAELIAELTVMVEWLGAFHPDSHVELDYGGLTRHVWPDDSVFDLWTLIDALGEGDEATA
+GVAQGRLNRRWAAVGMLARLT
+>GCF_020097155.1_00182
+MRTAAANLRVFQPLSAYPDAVAARMVAAAHRTRAEVEAEAAERARRRLLRLPADPFPAPG
+EDDLVRVLERGGSAFYCPDELALRMEMAAEMLEASAPEALYAAAVPAAARAMNRGRALVA
+LEDEWGLSPDPDAPAPDDPQDAAHQDQDADAGTHRLQTRTSLWGVPHAWLAAFDPEEPAR
+RLVDGEDVAYRRTPVAEAVERVGHAAAVLAGAAPDAELLGELAVMIPWLQAFHPDAVLEL
+DYGRALTSLVWPDDSVFDLWTLLDALEEGDEVGAGMAQERLNRRWARVGMHAHDG
+>GCF_023573625.1_00144
+MTHDDGGPPPGVARGTAHLRVFQPLAAFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA
+RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHEAAIPPA
+ARAMNRGRALVALEDEWGLSPDPDAAGQDPQDEGGAPEHHRVQTRTATWGVPHGWLTVFD
+PEEPVKRLVDGERTAYRRAPIVAARERAGHAAAVLARHAPDAELIGELTVMVEWLGAFHP
+DSWIELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWAAVGMLARLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000272.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000272.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aaaa7f8872abc2352586ca045405685b4e4713ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000272.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00139
+MSEIQHDDAVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRAQWQLLNTLTVAPQSR
+AELEAGFEEEQRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEAT
+ADVPRDQIDDAVRVLRRIARNLGHPDA
+>GCF_003691675.1_02153
+MSEIPHDDAPVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRVQWQLLNTLTVAPQS
+RAELEAGFEEEQRGAVSGQIEELVESHWVTVEGDLYTLTATGRTAGARVGEAVEALRAEA
+TADVPRDQIDDAVRVLRRIARNLGHPDA
+>GCF_005280335.1_00245
+MSEIPHDDAAVQHPSGLPLAHWLTLTEGLIAVRVAESLEEHGLTRAQWQLLNTLTVAPQS
+RAELEAGFEEEHRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEA
+TADVPRDQIDDAVRVLRRIARNLGHPDA
+>GCF_020097155.1_00179
+MTDNTQTPENRQTQAPRRDSHPSGLPLSHWLTVAEGLLAARVAASLEEHGLTRAQWQSLN
+ALTAAPLSAAEIGAGFEPEVRGAVVEQLDELVDAGWVTVEGDLFTLTSTGRTAGERVGEA
+VERLRGEATADLPAEHYEVTVATLRTIARNLGHPDA
+>GCF_023573625.1_00147
+MSEIQHDDAVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRAQWQLLNTLTVAPQSR
+AELEAGFEEEQRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEAT
+ADVPRDQIDDAVRVLRRIARNLGHPDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000274.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000274.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20c4b4f9c4f54683212293a2a505ca8ac264b991
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000274.fa
@@ -0,0 +1,37 @@
+>GCF_002008305.4_00141
+MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE
+DALAGGERAKLDRYGEDSFMVLHPARYIDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA
+AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR
+RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL
+SEQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNSALELDSTLASKRLAEQSIAQNEQ
+VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW
+L
+>GCF_003691675.1_02155
+MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE
+DALAGGERAKLDRYGEDSFMVLHPARYVDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA
+AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR
+RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL
+SDQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNNALELDSTLASKRLAEQSIAQNEQ
+VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW
+L
+>GCF_005280335.1_00243
+MIDNAVYVDGRRVHAPSTLEDTWEAAEASGGMAWLGLYRPDADELRAVADELHLHPLAVE
+DALEGGERAKLDRYGEDLFMVLHFQHAIRALPVIVEQLQGGARARLREEEHRREVGAPRT
+GDVHEWDQDELSEEGVFEVENLRRLRDVHDHAVQINERVAAMRQMLANALELDSTLASKR
+LAEQSIEQNEQVKQISSWAAIIFAPQLVGSIYGMNFDGMPELHWAFGYPFALGLMLAVAL
+TLFVLFKRADWL
+>GCF_020097155.1_00177
+MTLIDNAVYVDGRRVFAPTSLSDTWDAIERTGGMAWLGLYRPHPDELQEVADELPLHPLA
+VEDALTPGQRAKLERYGDDWFMVLHPARYIDATETVEFGELDVFTGKDYVVTVRHAEEPD
+LADIRAGMEQRHTDRLAQGPSQVAFEILDHVVDAYFPVAEGLEQDIREIEDQIFSGDAAV
+SRRIYELSREIIGFERATRPLPRMIEQLQEDMRARLGDAANGSHASHLEAPEPEPGEEER
+AELVETLRALRDIHDHAVQVTDRVAAMRQMLENALELDSTLASKRLAEQSIAQNEQVKRI
+SSWAAIIFAPQLIGSVYGMNFQHMPELEWPLGYPWALGLMLGVAVALYALFKKADWL
+>GCF_023573625.1_00149
+MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE
+DALAGGERAKLDRYGEDSFMVLHPARYVDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA
+AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR
+RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL
+SDQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNNALELDSTLASKRLAEQSIAQNEQ
+VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW
+L
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000275.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000275.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf0753b300d864a68e77c3db00747186b9aa608d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000275.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00142
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR
+>GCF_003691675.1_02156
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLATRGPAVTGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR
+>GCF_005280335.1_00242
+MNSPRHAAPVVRDGRTLLPAHAVTTAPIAAFGLIGGYLTARETGIRPLGGVVLAAAGAYA
+GRTWLAKRGPAVAGGLTALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDREGA
+R
+>GCF_020097155.1_00176
+MSKDTSTPVARDGKTLLPADAVTTAPIAALGLVGGYLVARETGIRWLGGVVLGAAGLYAG
+RTWAAKGGPAVAGTLGALYLGGFGASHPLAKKIGAWPSVLSVAAASAGAAYAAVDRKDGR
+R
+>GCF_023573625.1_00150
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000277.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000277.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d8783e87b854fbdaece081d844b4df3d28a4d05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000277.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00144
+MRAEQVTDPIAYHGEGPVWAASWGAAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTLAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
+>GCF_003691675.1_02158
+MRAEQVTDPITYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
+>GCF_005280335.1_00240
+MRAEQVTDPITYHGEGPVWAEHWGTAASGLAAGGGLRWVDMLAGDVLSLRADGAVERTHV
+GDVAAVVRPRAGGGAVLAVERGFALMSPEGELTTLPELWGPEAGLRMNEGGCDPDGRFHA
+GTMAYAKTPGAASLHRLSPGPDGGAGEVDVVLTGATTSNGLEWSPGGSLAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGEDLGTLYITTSWENMERGEDPLAGALFAVRPGVTGLPARPFAS
+>GCF_020097155.1_00174
+MRADQVTDPLCYHGEGPVWAESWGGLRWVDMLAGDVLSLGADGGVTRRNVDPKVCAVVRP
+RVGGGAVFAVERGFALEDPDGTLHRLPPLWDDAAGLRMNEGGCDPDGRFYAGSMAYAKTP
+GAASLHRLSPAPEGGAGEVDVVLEGVTTSNGLAWSPDGSLAYYDDTPTRQVAVFDYSREE
+GLTNRRVLVDVLDGEGKPDGLCVDAEGGIWVAVISHGRIHRYTPEGVLDEVVEVPVQKTT
+ACTFGGDDLGTLYITTSWEGMERGEDPLAGALFSVRPGVAGLPTLPFAG
+>GCF_023573625.1_00152
+MRAEQVTDPIAYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRTDGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000278.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000278.fa
new file mode 100644
index 0000000000000000000000000000000000000000..efe6787b83114bb88c4df2a463017207f0cc0196
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000278.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00146
+MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKHSVNIALHTDHCPQDKLEDFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVADGIATVEALGLGENGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGR
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
+>GCF_003691675.1_02160
+MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVADGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
+>GCF_005280335.1_00238
+MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGASVKDMVTGSLAMAAFAREVAKNYSVNIALHTDHCPKDKLDAFVMPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGKELLARTHANKQILEVEIGVVGGEEDGVAHEINDKL
+YTTVEDGIATIEALGLGEQGRYLTALTFGNVHGVYKPGNVKLRPQILEDIQKAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYAGVLKVDG
+EVGDKKMYDPRVWGAKAEEAMAARVVQACQELNSAGTSIG
+>GCF_020097155.1_00173
+MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAVRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAMAAFAREVAKKYSVNIALHTDHCPKDKLDGFVKPLLDASEAEVKAG
+RDPLFNSHMWDGSAETLEENLRIAQELLARTHANKQILEVEIGVVGGEEDGVANEINDKL
+YTTVEDGIATIEALGLGENGRYLTALTFGNVHGVYKPGGVKLRPQILQDIQQAVGEKFGR
+QRPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYDGVLKVDG
+EVGNKKMYDPRVWGAKAEDGMAARVVQACQELNAAGKSIG
+>GCF_023573625.1_00154
+MPIASPEKYAEMIDAAKNGAFAFPAINVTSSQTLNAAIRGFAEAGSDGIVQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVQDGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000279.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000279.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8079c5c064b6957838228d25aa89379aef3d893e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000279.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00147
+MDHGNGPPLVKNVTFFPKHVISSPVPSTVPRMMTRPLPEDSATVDTVALGRRVRHLRKQA
+GLTLDQLAERTGVSGSHLSLVENARREPRLSLVQRIAEVLGVPVEDLLTGRAPTRRAELE
+IEVERFARSEHYASLGLPPLRIGPRTPTEVLEVIAGLEAELRRRLEEQAATPEEARRANA
+QLRARMRAVDNHYPDLEAEAHRLLDAIGHTGGPLGLHAVSELAEHLGFTLRFVPDLPHST
+RSVTDLKHGRIHISGSRSSDHDRRTVVLQALAAAVLGHGEPRDYEDFLAQRVAVNYLAGA
+LLMPQRAASSLLRAAQKRRDLSVDDLKDAFGVSYEAAAHRFTNLATVDLGIRCHFQKVHE
+TGVIHKAYENDGIVFPADHTGAIEGQQACRKWGARQAFSRNDRFRAHAQYTDSPNGTFWC
+TSMIENGPDGLFALSVGTPFEHARYFRGADTRHRVTSTCPDPRCCRRPDPELEAAWGGHV
+WPAARMHAHLLAAMPTQTFPGVDEREVFEFLQAQEEREG
+>GCF_003691675.1_02161
+MMTRPLPEDSATVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGSHLSLVENARREPRLS
+LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL
+EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTG
+GPLGLHAVSELAEHLGFTLRFVPDLPHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQAL
+AAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQKRRDLSVDDLKDAFG
+VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRK
+WGARQAFSRNDRFRAHTQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADT
+RHRVTSTCPDPRCCRRPDPELEAAWGGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFL
+QAQEEREG
+>GCF_005280335.1_00236
+MMTRPLPEDSATVDAVALGRRVRHLRKQAGLTLDQLADRTGVSGSHLSLVENARREPRLS
+LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL
+EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAQRLLDAIGHTG
+GPLGLHAVSSLAEHLGFTLSFVANLPHSTRSVTDLKHGRIHVSGGRASDHDRRTVVLQAL
+AAAVLGHGEPRDYEDFLSQRVAVNYLAGALLMPQRPASALLRAAQKRRDLSVDDLKDAFG
+VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGLVFPADHTGAIEGQAACRR
+WGARQAFGRSDRFRAHTQYTDAPNGTYWCTSMVEHGPDGLFALSVGTAFEHARHFRGADT
+RHRITSTCPDPRCCRLPDPALEAEWGGHVWPAARMHAHLLAAMPTQAFPGVDEVEVFEFL
+ESQRDRTPGAPGADAPDGAGGVTP
+>GCF_020097155.1_00821
+MATPTDPAHEPPRVDPLVLGRRLRHLRRVSGATLSDVAEKVGVTASHLSLVENGHREPRL
+TLLTALADVHGVGVEDLLTPEAPSRRAALEVAVERAQRGPLFQRLGLPALKIGPRTPDEV
+LEVIAGLQAELDRQMAERVSTPEEARRANSALREEMRACGNHYADLERRAQELREAVDVA
+DGPLTHHHVSALAEHLGFAVRFVPDLPHSTRSVTDLKNRRIYLARARRPDHDPRAVLLQA
+VCSSVLGHGEPADYADFLRQRVYTNYLAAAMMMPERGTVRALREAKERRDLSVDDLRDRF
+GVSWESAAHRFTNLATEHLGLTCHFAKVHESGVFHKAYENDGIPFPTDHIGAIEGQTACR
+HWTSRQVFSVADHLGAFPQYTDTPAGTYWSAAVVEPTSTGFYSLTVGVPFDDAKWFRGRE
+TSARTRSTCPDPKCCRLPSAELEAAWGGQAWPAARANAHLLAAMPGGAFPGVEEVQVFEF
+LQTQESRWPPEGSGAA
+>GCF_023573625.1_00155
+MMTRPLPEDSATVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGSHLSLVENARREPRLS
+LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL
+EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTG
+GPLGLHAVSELAEHLGFTLRFVPDLPHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQAL
+AAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQKRRDLSVDDLKDAFG
+VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRK
+WGARQAFSRNDRFRAHTQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADT
+RHRVTSTCPDPRCCRRPDPELEAAWGGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFL
+QAQEEREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000281.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000281.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7201dc9ea10d6b82823467030f63658e693261c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000281.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00149
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDQID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVEPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFASQDDAAAKA
+>GCF_003691675.1_02163
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDRID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVVPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFAGQDDAAAKA
+>GCF_005280335.1_00234
+MTTTTVTSGRHHAAPALHHTDEPVDTAAHTPLPHDVSTQALPVVAPAGAAPVVTVHGPVT
+DRQAEILTEDALAFLGRLHRVAEDRRRRLLEEREFTRQRITEGWDPHFLRATKRVREDDS
+WRVAPLAPGLKDRRVEITGPVDRKMTVNALNSGATGWLADFEDSSTPSWERMLDGQVNLY
+DAIRGRIDFTSPEGKEYRLRGAELTDRPTIIVRPRGWHLTDDHLRVDGEPMAGGLVDFGL
+YFFHNAAELVRRGHGPYFYLPKLESHLEARLWNCVFVAAQDALGIPQGTIRATVLIETIT
+AAFQMEEILYQLRNHAAGLNAGRWDYIFSLIKNYRDRGPAYVLPDRAEVTMTQPMMRSYT
+EQLVRACHRRGASAIGGMSAVIPDRRDQAANEVAFAKVREDKTREARDGFDGSWVAHPDL
+VPVAREVFDEVLGEAPNQIRTRRREDVEPDEAGLLDVAATTGSVTEAGVRRNIEVAMRYV
+ESWLRGQGAAAIHGLMEDAATAEISRSQIWQWAHNRTAVALEDGGTRTASREWMEQLVRE
+EHARILAGPLPEGHRFEDARRVFCESALPPEYPAFLTLGAYRRHFSAERA
+>GCF_020097155.1_00819
+MMTLQTTHSDTTVNGVRVLGEPVPGQDRVLTSAALEFLAALHRGVEGRRRELMDERAARR
+RRIAEGETLDFLPATRKVREDDSWHVAPLAPGLRDRRVEITGPVDRKMTINAMNSGAKCW
+LADFEDSSTPSWENVIAGQVNLQDAIRRTISLTTPEGKEYTLGGVQLVDRPTIIVRPRGL
+HLMEDRILVDGQPVSGALADFALYFFHNAKELLRRGRGPYFYLPKTESHLEARWWNCVFV
+RAQDLLEIPQGTIRATVLIETITAAFEMEEILYQLRNHAAGLNAGRWDYIFSVIKTFRER
+GEDFVLPDRSEVTMTQPMMRAYTELLVRTCHRRGASAIGGMAAQIPNRKDPEANAAALEK
+VRSDKTREAGDGFDGSWVAHPDLVPVAMEVFDAVLKDLPNQIRTRRREDVVPDAAALVDI
+KSTTGSITEQGLRMNIEVGIRYVESWLRGNGAAAIHNLMEDAATAEISRSQIWQWIRTGS
+TARLTDGGERTVTREWVEQVTEEEFGRIERTEGDRFDDAREIFTSVALAEDFPDFLTLPA
+YERFLSAEARRRAGHGA
+>GCF_023573625.1_00157
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDQID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVVPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFAGQDDAAAKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000282.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000282.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53bd87b7e37d89206f81fb306dfe855a0938b627
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000282.fa
@@ -0,0 +1,39 @@
+>GCF_002008305.4_00150
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSASASASPSPSTSGD
+>GCF_003691675.1_02164
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSASASPSPSTSGD
+>GCF_005280335.1_00233
+MREARESASAEGTPRAQPRQALETLGPGIRDGAATTAWENTAAVRNDTVSVMDCTRDVLD
+QRTLDAVATHIPDGSNIEIVQLFAAQDETHEFLTCAYNGYFEYSPGMPLAQVQYQHNLDS
+TRLDWCEDEPATVADEYTFDPETGKGLLALLRPGMIGGQDGAPLMPQRTAWACSEDGTEL
+VSVTMGSMEGYGDANGGLTQVENSPVAGSTTLVTEARDHLADTVLKDASRFHEVIKLSSP
+FFLNASMDEESLAKAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPPRPFQGAAREA
+AESQRAAEASASAAEASASRAASGSGTPSPSSTPASRTPSPSGTGG
+>GCF_020097155.1_00172
+MTHPTSAPHRAAAALGAAALALTLAGCSDSGQPSPASSTSTATAAAGSSASATGDPQSPA
+SAAASEIRAARASEKADGSERPQPREALETQGPGITSGAASAGWKSVAARYNDTVSVMDC
+TQDVLDQTTLDAVATHIPVANDIGIVQLFASRDQTHEFLTCQYQGSSSRSEGAPLVMVHY
+QHNLDGRRLEWCRPEAPVMADEYSYDESTRKGLLALLRPGMVGGADGAPLLPQRTAWACN
+EDGTQLVSVTFGAMKGYGSVNEGLTQVTNSPIANSTTLATQARDHLADTVLKDPSDFQAD
+IETSSPFFLNAQTDQETLDKAKGLPTGIIPQDQLSDQSTIDRPEGAPEPVAPGQPPRPFV
+GAARDAAESAAAESAASSSGSDSASPSDDGDGNPVVSESGTPSPSNTTD
+>GCF_023573625.1_00158
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSTSASPSPSTSGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000283.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000283.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b44f8c4c00f1f72cc003a008dd6c62a2a34f812
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000283.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00151
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEAGQGRARG
+>GCF_003691675.1_02165
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNHGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEAGQGRAQG
+>GCF_005280335.1_00232
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDVVPVAPESSLVWALMAEDAWSEGR
+TVDSYAYARVGYHRGLDALRKAGWRGAGPVPYDHEPNRGFLRALYSLGRAAAGIGESEEV
+ERIRTFLKDSDPTAAEKIEATQGRSGS
+>GCF_020097155.1_00171
+MSESLIGKNLMEPPATLLPEEPEVLARLDAGDLPEDLVPLAPESSLVWALMAEDAWSEGR
+AVDSYAYSRVGYHRGLDALRRAGWRGAGPVPWSHEPNRGFLRALYALGRAAAGIGESAEV
+DRIRTFLKDSDPTAAQQIEAAQA
+>GCF_023573625.1_00159
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEADQGRAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000284.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0d415707c1924842bd23ec16ed98f0912e96faa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000284.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00152
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG
+>GCF_003691675.1_02166
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG
+>GCF_005280335.1_00231
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEDEVVSRLGVTRTVDF
+LVPAGAGVRELFRRHASGDDPDALVDHVDAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRCFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVNPATGAEHF
+VFEGDQVAIDGVEVTYESLCGSCYLAESGGRLG
+>GCF_020097155.1_00170
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPAVDTKGDAAVVSRLGVTRAVDF
+LVPAGADVLALFRAHAAGDDPDALVDHVDAPPVACLLVDEAQFLEAGQVDDLLRIAVLED
+VPVMAYGLRTDFRTHSFPGSARLLELAHSLEELKTICRCGRKAVLNTRKVVDAATGRSRF
+VFEGDQVAIDGVEVTYESLCAACYLEESGGRLG
+>GCF_023573625.1_00160
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000285.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d33ee22cfd8239492b3732cf17941b9745236985
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000285.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00154
+MATPLLELAASRGVCFPLRARRLTLTPFRGLDAPAVWSFCRLEQVWSWTSGRPESENALR
+ESYLGAGDRLTVRAGDVIVGVGKVAVQDAWSQDGPQEEARDAQAELGWTIDPRQAGQGYG
+TELARALLGFAFDDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG
+ATYAMLASEFHSPLTQE
+>GCF_003691675.1_02168
+MATPLLELAASRGVCFPLRTRRLTLTPFRGLDAPAVWSFCRLEQVWSWTSGRPESENALR
+ESYLGAGDRLTVRAGDVIVGVGKVAVRDAWSQGGPREEGRDAQAEIGWTIDPRQAGQGYG
+TELARALLGFAFDDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG
+ATYAMLASEFHSPLTQE
+>GCF_005280335.1_00470
+MATPLLDLAARRGVVFPLRTERLTLTSFAADDAPAVFDFCRLEEVWTWTSGRAGSAGELR
+ESYLAAGDRLTVRAGEAIIGVGKLAVQDAWSQGGPREEARDAQAEIGWTIHPTHADQGYA
+TELAGALLKLAFTGLGVHRVEAEAFADNAPTLRVMEKVGLRHEGTFREESLHLTRGWVDG
+VTYAMLASEFLARV
+>GCF_020097155.1_00420
+MATPLLDLAARRGVAFPLRTERLTLTPFTAVDAPAVWDFCRLEEVRTWTSGRAGSAAELR
+EEYLATGDRLTVRDGAGDVVGVGKLAVQDAWSQGGPHPDARDAQAELGWTVAPEHAGRGY
+ATEIGRALLDLAFRGLGVRRVEAGAFADNAPSLRVMAKIGLRHEGTFLGESLHLTRGWID
+GVTFALLASEYEGGAAASRA
+>GCF_023573625.1_00167
+MAPPLLELAASRGVCFPLRARRLTLTPFRGLDAPAVWGFCRLEQVWSWTSGRPESEGALR
+ESYLAAGDRLTVRVGDVIVGVGKAAVQDAWSQGGPREEARDAQAEIGWTIDPRQAGQGYG
+TELARALLGFAFNDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG
+ATYAMLASEFHSPLTQE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000287.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000287.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03548359149c9db10926cde7ba20e06e95b26f37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000287.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00178
+MSTAAPHTQHSDFPSPTPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM
+TVIYMVFGALPHELVLMVLVGSLFLLPRVNPQDEQRGGIRLGRLLHTLLGVSWGSFALAA
+IIFPDGGDHPDSGATTPVLMDLLGKSTAMDVGIVGGLALVAVSALTGLAVIVVCVVRRIR
+AVR
+>GCF_003691675.1_02174
+MSTAAPGTQHSDFASPTPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM
+TVIYMVFGALPHELALVLMVGSLFLLPRVNPQDEQRGGIRLGRLLHTLLGISWGSFALAA
+IIFPDGGDHPDSGATTPVLMDLLGKSTAMDVGLVGGLALVAVSALTGLAVIVVCVVRRIR
+AVR
+>GCF_005280335.1_00223
+MSTAAPHTQHSDSASPAPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM
+TVIYMVFGALPHELFLMLMVGSLFLLPRVNPLDEQRGGIRLGRLLHTLLGVSWGSFALAA
+ILFPDAGDHPDSAATTPVLMDLLGKSTAMDVGSVAGLALAAVSALTGLAVIVVCVVRRIR
+AVR
+>GCF_020097155.1_00169
+MAVPHPVMPPPGTPLPHQLRPAGPSVGTPRWLPAVLWIVAFALLPLCVIVGRFATENGGW
+LLFTYIMFGWMVQGGLGVLAAASLFLLPRVNPPVERRAGVRTGVVVHLLLGASWLTGLLG
+MLAFGDYGDAPGSETAPAPLVDLYGMDRAVEIGDAVGPPLVGISLLTGLAAVVLVVVRRL
+AAAVRS
+>GCF_023573625.1_00175
+MSTAAPGTQHSEFASPAPARKGPSVGTWRPWAVLPWALALLALPLIALALRSDFGANGWM
+TVIYMVFGALPHELVLMVLVGSLFLLPRVNPQDEQRGGLRLGRLLHTLLGVSWGSFALAA
+IIFPDGGDHPESGATTPVLMGLLGTSTAMDVGIVGGLALVAVSALTGLAVIVVCVVRRIR
+AVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000289.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000289.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6668e4ba5d7f59594a0964b5e911e8bf77a94ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000289.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_00180
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDQKAG
+AADPEAVDPRVIKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVSRLTE
+LLPAHRVWDRFPTTGRLAD
+>GCF_003691675.1_02176
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPSLDQKAG
+AADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVSRLTD
+LLPAHRVWERFPTTGRLAD
+>GCF_005280335.1_00221
+MTTQQPDIPGTPGPRTPDLEERTAPTSSDDAAMPAPDQRGPASVSPTGQDTGADPATAAQ
+GCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAH
+GMFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGTW
+DLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIWN
+MSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPD
+YHRRDLADAIEAGAFPEWELGVQVFEDTEEQMFEGIDLLDPTKLVPEELVPVQPLGRMTL
+NANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWTQLPINR
+PHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKERA
+HAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLAQ
+QVADGLGIPVPAPTETPADVQPSPVLSQIGGVWPLDGRQVGVVVGESVDEKELDALVQGI
+HGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDEKAGA
+AASEAVDPRVVKVLQEMWRHSKAILALEPAEGVLAAAQVSGKGVESAADGASAVSRLTEL
+LPAHRVWERFGTTGRFAD
+>GCF_020097155.1_00166
+MAEQPKIPGTPGPITPDLEEHTALTDPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAAQ
+GCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAH
+GVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGTW
+DLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIWN
+MSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPD
+YHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELVPVQTLGLMTL
+NANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWTQLPINR
+PHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKERA
+HAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEETIRVRQLQNLGAIDPRLAQ
+QVADGLGMPVPAPADAPADVQPSAALSQVGGTWPLDGRQVGLVVGPQVDEKELGDAVQGI
+HGAGMVPLVIAPKGGPVAGEVVAQRAYLTAASIELDAVVVLGATPPAGDAQHGLDAKAAA
+DAPDAVDPRVAKLVQEAWRHAKAIVAVGEGTSVLDELGLTGTPGVLTVDAGADAVAQLKE
+LMPAHRVWERFPTTGRLAD
+>GCF_023573625.1_00177
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDQKAG
+AADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVAALKQ
+LLPAHRVWDRFPTTGRLAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000290.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000290.fa
new file mode 100644
index 0000000000000000000000000000000000000000..820e8c3f9aa8d1b9c16f00deb7e2ee9faaafa88a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000290.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00181
+MRISVGQFGPVGDVEENLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVATAEVTR
+ERIDEVREFLPSLANRRTDVL
+>GCF_003691675.1_02177
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVVTAEVTR
+ERIDEVREFLPSLANRRTDVL
+>GCF_005280335.1_00220
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGAELLVLPEEAMLGAREVGEEFPDAIAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRISPGDGGVAAIELDGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVVELADEREAVVTAEVTR
+ERIDEVRKFLPSLANRRTDVL
+>GCF_020097155.1_00165
+MRIAVGQFGPTGRVEDNLEAMGRLAARAAAEGAGLLVLPEEAMLTFREVEDEFAHAVAGS
+WEPFTEGLARLARQHGLAIVAGGYEPSATDRPYNTLVAVDADGAVAGAYRKLHLYDAFEH
+RESELITPGDRGLVTVEVGGLTVGLQTCYDLRFPEVSRALALAGAQVLAIPAAWFAGEHK
+VDHWRTLLRARAVENTVWVAAADTASAATVGHSAIIDPLALTLAEADDDAAPETLLCADV
+TAERVEEVRRTVPVLANRRTDVLTPPVDVEPGG
+>GCF_023573625.1_00178
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVVTAEVTR
+ERIDEVREFLPSLANRRTDVL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000291.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..487990686a25117917b43929c814769f75ac3dfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000291.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00182
+MTINADGSHAVQPHTANAHTTPARPVRHAVVEEEVLEPLRPVDGWGFTNRVILVSVLVVI
+IGNVVRVLTGGLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVVYGSGVHLFWMLPVAGLLGGLWAGLVSSRR
+>GCF_003691675.1_02178
+MTINADGSHAVQPHAANAHTAPARPVRHAVVEEEVLEPLGPVEGWGFTNRVILVSVLVVI
+IGNVVRVLTGDLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVLYGAGLHLFWMLPVAGLLGGLWAGVVSSRR
+>GCF_005280335.1_00219
+MTINADGSHAVQPHSANAHTAPASPARHAVVEEEVLEPLRPVDGWGFTNRVILVSVLVVI
+IGDVVRVLTGGLGDPNGSVALGETGRGWVVLVQSFMFGLVGGALAGAAGYLIVLLMGGAA
+RSVVPYVVGGVVGGFLGAVGVFAVFSNTALYGSGLHLYWMLPVAGLLGGLWAGVVSSRR
+>GCF_020097155.1_00164
+MNTQAHGAHAVQTVGGTAAPQAPARRAVVAPEAVEPARPVDGWGFVNRILVVATVLIVAF
+ELWRAATGLLSDGPRVLGEDGVGWVAVLEAFMFALVGGAIAGAAGYGIVLLMGGAARSAA
+RYAIGGLIGGFLAAVGVIFVFSNTAALSVGGHLFWMLPLAGLIGGVWAGITSAKS
+>GCF_023573625.1_00179
+MTINADGSHAVQPHAANAHTAPARPVRHAVVEEEVLEPLGPVEGWGFTNRVILVSVLVVI
+IGNVVRVLTGDLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVLYGAGLHLFWMLPVAGLLGGLWAGVVSSRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000292.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000292.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76992762816348adac1c31bf4b96a6ea61fcd03c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000292.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00183
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVATPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKARS
+>GCF_003691675.1_02179
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATGELAHLLGAADTPRERPADSPGKPKASS
+>GCF_005280335.1_00218
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPASAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATDELAHLLGAADTPRERPADSPGKPKASS
+>GCF_020097155.1_00163
+MPTTPPASTRTVDRALALLAAVVAQPRLSLAEAARATDLPASTALRLLRSLETAGFVDRQ
+EEGEYRPGARLIQLGARAFSREPLVRLARAPMDGVAEATGESVYLSLRNGAQEAVYIAIV
+EGTHSVRHASWVGRTVPLEGTAVGEVYRGEVPPGGYAHGGHSVEQDVTALSSPVVVGGRV
+VAALSALVPDYRCTAEHADRCGRALAGATTRLASALGEEAPPEDAD
+>GCF_023573625.1_00180
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKASS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000293.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000293.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab85100438356555bea9bb05de4b0ea5f1154211
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000293.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00184
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLQGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKNDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEVAKERGVRVPMEATIRD
+>GCF_003691675.1_02180
+MAEGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLQGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAVEVAAERGVRVPMEATIRD
+>GCF_005280335.1_00217
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLKGTLTLTGGCGGM
+GGAQPLAVTLNGGACLIVDVSEGRLRRRMGKRYLDEVVTDIDKAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKRGEIEIDIVTDQTSAHDPLSYLPIEIDEADWQAEAEGDPETF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEIAAERGVRVPMEATIRD
+>GCF_020097155.1_00162
+MAAGFTQHDPSRTIRAPRGTELNAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAFDAIVETLKDLEEDETLLVQSGKPVGVFRTNVWAPRVLIANSNLVGDWADWKTF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKKYDGTLKGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEERLRRRMGKRYLHEVETDIDAAIARVMQAKRDGEAVSV
+GLVGNAAEVFPELLKRQKAGEVEIDIVTDQTSAHDPLSYLPIEIEEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLTALLTNDPGMGVIRHVD
+AGYSRAVEVAAERGVRIPMEPTVRD
+>GCF_023573625.1_00181
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVVKTNVWAPRVLIANSNLVGDWADWKTF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLKGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIERAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDAALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEVAKERGVRVPMEATIRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000294.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000294.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25c6638b1c039634cc1a95f1113fc8e61ab0c9c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000294.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00185
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF
+GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPEQAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLGARFVIGVVCVSAIIFFSAVVPAI
+LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT
+>GCF_003691675.1_02181
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF
+GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAAGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLVVTFAVTAITVRIPPLSRIPDEVYPGAVHSPELAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPIPLWKLVVIWAERVALTILLAMPVAHLVAALT
+>GCF_005280335.1_00216
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIATGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF
+GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFSALVVTFVVTAITVCIPPLSRIPDEVYPGAVHSPEQAVTRDRFRVALRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGMIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT
+>GCF_020097155.1_00161
+MTHAHPADGELHTDTTAMAAIEADSPRPPARWRMVVYSLIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRYVALALIAAGAVFPFATGRWRQSVTTTVFAFLGVVGLLTACMVVF
+GFGPSWVLDKGIGPFLLDKLVIPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+DLMDHWLWYFFGTLVVTFVVTAITVRIPPLSRIPDEPFPGAVHVPEEAVTQDRFRVARRA
+AEQTLAEAPSLGRNVWLNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWVGLIFQPV
+FWALGFSDPALMASASATSIAEMFIPATMLAGHEDFVARFVIGVVCVSAIIFFSALVPAI
+LATDIPVKLWHLVVIWVERVVLTVLLATPLGHLVAALTS
+>GCF_023573625.1_00182
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF
+GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPELAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPIPLWKLVVIWAERVALTILLATPVAHLVAALT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000295.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000295.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b65a99ff76f14cdb470d0d8f67304639f3ff9251
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000295.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00186
+MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPEADDRVSVEGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDARLAELVRGRVADAVA
+GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLAAVREHVGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDADVEALAGTWADWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGALGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
+>GCF_003691675.1_02182
+MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPEADDRVSVEGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDARLAELVRGRVADAVA
+GGTTYLETKTGYGLTVAEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLAAVREHVGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDADVEALAGTWADWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
+>GCF_005280335.1_00215
+MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPDADDRVSVEGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDDRLAELVRGRVADAVA
+GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLEAVREHAGWADVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDTDVEALAGTWTGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGALGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
+>GCF_020097155.1_00160
+MASTLITDIAELTTVDPEGRVLRDAAVVLDDEDVAWIGPAAQAPAADERVSVAGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGLTMEATRAASDERLRELVLGRVADAVR
+GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDVEDYLDDVV
+GPMLEAVREHVGWVDVFCDTGAFDAAQTRRVLAAGVAAGLRARLHGNQIEQGPGVALAVE
+FGAASVDHVNHLSDADVEALAGTWSGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
+>GCF_023573625.1_00183
+MRSTLITDIAELTTVDPEGRVLQDAAVVVEDERIAWIGAAADAPDADDRVSVGGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDDRLAELVRGRVADAVA
+GGTTYLETKTGYGLTVAEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLEAVREHAGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDADVEALAGTWTGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000296.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000296.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f2bb13f4c3d37dd286011b2d6bd9390f6a83a44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000296.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00187
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGTDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
+>GCF_003691675.1_02183
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGEDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
+>GCF_005280335.1_00214
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGADGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAWKSEGTEAEGH
+>GCF_020097155.1_00159
+MTTTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTG
+FGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVV
+VETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGADGALRPAGEALAE
+AGIEPVELREKEGLALVNGTEGMLGMLIMALADLDELVDTVDLTAAMSVEALLGTDRVFV
+PELHLPLRPHPGQAASADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTL
+AYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTD
+RMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQEDH
+VSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGVPGP
+GPDQYMAPQLAAAEQALRDGSVLAAVAEALAGASADAEPQDLAEESAGAEAEGH
+>GCF_023573625.1_00184
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGTDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000297.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000297.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b24ef873922001f6974d34cc71559b42b0005758
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000297.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_00192
+MTSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTPQRDPGAGAPTSGARST
+ALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVAAGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE
+QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE
+ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDASLLA
+>GCF_003691675.1_02188
+MTSELPSPSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST
+ALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGAGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE
+QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE
+ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTVVSRHRTDASLLA
+>GCF_005280335.1_00208
+MTSELPSPSLSSAWAGRTDGDAPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST
+ALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGEGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRVLFDTAREHGVTWVTDE
+QAQIADVTGVRRWVRSFIDAVDVLYLTVDLDVLPAAVAPGVSAPAGFGVPYEVIHACAVE
+AATSGKLALADVVELNPSLDVDGRTAKAAARLIHTIVSRHRTDASLLA
+>GCF_020097155.1_00155
+MSGVVRPSLRTRPSMAWNGAMTADRASELPSAALSPAWTGRTDGDAPEHLRWHQVVRSAD
+GGAPAQTVDAAPARSTALVGFASDEGVRRNHGRVGAEDGPDALRGALASLAYLEGTGALV
+DAGDVSVDRGDDDAPGELEAGQAELATVVSGLLNAHDLAVVLGGGHETAYASITGLTGST
+RVAAGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEEAEHQLSYAVVGISEANNTRA
+LFDTARERGVTWVTDEQAQTADVTGVRRWVRSFIDAVDVLYLTIDLDVLPAAVAPGVSAP
+AGFGVPYEVIHACTLEATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDA
+SLLA
+>GCF_023573625.1_00192
+MTSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST
+ALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGAGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE
+QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE
+ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDASLLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000298.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000298.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dcf0912078a77b0d12ada7dfad37d6ae0ede8bd2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000298.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00193
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDGLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>GCF_003691675.1_02189
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>GCF_005280335.1_00207
+MSATHPERTWTGPSAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGQEILGHRVYASLDDLPVTPDLVEVFRKASDAPEMVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEIVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>GCF_020097155.1_00154
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEIVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>GCF_023573625.1_00193
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000299.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000299.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88683348f43ecb1ae556874c58f1cf638655f1bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000299.fa
@@ -0,0 +1,49 @@
+>GCF_002008305.4_00194
+MITQPALHATGRRRVTLCDVPTLPPARLARDNGADCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAAAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKTVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSIGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPEDLIRISVGIEDTEDILWDLDQ
+ALTEATGRTRDDDGAPAAPKEA
+>GCF_003691675.1_02190
+MITQPALHGTGRRRVTLCDVPTLPPAHLARDNGRDCPEASIERTPVADHEFGFRTQALHA
+GAVPDTVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAAAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKTVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPEDLIRISVGIEDTEDILWDLDQ
+ALTEATGRTRDDDGAPAAPKEA
+>GCF_005280335.1_00206
+MADHEFGFRTQALHAGAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRI
+GNPTVAAFEERVATLEGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLD
+VSLRRFGVETTFVDSVEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVP
+LVVDATLTPPYLIRPIEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTE
+PVPSYGGVSWWGNFGEYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLAN
+ARAVATWLDEDPRVSWVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASG
+PEAGRATASRFISALQLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRIS
+VGIEDLEDILWDLDQALTEATGRTRDGAVVPAEQEA
+>GCF_020097155.1_00153
+MITQPALHGTGLRRVTLCDVPTLPPAHLARDNGTDCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANARAVATWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRISVGIEDLEDILWDLDQ
+ALTEATGRTRDGAVVPAEQEA
+>GCF_023573625.1_00194
+MITQPALHGTGRPRVTLCDAPTLPPAHLARDNGTDCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRISVGIEDLEDILWDLDQ
+ALTEATGRARDGAVVPAEQEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000300.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000300.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9df07e3e37a2bd4c706c97207540452158f7cfc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000300.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00195
+MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGIPDPCAPDGAAAL
+VRLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRTDLDGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIADGDHLVRPPWTPTGRADPVATVSELS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRGARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG
+LVRRRLARTR
+>GCF_003691675.1_02191
+MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGIPDPCAPDGAAAL
+VRLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRTDLDGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIADGDHLVRPPWTPTGRADPVATVSELS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRGARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG
+LVRRRLARTR
+>GCF_005280335.1_00204
+MTARAPLPPALARAAFGVDELLDAGLPWDRTRAADLHRIWRGVYTAADPAALTWDRAAAL
+CRVTGGVISHTTAAAWHGIPLPRRLEASEELHLTVDRGRRQHRSARPGVVTHRLRLPPQE
+IRQVGGGLRVTSPERTWLDLAVLLRPWELDWLVVAGDHLVHHPWHPDGRRPSATTPALLD
+AALGRHVGRHGIRRAREALADVRVGADSAPETRLRLALIRAGLPEPALQIAVDPSDPRSP
+EADLGYRDARIALQYDGAAHRTPEQQARDARREAYCLELDWLPLRCTQEDLREGFIRVIG
+LVRRRLGPRGAFGATSRR
+>GCF_020097155.1_00152
+MTARTPLPPALAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGVPDPCAPDGAAAL
+ARLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRSDLGGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMFRPHEVDWLIAAGDHLVRPPWTPTGRADPVATVPGLS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRAARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG
+LVRRRLARTR
+>GCF_023573625.1_00195
+MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGVPDPCAPDGAAAL
+VRLTGGVVSHVSAALWHGLPLPPRLTRPAGLHLTFDRSARTHRTDLGGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIAAGDHLVRPPWTPTGRAHPVATVPGLS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRGRAWPSSTTAPATARLSSRRGTPVGTRTASSGNGRPCAAPGRTSALGSGGSWG
+WSGVGSPARADPPPRPTRVELSRVPSNAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000301.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000301.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d346581e52891c965e8ca1ecb0118f98d39fdb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000301.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00196
+MPDDVAVRLLLIADTHIPRRARALPAQVWAEVARADVVLHAGDWVTEDVLDDLDARAARL
+VGVWGNNDGPKLRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPDTANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVSVDRTP
+>GCF_003691675.1_02192
+MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL
+VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP
+>GCF_005280335.1_00203
+MTTETRLLLLADTHIPPRARAMPAQVWDEVARADVVLHAGDWVEESVLDELEARSRRLVG
+VWGNNDDGALRARLPEVARVEIGGVRIAMVHETGAARGRERRMAEAFPDADVLVFGHSHI
+PWDTVAGPETANPGLRLLNPGSPTDRRRQPVCTLMRAVVRDGGLADVELVPVDRTP
+>GCF_020097155.1_00151
+MTTRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDAQAARLVGVW
+GNNDGPRLRARLPEVARVEIGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHSHIPW
+DTVAGPETANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVPVDRTP
+>GCF_023573625.1_00196
+MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL
+VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000303.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000303.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c2ae764ba5cfe3f5ef49d2d0c4788329350e947
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000303.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_00202
+MTAGDDGGRGAVVGVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAEADRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGAAVPVKANADEAVSGDNAIEHILVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPNPARRDDDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDGIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPAMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPEVIEAGVCPVPHETTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+ALGDTTSLQNEPCVGQIAEVLRAGRRAQDAGTGAVRSASSAST
+>GCF_003691675.1_02197
+MTPTEDPARPDPAEEGASGAVRGPNDGVPAAALATLPGPLPQALVDAADPDVHPGRPADR
+LHGGRGDGRPVAEADRLAFWEAAGRRLSWERPFTRTRSLTAPDPAAERGPEIRWYEDGTL
+NVAVNCVDRHVAAGRGEKVALYFEGEPGDRRAVTYAQLQREVAQAANALEELGIEAGDRV
+VVYLPVLVETIVITLACARIGAVHSLVFGGFSAEALRFRVEDTGAKLLVTTDGQFRRGTA
+VPVKANADEAVSGDNAIEHVLVLDRTGHRDIPWTEGRDLWWHDVVDRQPDTHTPRAFDAE
+HPLFIMYTSGTTGQPKGLVHTSGGYLAAASWTHDFLFSHPDPARRDDDVHWCTADLAWVT
+AHTYEIYGPLSNGVTQVIYEGVPNAPHPGRHFEVIERYRVTSYYTAPTLIRSLKGWHPDG
+IPAHADGGPDLSSIRLIGTVGESVNPEAWTWARTQIGRDTPDLPMVDTWWQSETGATVLS
+PRPTDTAFKPGCGSRPLPGVDVAVVDDDGTPTPEGLQGRIVVTRTSPSMARTVWQNPARY
+FHSYWEDYADQSEAGWFLAGDGAKRDEDGDVWILGRVDDVINISGHRLSTIEIESALVAH
+PEVIEAGVCPVPHETTGHAAVAFVVAHESWLAGDDGPGASAADRAEELRRHVGRVIGPVA
+KPAEVVFVPDVPKTRSGKIMRRLLTQLHQGTALGDTTSLQNEPCVGQIAEVLRAGRRAQD
+AGPGAVRSASSAST
+>GCF_005280335.1_00190
+MTPSPLDAATRARSSAPASPGDAPTAPDAPVRRPNDGVPAEALATLPGPLPQAVVDAADP
+DVHPGRAEDLAHGGRGDGRPVAEEDRLAFWAAAGRRLTWDREFTRVSTGTPADPAAERGP
+ALRWYEDGRLNVAVNCVDRHVAAGRGEKVALYFEGEPGDREAVTYADLQRRVAQAAHALE
+DLGIGPGDRVVVYLPVLVETIVIALACARIGAVHSLVFGGFSADALRFRVEDTGAKLLVT
+TDGQHRRGQVVPVKENADAAVAGDNAIEHVLVIARCGLTGAGEIPWTEGRDLWWHDVVET
+KPTEHAPASFDAEHPLFVMYTSGTTGRPKGLVHTSAGYLAAASWTHDFLFSHPDPARRHE
+DVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRHFEVIDRYRVTSYYTAP
+TLIRSLMGWHPDGIPAEHSLESIRLIGTVGEAVNPEAWTWARTQIGRAALARTGEPVPMV
+DTWWQSETGSTVLSPRPTDHTFKPGCGSRPLPGVEVAVVDDDGAPVPAQTQGKIVVTRTS
+PSMARTVWGDPARYFHSYWEDCAEQGWFLAGDGAKTDEDGDVWILGRIDDVINISGHRLS
+TIEIESALVAHPHVVEAGVCPVPDARTGHAAVAFVVPGREWAPGPEGDEAAAALAAERAE
+ELRRHVGTVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHTGTALGDTTNLQNEVCVG
+QIAQVLADRPGR
+>GCF_020097155.1_00144
+MTAGDDGGRGAVIVVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAEADRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGAAVPVKANADEAVSGDNAIEHVLVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPDPARRDGDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDGIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPSMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPHVVEAGVCPVPDPKTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+TIGDTTSLQNEWCIPQIAEVVAARR
+>GCF_023573625.1_00204
+MTAGDDGGRGAVVGVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAESDRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGVAVPVKANADEAVSGDNAIEHVLVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPDPARRDDDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDKIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPSMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPEVIEAGVCPVPHETTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+ALGDTTSLQNEPCVGQIAEVLRAGRRAQDADTGAVRNASSAST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000306.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000306.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6fe08af176cb86567709d744fd4e8026987a6e0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000306.fa
@@ -0,0 +1,27 @@
+>GCF_002008305.4_00208
+MAAAPCLGRQQPQEENMQRRRAVRAAGLGVVGALALAGCASEPQSAGEAWHQARTQLDEA
+ETVRLETAYTTGRQGPHSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR
+VDVDGSDVPDDVQVMYSDPQWRRVPAGEGQEPPLKALLDQVGFPAADALDGAEVRAEEVD
+WDDGTAYRYAVPEEVADAAMVEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ
+IEPAEAPEEVAE
+>GCF_003691675.1_02201
+MQRRRAVRAAGLGVVGALALAGCGSEPQSVGEAWHQARTQVDEAETVRLETAYTTGRQGP
+QSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVRVEVDGSDVPDDVQLMY
+ADPQWRRVSAGEGQEPPLKSLLDQVGFPAADALDGAEVRAEEVDWDGGTAYRYAVPEEVA
+DAAMAEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQIEPAEAPEEVAE
+>GCF_005280335.1_00183
+MQRRRAVRAVGLGVAGVLALAGCAAEPQSAGEAWQQARTQLDEAQTVRLETAHTTGRQGP
+NTVRWDIAGRLDGSNGDAKGVIQAGHESHMTMETRTVGEDSYVRVSIDGADFADDVQLAY
+ADPQWRRTPAGQEQERPLKELLEQIGLPSADALEGAEVRAEEVGWAGETAHRYAVPQEVA
+AAAMGQGDSTLLHSFTVDDDGGLLALTVDDGRSLRQYALSDWNEIDPAEAPEEVAE
+>GCF_020097155.1_00129
+MQRRRAVHAAGLGVVAALTLAGCGTDQQDVGEAWQHARAQIDGAESVRMTMASVNDSQGP
+SVVAWDVAGPLEGADGTTTGRMQVGRDSWMTVRSVSADGKTWARVDTEGQDVPEQIASMY
+RTDGWTETQQSGQNALRATLDAVGLPAADALDGVDVQPEKVDWSGGTAYRYAMPGDVASA
+ARGDSQFSVRAFTVDEDGDLVGLRVEDGGVIQEFALSDWNEIEPAEAPEEAQH
+>GCF_023573625.1_00208
+MAAAPCLGRQQPQEENMQRRRAVRAAGLGVVGALALAGCASEPQSAGEAWHQARTQLDEA
+ETVRLETAYTTGRQGPHSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR
+VDVDGSDVPDDVQVMYSDPQWRRVPAGEGQEPPLKALLDQVGFPAADALDGAQVRAEEVD
+WDGGTAYRYAVPEEVADAAMAEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ
+IEPAEAPEEVAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000307.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee6e169cb6433d1727343d360036bde1f03ac87f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000307.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00209
+MRQRQTQTRRTRRGLSLAALGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR
+SEAPSNGRAVPDAVDISGPVDGSSMRYVSVYKDDGLITRDESRIVDGTAYSRFTVERVGA
+SGEDHPAYAERWTATPYEGDPSATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA
+IRYVLDEPVSGPQEGVELTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGGVDPVQAPPA
+DEVLKQDG
+>GCF_003691675.1_02202
+MRQRQTQTRRTRRGLSLAAVGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR
+SEAPSNGRAVPDSVDISGPVDGSSMRYVSVYQDDGLITRDESRIVDGTAYSRFTVERAGA
+SGEDRPAYVERWTATPYESDPRATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA
+IRYVLDEPVSGPQEGVELTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGGVDPVQAPPA
+DEVLKQDG
+>GCF_005280335.1_00182
+MPRQNPTGRARRGLPLAALGAAAALVLTGCGASGEDASAAWDRARTQLEETDSVRMVTEL
+RSDAPQAGNRTPESVDLSGPVDGSSMRYVSTYEDGDLITRDESRVVDGTAYSRFTVERRG
+ASGEDRPAYVERWTAAPHTGDPRATGMGAMVSSLLGSLPESGGLEDVAVDADGIRRSGQD
+AVRYVLDEPLSVADDGVAMTAFTVSEEDGRLLTVETESAGTKAVVTVSEMGDVEPLQAPP
+SDEVLPQQQGQGAPGAVPPGGAPQDGTAPGGTPAEPVPPTDG
+>GCF_020097155.1_00128
+MRPTTPRTPAPHGGARRRALSLAALGAAAALSLSACGASGEDASAAWDAARTQLQDASSV
+RLTTEARNDSGAAPGTPDGVEIAGDVHSSDLSYTGVFRTDGYITRDESRTVGGQRYERFT
+LEQPGGVSGEGRPAFAEKWKKAEPLPGDASMRSILDGVLTAVPQAGALQGADVRATDIRR
+QGRDATRYVLDTPVKGGTTDSSLTAFTVADDDGTLLTVETTGPGTRGTVTFSDWNAVEPV
+TAPATEDMAQDTATAK
+>GCF_023573625.1_00209
+MRQRQTQTRRTRRGLSLAAVGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR
+SEAPSNGRAVPDSVDISGPVDGSSMRYVSVYQDDGLITRDESRIVDGTAYSRFTVERAGA
+SGEDRPAYVERWTATPYESDPRATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA
+IRYVLDEPVSGPQEGVALTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGEVDPVQAPPA
+DEVLKQDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000308.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000308.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acbb1f305bfde9aeecd33c2915132f930a4fdb29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000308.fa
@@ -0,0 +1,19 @@
+>GCF_002008305.4_00210
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNITSAARHGAEPDTISDPSTPLGD
+EGPLTR
+>GCF_003691675.1_02203
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNITSAARHGAEPDTISDPSTPLGD
+EGPLTR
+>GCF_005280335.1_00181
+MRLITLGLGAALGYLLGSAEGRRNLEKMSQNAQKFWNDPKTQQKVGNLQETAQQKFADVK
+NSEQVQKATAKVEDTMNKNGSKDQVRDDRVTESNNENTTTASAHGADPDIVSDPSTPLGD
+EGPQTR
+>GCF_020097155.1_00127
+MRWFTLAVGAAAGYLLGSAEGRQNLQKMTANAQKVWNDPKTQDKVGVVKDKAQVVASDAK
+DKAASAASDAKQAVQEKTSSNQPSPASNNETVTTGNAHGADPDVVSDPSTPLADEGPAA
+>GCF_023573625.1_00210
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNVTSAARHGAEPDTVSDPSTPLGD
+EGPLTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000309.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000309.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6eac8dc190f4835c13e6912dfd5aefae22eaa1bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000309.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_00211
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQDL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG
+>GCF_003691675.1_02204
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQDL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG
+>GCF_005280335.1_00175
+MSQQFSIETVADAAANPDIEQPWAELGLKENEYAQIREILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGLGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFAGSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPDNVAAFEAVMAKWDVEYSWL
+GEVTGDGRLVITWDGEVIVDVDPRTVAHDGPVYERPYARPGWQDRVQADTFRASEAGADL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTAMAAPDDAGVVRVDEETGMGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPENPDVMWQFAEA
+VRGLADGCQVLGIPVTGGNVSLYNQTGATPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGVPPKVDLAKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRHGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYTVTRIGVVDADSAALEVQDAFTLPIAELREGWEATLPKHFG
+>GCF_020097155.1_00124
+MSTQFTIETVEQAAANPDVAQPWAELGLKEDEYARIREILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGDTLTEEMKEHMMVGIGENAGVTDLGDGWAVTFKVESHNHPSFVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAVDHPDTARVVHGVVAGIGGYGNSLGLPNI
+GGEVAFDPSYQGNPLVNALAVGVLRHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDDGGKPAKRPSVQAGDPFAEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEHSWL
+GEVTGDGRLVITWDGETIVDVDPRTVAHDGPVYERPCHRPSFQDALQADTFRSSAAGQDL
+PATGEELKAAVVELMASPNMADVSWITRQYDRYVRGNTALASPDDAGVVRVDEETGMGVA
+VATDCNDRYAYLDPYAGAQLSLAEAYRNVTTTGAVPLAVTDCLNFGSPEDPEVMWQFAEA
+VRGLADACQVLGVPVTGGNVSLYNQTGGVAIHPTPTVGVLGRFDDVLRRTPSGFGTDADG
+QAVYLLGVTADELDGSEYANLRGHLGGVPPKVDLAQERLLGELLVNMSRDGMVDAAHDVS
+KGGLAATLADMVLRFGVGARIVLDEVVRRDGVDVFTALFSETQGRTVVSVPRTEEVRFTD
+MTTARGYTVTRIGVVDAQSDALEVQGQFTLPIAELREAWEATLPKHFG
+>GCF_023573625.1_00211
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQHL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGMGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPITELREAWEATLPKHFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000310.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000310.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54d7c03822c0442033e274f40a0b408b26ae4bb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000310.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00212
+MTELPLIGDYSTPATPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT
+LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQELVVESTDTVWTRDFEQGQTITVPLKNQDGQYVADET
+TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVETGFGPDTAAGP
+RSGVDGLGFFTSVLTTLASRGGHA
+>GCF_003691675.1_02205
+MTELPLIGDYSTPTTPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT
+LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQELVVESTDTVWTRDFEQGQTITVPLKNQDGQYVADET
+TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVETGFGPDTAAGP
+RSGVDGLGFFTSVLTTLASRGGHA
+>GCF_005280335.1_00174
+MTTDLPLIGDYSTPTTPLNGARIGVITFPGTLDDVDALRAVRLTGAEPVSLWHADEDPQR
+TLAGVDAVVIPGGFSYGDYLRAGAISRFAPMMDAVATAAGGPEGAADGLPVLGICNGFQI
+LTESHLLPGSMIKNDHLHFICRDQELTVENTDTAWTRDYERGQTITVPLKNQDGQYVADD
+ATLDALEAEGRVVFRYRGWNPNGSRRDIAGIANAAGNVVGLMPHPEHAVEPGFGPDTADG
+PRTGTDGLGFFTSVLTTLASRGGHA
+>GCF_020097155.1_00123
+MTEIPLIGDYSTPSTPLNGARIGVITFPGTLDDVDALRAVRLTGAEPVSLWHAEADAAAT
+LATVDAVVIPGGFSYGDYLRAGAISRFAPMMGAVAQAAGGPEGSEDGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQQLAVESTDTAWTRDFEQGEVITVPLKNQDGQYVADEK
+TLDALEAEGRVVFRYVGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVEAGFGPDTEAGP
+RSGTDGLGFFTSVLTTLATRGGAA
+>GCF_023573625.1_00212
+MTELPLIGDYSTPTTPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT
+LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQELVVESADTVWTRDFEQGQTITVPLKNQDGQYVADET
+TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVEPGFGPDTAAGP
+RSGVDGLGFFTSVLTTLASRGGHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000311.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000311.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97fea551b5a00c3420e26232b85b2f2ac75f5332
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000311.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00213
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDEILAQAR
+TAAEEMLSNPVIEDVVNVAVLDEAEGAR
+>GCF_003691675.1_02206
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGKVTDEILAQAR
+TAAEEMLSNPVIEDVVNVAVLDEAEGAR
+>GCF_005280335.1_00173
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDAVLDQAR
+RAAEELLSNPVIEDVVNVAVLDEAEGAR
+>GCF_020097155.1_00122
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTEEVLAAAR
+TAAEEMLSNPVIEDVVNVAVLDEDAA
+>GCF_023573625.1_00213
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDEILAQAR
+TAAEEMLSNPVIEDVVNVAVLDEAEGAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000314.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000314.fa
new file mode 100644
index 0000000000000000000000000000000000000000..933dbfdb3b35149b7642fbac3a20f68625b82b2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000314.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00218
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGVVGAAIYPDRPDAFV
+CGLDEDELAGAGLRVRREPGDPSDPHSAEFPHVYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAAAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPRTDGSRHEPLPDDLEARLSTPAGLAVGAFEGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATLLATHARGGRQWGTGGAEANAASLRMNTALGFRL
+EPAWLGLTPPMTWEEFARAPASSSLDDKVT
+>GCF_003691675.1_02212
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGMVGAAIYPDRPDAFV
+VGLDEDELAGAGLRVRREPGDPSDPHSAEFPHIYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAVAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPHTDGSRHEPLPDDLEARLSTPEGLAVGAFQGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATVLATHARGGREWGTGGAESNAASLRMNAALGFRL
+EPAWLGLTPPTTWEEFARAPASSSLDDKVT
+>GCF_005280335.1_01604
+MILHIALPEDWAAARAAGHYTVSTRGATVDRVGFLHASEDAAQVGIVGPAVYADRPDAVV
+LAMDEAALEAAGLTVRREPGVPGDPHSPLFPHVYGGPVPVGLMTPLPRADVDPRVVREDD
+AEAIRLQDAGWTPASTSWGARLHLADDADLAPYERRVAAVRAAGFQVRRLTPDDVGQVRR
+LDGETAADYPATAASSHSPLPEDLAVRLTLPGHRGYGAFRDGVLAGFTLLDRLDDRWDVD
+RTAVHPTGRRRGLAAAVKALSVLETHREDGARTWGTGGAGANAGSLAMNRKLGFELEPLW
+LALVPALTWPEAAATSGTP
+>GCF_020097155.1_00616
+MILHLTLPEDWAAARAAGVYTASTRGAGIAEVGFLHASEDERQAGAVAAAFYADRPDAFL
+VALDEDALAAAGLEVRREPGNPADPQSELFPHVYGGPIPVALMRPLRPSLTLRPYAPDDA
+AATLDVFRAAVTGTAAAHYTPEQIRAWCPADVDADAWAARRAAAWTVVAVDGAGRVLGFA
+DLTADGVLDMLFVHPEAGGRGASHLLVGAVLAEARRRGLLRVDVRASRSARPVLEALGFT
+VDGEDPGNTVRGVVVPNTRMHADLAGSAGSPAPPGLWS
+>GCF_023573625.1_00219
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGMVGAAIYPDRPDAFV
+VGLDEDELAGAGLRVRREPGDPSDPHSAEFPHIYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAVAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPHTDGSRHEPLPDDLEARLSTPEGLAVGAFQGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATVLATHARGGREWGTGGAESNAASLRMNAALGFRL
+EPAWLGLTPPTTWEEFARAPASSSLDDKVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000316.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000316.fa
new file mode 100644
index 0000000000000000000000000000000000000000..605acac9bf00b41c707e7157b29317c986ff1ce4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000316.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00222
+MSLIVQKFGGSSVADAAGIQRVARRIADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR
+VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW
+IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI
+DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG
+MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAESKLDDAVRAVHAAFGLDAEEEA
+TVYGGTGR
+>GCF_003691675.1_02235
+MSLIVQKFGGSSVADAAGIQRVARRIADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR
+VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW
+IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI
+DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG
+MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAESKLDDAVRAVHAAFGLDAEEEA
+TVYGGTGR
+>GCF_005280335.1_00158
+MSLIVQKFGGSSVADAAGIQRVARRVADTVRAGHRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMMTDTSYGRARIVKVNPHR
+VQEALDAGGVAIVAGFQGVSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPSARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPIHVRSSFSDHEGTW
+IMPDPNDTITLKEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAESNVNI
+DMIVQNVSREGSGTTDISFTLPIVEGKDAMAALRAAQERIGFQDIVSDKEIGKLSLIGAG
+MRSNPGVSATFFKALSDAGVNVDLISTSEIRISVVTAEDKLDDAVRAVHTAFGLDAEEEA
+TVYGGTGR
+>GCF_020097155.1_00116
+MRLIVQKFGGSSVADAEGIQRVARRIVATQQAGNQVCVVVSAMGDTTDELLDLAAELTAD
+APAREMDILLSAGERISMSLLAMAIDAQGVPARSFTGSQAGMMTDAAYGRARIIEVNPHR
+VRAALDEGAVAIVAGFQGMSRESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVSSARKLPQLSSEETLELAASGAKVLHLRSVEYARRFGVPIHVRSSFSDHEGSW
+IMPDPNDTIHLKEGAPMEQPIVAGVAHDRSEAKVTIVGVPDVPGKAAEIFRVIAESNVNI
+DMIVQNVSRQDSGRTDISFTLPIVEGKAAIEALRAAQESIGFEEIVPNKEIGKLSLIGAG
+MRSNPGISATFFKALSDAGVNVDLISTSEIRISVVTSEDKLDDAVRAVHTAFGLDTDVEA
+TVYGGTGR
+>GCF_023573625.1_00223
+MSLIVQKFGGSSVADAAGIQRVARRVADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR
+VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW
+IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI
+DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG
+MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAEDKLDDAVRAVHAAFGLDAEEEA
+TVYGGTGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000317.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000317.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72fac5dd6495c0d0582ae3e987b0329938b5bcd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000317.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00224
+MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV
+TLGALGLRGLGVAEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI
+SGDRAGGTLAITQVTLLRTGHLMAGKWLAAWIASAAFPAAALPWLAVAAVVGRVSPWAVL
+VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV
+RANEADYGSTTAEPFTEAELEKMTPEEAEQAWAEWEAAHPELYDGIADRCVGPVTTRTIP
+DPRRSGWLLAANPYAVLADASPWEGGLLEDGTRAEPGPLNLLSVGLRWTQRDPVRDVECL
+DGELRGLDQSGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA
+>GCF_003691675.1_02237
+MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV
+TLGALGLRGLGVAEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI
+SGDRAGGTLAITQVTLLRTGHLMTGKWLAAWIASAAFLAAALPWLAVAAVVGRVSPWAVL
+VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV
+RANDAEYGSMTAEPFTEAELEKMTPEEAEQAWAEWEAAHPELYDGIADRCVGPVTTRTIP
+DPRRSGWLLAANPYAVLADASPWEGGLLEDGTRAEPGPLNLLSVGLRWTQRDPVRDVECL
+DGELRGLDSTGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA
+>GCF_005280335.1_00156
+MSTVVADPTRQGPPPLRPPGGGRLSTASAVRTVVGMELRQRLRSRGWYVLLGVFFLVVGA
+VTLGALGLRATTLGDLQSQGMDPAAAEVQMRSAGQWLFDGVLLFVLTLSLLVSPVLAANA
+ISGDRAGGTLAITQVTLLRTGQLMAGKWIAAWIASAAFLVAALPWLAVAAVVGRVSPLFV
+LVGLLMILVEFGVITGIGVAVSAIAGRTLFAVVVTYLIVAALSIGTLVAFVLSLQFLQTD
+VRANMPEHDGMTMADPLEGQDVENMTQAEIDAAWAEWERQNPDAYDGIADACVGPVGVQS
+VPDPRRVGWLLAANPYAVLADASPWDPTGASMQFTPETGPLNMMSAALRLTQQDPAETTE
+CLDGQLRRIDTTSVPDREGTWPVWPLGLAMQAALTGGLLWWGHRRLDTPAGRLPAGTRVA
+>GCF_020097155.1_00114
+MSAVLHTPPPAAAPAGGPTPLGSGRLGVVDALRTLVGMELRQRLRSRGWYILLGVFFLLV
+GGVTLGALGLHAWTGGNSPDSTMVFGRWLYDGVLLFVLTLCLLVSPALSANAISGDRSAG
+TLAITQVTLVSTWQLMLGKWLAAWIAAVAFLVAAAPWLIVAAVVGQVPPLAVLAGLAMIL
+VEFAVVTGIGVAVSAITGRTLFAVVVTYLLVAMMTIGSLIAFTISLQFIETRLQTNQVTY
+GYAEDAGSTKSCAGPLRDTTVPDPRRVAWLLAGNPYVVVADAVPLPELREDSAGEEFGAL
+NLISLGMRVAQIDPREYTDCVDGQVNEGSVTDSPVTLVDRTWPTWPLGMLLQGGFLAALL
+WWGRRRLDTPAGRLPTGTRVA
+>GCF_023573625.1_00225
+MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV
+TLGALGLRSLGVTEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI
+SGDRAGGTLAITQVTLLRTGHLMAGKWLAAWIASAAFLAAALPWLAVAAVVGRVSPWAVL
+VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV
+RANDAEFGSMTAEPFTEAELEKMTPEEADQAWAEWEAANPELFDGIADRCVGPVTTRTIP
+DPRRSGWLLAANPYAVLADASPWEGGLVEDGTWAEPGPLNLLSVGLRWTQRDPVRDVECL
+DGELRGLDQSGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000318.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000318.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dbf993debfd01f56ac0d801dacb182d76d52cf61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000318.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00225
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF
+NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>GCF_003691675.1_02238
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF
+NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>GCF_005280335.1_00155
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDKVRLCSVCF
+NVSEDEVCSLCRDERRDASQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>GCF_020097155.1_00113
+MYEGAVQDLIDELGRLPGIGPKSAQRIAFHVLEADAADMLRLADAIRTVKDKVRLCSVCF
+NVSEQEVCHLCRDARRDDSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>GCF_023573625.1_00226
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF
+NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000319.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000319.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76e6d54dc824cc259769386f8c21739c1b062803
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000319.fa
@@ -0,0 +1,107 @@
+>GCF_002008305.4_00226
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV
+RLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADITNLALTDMVGATSPRLHLELLMA
+RLLLPASDETHRGLAARLEALERRLELGGAAPVEDGAPEGTTTPARSGTPAKDGGGSAGD
+ADGSGPLTGAALARAAMRRPEEPAPTAPTAPPERWTPPAPQSVAEAPEGDAAAGATGSER
+PQQPPQPKRPEPAEVGARSGDTRRPEAGSRAEPEGRPEGRPQAQDRTGAAPSSPAPAPAA
+SQVEMIRRAWPDILTALEDASRLVWMLVKDNASVAGYDGSLLTIGFQQDGPRQSLLGRGG
+DRVLGEAVHQVLGIRPRLDLILGGDAPTGDARAQSGARPAGPARTDRPERPAPQQGRPDR
+PTAQPNRPAPAPGQAPREPESSRPTPPRSAAPSTAEDDPAPPAAPPRATQQRQTPEPSPA
+WTPAAPATSWGPTPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPEEDPWDSLPAFDPDA
+EQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAPAPGGAAPDAGQDSP
+VQPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELRAEFAKRFGATRPAG
+FDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSSDEQRRPTGAPTADA
+TPDPGVPADDADATPRTAAGPTGSDFPGSGHPASMYPRLMERLRAGGPLEPPVNAGSSGG
+GGTGGGPGAPGGPDPDASPGSPAGGRPSAASLGARPADVEPAGGASAPPSLDARAAAIHA
+AREAAQGRGPTRPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLVGRAVVERVLGGRLL
+EERPNDA
+>GCF_003691675.1_02239
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV
+SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLLLPTSDETHRGLAARLEALERRLELGGAAPVEEGAPEGTTTPARSGTPAADGGGSAEN
+AEGSGTLTGAALARAAMRRPEEPAPTASTAPPERWTPPAPQSVAEAPEGDAAAGATGSER
+PQQAPQPKRPEPAEVGARSGDARRPEAGSRPEPEGRPEPEGRPQAQERTGAAPAPAHGPE
+ETAAPSSPTPAPAASQVEMIRRAWPDILAALEDASRLVWMLVKDNASVAGYDGSLLTIGF
+QQDGPRQSLLGRGGDRVLGEAVHQVLGIRPRLDLILGGDAPTGDARAQSGARPAGPARTD
+RPERPAPQQGRSDRPTAQPNRPAPAPGQAPREPESSRPTPPRSAAPSTAEDDPAPPAVPP
+RATQQRQTPQPSPAWTPAAPATSWGPAPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPE
+EDPWDSLPAFDPDAEQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAP
+APGGAAPDAGQDSSVRPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELR
+AEFAKRFGATRPAGFDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSS
+DEQRRPTGAPTADATPDPGVPADDADAAPRAASGPTGSDFPGSGHPASMYPRLMERLRAG
+GPLEPPVNAGSSGGSGTGGGPGAPGGPDLDATPGSPAGGRPSAASLGARPADAEPAGGAS
+ALPSLDARAAAIRAAREAAQGRGPARPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLV
+GRAVVERVLGGRLLEERPNDA
+>GCF_005280335.1_00154
+MSTALYRRYRPDRFEEVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAHLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQDGGVSYELAV
+SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLLLPASDDTHRGLAARLEALERRLELGGVPVASADESAGGTTTSARPGAPAAAGGGSAG
+SGGAGGGEPLTGAALARAAMRRPEVQEAPTPPAQETARSEKAPAQPEPTPMPSPVGQAAP
+PAQPAQSEHPRPERWAPPAAASSPEADAPAQRPDAARPEQPAQQDRPQRQTPPPAPAGQP
+EQRQQQTAQAERPTTTERPAERPAAGAPEASPASTRPQAAERAAERPQAEADAAGSAVPS
+SAAPAPTPSQVEKVRRAWPDILAALEDASRLMWMIVKDNASVAGYDGSLLTIGFQQDGPR
+QMLLGRGGDRVLAEAVHQVLGIRPQLDLILGGDAPQGGSRHAQGQAQTPSAPRAESRADA
+PTSRPDAGEAAPTRQDRPQQQGGEPDRGQQQDRGQQQGRGQASDLGPAQGGSPSGRPTGQ
+AAAPTPGRGPSSPAPAQRPTAPQAASTTPPGAPPSDGWGRADEEPPAWDDAPPPEEDPWD
+SLPEFDPDADMDDSDGPEGWTPPAAGQDDAPVGAAGWDGPVPAAEDWGAPPQGGAPAPDG
+RRDERPAAAQGSDAPSEQPTPQGSADAGPAAETDAEPSAEEVRRAYDPGPLVREEEHTIP
+VFARPEAELRAEFAQRFGATRPAGFDDGAGAGADAESTRAAAPSPGPDDLPPGQGDDPDA
+TARRDTHPAASASGPSSAADHGSSGEPTADGTPDPGVPAEDHEHTSASDADDDGSPERAA
+GSGHPASMFPRLMERVRAGGPLEPPVNAAPPGGATPPGGGPGGGAGPSGPGSAPGSDQGP
+RPGGAPSDAQGPGAPGPDAPRGGRPSAAALGARPGGETGSPAGASAPPSLDARAAAIRAA
+REAAQGRGPARPAGNGPAAPSAPAVGWEDEVASDDDVALEDSGLVGRAVVERVLGARLLE
+ERANSA
+>GCF_020097155.1_00112
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLERLCQEEGVRVEPGVLPLVVRAGTGSVRDTLSVLDQLIGGAQQGQVSYDLAV
+SLLGFTPEALLDDVVDAIAADDTPTVFRVADRVVQSGQDPRRFVEDLLERFRDLVIARAL
+PDEASSILHGMPEDQVRRLAAQASQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLMLPATDDTHRGLAARLEALERRVAGGAAFSPDDDASSGAEGPAAGGAGQGGAALSGAA
+LARAAARRAEPEQAREQEPGAGSDKRAAEPATPKPATPEPVAAAPAPERPVERPAEAPAP
+SSSAPAAPAAPTAHTPSQVEKVRRAWPDILAALESDSRLMWMLVKDNATVAGYDGELLTV
+AFPQEGPRRTLQSRNGEQVLGEAVHRVLGIRPRLDLILGGDTPRGEERPKAEGRPAAAVS
+EAPAAPSTSAPPPAPQGQPTQAQPPRAQPSPEDGRRPAASAPRPQDVAVATSWDQAPAPS
+AAPWQPAPSRPAAASPAPQTGPAAPSTPDPRQDAHPGTRPGPADTTPPAAPPSDGWGHVD
+EEPPAWDDAPPPPEDPWDSLPEFDPDADMEDSPGPEGWTPGAGDDAVHGSAGSAPTSAPE
+AWGGAVPTPQDWGAPRPQDPVESPAPQGPEAGTQGTAPDAAAQGAPSPAAPAEAVPEDPE
+TARRAYDPGPLVREEELTIPVFAKPEAQLRAEFAARFGGTRPAGFDSTAASDAAAPDAQG
+PGAAARAAAHGEPVRGGQDAAEPAADREAEPEEDPQAAASAPEHPVRPSPARPTADDTPD
+PGVPQEDHAEDAAPPSATAPDDRGSGHPDSHYPALMERLRASGPLEPPVNARPAGQGGAR
+EEQVPAPVDAAPSPGRPSAASLGRPTGDPQAAIAPPAEDPRASGARAAAIQAAREAARGA
+GPRPADGAPGGPATASGPSVDWQDEVASDDDVALEDSGLVGRPVVERLLGARLLEERPLE
+PGL
+>GCF_023573625.1_00227
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLVQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV
+SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADITNLALTDMVGATSPRLHLELLMA
+RLLLPASDETHRGLAARLEALERRLELGGAAPVEDGAPEGTTTPARSGTPAPDGGGSAEN
+AEGSGPLTGAALARAAMRRPEEPAPTAPTAPPERWTPPAPQPVAEAPEGDAAAGATGSER
+PQQPPQPGRPEPAEVGARSEDARRPEAGSRPEPEGRPEPEGRPQAQDRTGAAPAPAHGPE
+ETAAPSSPTPAPAASQVEMIRRAWPDILAALEDASRLVWMLVKDNASVAGYDGSLLTIGF
+QQDGPRQSLLGRGGDRVLGEAVHQVLGIRPRLDLILGGDAPTGDTRGQSGARPAGPARTD
+RPERPAPPQGRPDRPAAQPNRPAPAPGPAPREPESSRPAPPRSAAPSTAEDDPAPPAAPP
+RATQQRQTPQPSPAWTPAAPATSWGPTPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPE
+EDPWDSLPAFDPDAEQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAP
+APGGAAPDAGQDPPVRPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELR
+AEFAKRFGATRPAGFDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSS
+DEQRRPTGAPTADATPDPGVPADDSDATPRAAAGPTGSDFPGSGHPASMYPRLMERLRAG
+GPLEPPVNAGSSGGPGAPGGPDPDASPGSPAGGRPSAASLGARPADVEPAGGASAPPSLD
+ARAAAIHAAREAAQGRGPTRPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLVGRAVVE
+RVLGGRLLEERPNDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000320.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97536c0230d3b920cbfa87ff49b410cc103e56e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000320.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00228
+MPAGRYAPSPTGSLHLGNLRTALVAWLAARATNRAFLLRVEDLDRVRSGAEADQRADLAA
+VGLDWDAEPVRQSERTALYDAAVAALRAVHGPDAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGAVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDVAKVAGLPAGETPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CAARGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLEDLSAQDPAWTPERVRDRLLESLG
+LPAGPLAAAVPAFDPAALPRVPWVFTGL
+>GCF_003691675.1_02241
+MPAGRYAPSPTGSLHLGNLRTALVAWLAARATDRAFLLRIEDLDRVRSGAEAGQRADLAA
+VGLDWDAEPVRQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGAVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDAAKVAGLPAGEIPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CDGRGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLEDLAAQDPAWTPERVRDRLLESLG
+LPAGPLAAAVPAFDPAALPRDPWVFTGL
+>GCF_005280335.1_00153
+MPAGRYAPSPTGALHLGNLRTAIVAWLAARATDRTFLLRVEDLDRVRSGAEAAQLSELAA
+VGLDWDAEPVRQSERTGLYDDAVAALRAAHGADAVYECFCSRKDIAEATSAPHPAPADDD
+GAPGPAGAAPLRPPGFYPGTCRGLTAAQRAERRRVRPAALRIDAVQVAGLPEGEIPRAEA
+VDLLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSTPRQRWLAA
+ALCAARGEALPQTSYLHVPLVLNAEGRRLAKRDGAVTLEDLAAADPSWTPERVRDRLLSS
+LGLPPGPPADAVPAFARMLEDGSLPREPWMFDPAAFAGA
+>GCF_020097155.1_00110
+MPAGRYAPSPTGTLHLGNLRTALVAWLAARATGRTFLLRIEDLDRVCSGAEAGQLADLAA
+VGLDWDGEPVHQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGTVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDAAKVAGLPAGEIPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CVARGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLGDLAAQDPAWTPARLRDRLLESLG
+LPAGPLAVAVRAFDPAALPRDPWVFTGL
+>GCF_023573625.1_00229
+MPAGRYAPSPTGSLHLGNLRTALVAWLAARATDRAFLLRVEDLDRVRSGAEAGQRADLAA
+VGLDWDAEPVRQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGTVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDVAKVAGLPAGEIPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CSARGEPTPAVEYLHVPLVLNAAGRRLAKRDGAVTLEDLAAQDPAWTPERVRDRLLESLD
+LPPGPLAAAVPAFDPAALPRDPWVFTGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000324.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000324.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7f9355a3dc013c87aa8fd72684db8d915dadca0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000324.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00233
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAVVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLLAYAVWQFLASAQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLMWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR
+>GCF_003691675.1_02246
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAVVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLLAYAVWQFLASAQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLVWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR
+>GCF_005280335.1_00138
+MSTATDLGPHRSTFGPDAAGRVPSSGTGLASTGGRVAMLLVVLAALVAAFLGAGVVAGFT
+PVAEASGGWLGPDATWVAPASPAFSIWSVIYAGLLAYAVWQFLPSAQSARHDRLRPWILV
+SVLLNAAWIWTVQLGLLGLSVVVIVLLLASLCRILMLLESARAHSWGERILLDGVQGLHL
+GWVSIATVANVAAWLASTGWTGDPFQPTTWAKIMIVVAVLVGAFTAVYDGGRPAPAFALA
+WGLVWIGVGRADGSGLLSGSLAVLAWGGAAIVLLCWVAALLLSRRSATGEARDLVLDALD
+GGDDPVDGRR
+>GCF_020097155.1_00103
+MSTAIDAGPQGTVPIDAAQAPSSGRGLASPGGRWAMLAVVVLGLVGAFLGAGVLPGMTPT
+SDAAGGWLGADSTWIAPATPAFRIWSVIYLGLLAYGVWQLAGSAQSARHDALRTWIMASI
+VLNVAWLWVVQVGWLGLSVVVIFLLLAVLCRILVLLETGRPRGWAARILLDGVQGLHLGW
+VSIAAVTNVAAWLASLGWFGAPLEPTRWAQIMIVVAVLVGAFTAVYSGGRFAPAAALAWG
+LLWVGVGRSDGSGLLSGAVALTAWGAAAIVMLCWLVSLWLSSRSATGEARDLVLDALDGG
+GDPVDGVR
+>GCF_023573625.1_00234
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAIVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLFAYAVWQFLPSGQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLVWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000325.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000325.fa
new file mode 100644
index 0000000000000000000000000000000000000000..892a76b7ecbdb764d9aa5533b098b97565cff4e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000325.fa
@@ -0,0 +1,39 @@
+>GCF_002008305.4_00234
+MPLARLRAALPAAALSLLLLTGCTATDDGVTPASDADTSASVSTMPITSTPSVDAAATSR
+AAASSLAASSSAAQSSRAAASSSSGAAESRAAEGSRSAEPAAPAAPADVEGDVVTVESIS
+DGDTLRVTLGEVSTRVRLLNIDTPETHHPSKPVECMGPEATAALKSMISPGDTVVLRYDR
+RLYDRYDRLLAGVYADGVLLNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQARANGVGRF
+SGECGTAAEPIPEAAPAPAPEAAPAAGDAGPVSGADSVCPDSHPVKANDNSGIYHMPGQQ
+HYGKTNARHCYASASAAQAGGYRAARR
+>GCF_003691675.1_02247
+MPLARLRAALPAAALSLLLLTGCTATDDGVTPESAADTSASVSTMPTTPTPSVDAAATSR
+AAASSLAASSSAAQSSRAAASSSSGAAESRAARAAEESRTAEGSRSAEPAAPAAPADVEG
+DVVTVESISDGDTLRVTLGEVSTRVRLLNIDTPETRHPSKPVECMGPEATAALKSMISPG
+DTVVLRYDRRLYDRYDRLLAGVYADGVLVNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQ
+ARANGVGRFSGECGAAAEPIPEAAPAPAPEAAPASGDAGPVRGADSVCPDSHPVKANDNS
+GIYHMPGQQHYGKTNARNCYASAAAAQADGYRAARR
+>GCF_005280335.1_00137
+MTPRLFPRAGLVAAAALSLVLTGCTPAASGDDVAAPASAGAPSSGAAATTAAPAVSSTAS
+AEAADRSRAAESSRAAAQASEAEQSRRAEESRAAEARRAEESRAAEASREAERSRRAEES
+RAAAAAAAEEEDLDAAGSAEDAAWGGTAGVEGDVAVVQSVADGDTLRVSLDGVSTPVRLL
+NIDTPETVHPSKPVQCQGPEATAALKSMIGPGDTVVLRYDRRVYDRYDRLLAGVFADGRL
+VNAEMARLGLGEPVVFDGNVRFLPEVEAAWEQARADGVGLFSGECAVEEAPEPVEDEAPT
+AVAEPAPAPAAGSGPVPGADFVCPDDFPVKGNDNSFIYHVPGQQHYGRTNARNCYASAAA
+AEVDGYRAAKR
+>GCF_020097155.1_00102
+MPSSRPPAPRVRTRLLVSAALVLLAATGCTASPATSSSTSSTSSAAPAALAASASPPASG
+ASSAAAVEGDAATVVRVVDGDTVDVRRGAEDVRVRLLNIDTPETKHPSRPVECLGPEATR
+KLEELLRPGDEVVLQYDEERFDRYGRTLAGVVEGETLVNAEIVRAGLGVPVVFEPNRRFL
+PPVEAAWAEAQREGAGLNQPGLECSLQTLQESVAQDPAPAAVSELAQALEAVEAEGQEWM
+KVHYAAVIPLAVSLVQQHGGRADVPSAGAASVAPRASTAPAVPAAPQAPAVGAGSDAAER
+DRQRAAEAQAAADRAERKRQAEARAEAQRQAQAQEQVQARERAAQASREAEAAASAREKQ
+KGASSGSSTAKGFADTSARDTSSGSPSSSGGTSQKAPNRCYAPGGETFVYCGEGSTGSSS
+GGSSSSASAGASSSGAGTSSGGAGGPVSGADGVCPAGYPVKVSSSGKYHVPGGQYYDDTS
+AKRCYASTAAAAADGAVASKR
+>GCF_023573625.1_00235
+MPLARLRAALPAAALSLLLLTGCTATDDGVTPESDADTSASVSTMPTTPTPSVDAAATSR
+AAASSLAASSAAQSSRAAASSSIEAAQSRAARAAEESRTAEGSRSAEPAAPAAPADVEGD
+VVTVESISDGDTLRVTLGEVSTRVRLLNIDTPETHHPSKPVECMGPEATAALKSMISPGD
+TVVLRYDRRLYDRYDRLLAGVYAEGVLLNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQA
+RANGVGRFSGECGTAAEPIPEAAPAPAPEAAPAAGDAGPVSGADSVCPDSHPVKANDNSG
+IYHMPGQQHYGKTNARHCYASASAAQAGGYRAARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000328.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000328.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7cd4ddbd6e22f5c5a16ac2b722f222f826a05312
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000328.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00238
+MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV
+ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT
+VSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELIGTVATSDADVRAAVALPAVASLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKI
+TDDGTAAERLVEFLAGRGLV
+>GCF_003691675.1_02251
+MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV
+ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT
+LSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELTGTVATSDADVRAAVALPAVAGLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKV
+TDDGTAAERLVEFLAGRGLV
+>GCF_005280335.1_00133
+MKILVLAKQVPDTWQERELSLDTGWVVRDGAAEPVPDEISERVMEVALGWRDAGTDAEIV
+ALTVGPEDSSKTLRKMLAMGADAAVQVTDDALVGSDAVETARVIAAAVEREGADLVLAGT
+VSTDGGTGVVPAMVAELLDRPYLPHAEAPQLADGELTGTVATSDADVRAAVALPAVAGLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGAKV
+SDDGTAAQQLVDFLAGRGLV
+>GCF_020097155.1_00098
+MKIAVLAKQVPDTWQERTLDMETGMAVRDGAAEPVPDEIGERVMEVALAAREAGLEAEIV
+AVTMGPADATKTLRKMLAMGADSAVHVVDDALDWSDAVQTARVLAAAVEHLGVDLVLAGS
+ESTDGATGVVPAMVAELLDRPLLPSVEAVEITPEEVRGVLVTEDARLRASVPVPAVVALT
+EKTAEPRFPNFKSIMAAKKKPLETLTLADLGLTAGPLDADRRSVMVSAAARRERAAGEKI
+VDDGTAGEQVAAFLAARGLV
+>GCF_023573625.1_00239
+MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV
+ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT
+LSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELTGTVATSDADVRAAVALPAVAGLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKV
+TDDGTAAERLVEFLAGRGLV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000329.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000329.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5b37d979b9de9b4f6ddcbdc4c87cdb1d79c744b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000329.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00239
+MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPVVAELLGAAATVGVPEAVLVTGA
+EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAAAARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCTDAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITMRPGAVAD
+RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG
+FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG
+>GCF_003691675.1_02252
+MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPIVAELLGAAATVGVPEAVLVTGA
+EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAATARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCADAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITVRPGAVAD
+RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG
+FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG
+>GCF_005280335.1_00132
+MSANVEESEMTMQNDAANSGQTVLVHAELGADGALRPVVAELLGAAATVGVPEAVLVTGA
+ASQDAAVARLGELGAARVHVLVAEDAAGTLGDAAVQALAAVTARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCADAVALRWADDEVIARHSVFGGDFLSESTGEGGPRIITMRPGAVSD
+RAPAVASPEVVEVAAAELGAVTAGARVLETTRRVQQADRPALRGAKTVVSGGRGVGSEEG
+FAIVEELADALGAAVGASRAAVDAGYTAADRQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEYADFGVVGDIFKVVPQVIEQLRARRG
+>GCF_020097155.1_00097
+MTDLPVTPVLVLAELTAAGDLRPAVAEALGAAARVGVPHAVLVTDADADDALVARLGELG
+AAVVHTAVAQDPAELGTAQVAALAAAVDAVLPEAVVLPNTPESRAVAGRLAVRARGAVTA
+DAVGLHRADGEIVARHSVFGGDVLAESTVEGGPNIVTLRPGAVADRARPVAAPEVRPLDV
+AGRTVTAGARILSSEPAAPSADRPDLRTARAVVAGGRGVGSAEGFTTLVEPLADALGAAV
+GASRVAVDSGFTAPEGQIGQTGVTVAPDLYVALGISGAIQHLVGMKTSGTIVAVDSDEDA
+AIFEHADLGVVGDVNEVVPQLIAALAARRG
+>GCF_023573625.1_00240
+MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPIVAELLGAAATVGVPEAVLVTGA
+EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAATARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCADAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITVRPGAVAD
+RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG
+FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000330.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000330.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00983e7b94b24605687bdfa8efa02b4dbf52b8f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000330.fa
@@ -0,0 +1,52 @@
+>GCF_002008305.4_00240
+MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPFAREGEWFTELAAVGGPTAPE
+MVAQEVDAPEQATAEPTAEPAAAAPARPVVAELADVEPADAEPAVAAPVAAASAPEPAPT
+APDTRSAPPASAVQPPRAATGTPARTAETDAAESAVPSRLRKALPAVAGVVVLALLAVLA
+ARWLRSLDPVADFIATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHET
+RPPANFTPTKDGLFSARGNTPKKFSLTIWMHQALDALWLLNGLIFVVLLIATGHWARIVP
+TDPHVFQHALSAGIQYLSLDWPTENGWVHYNALQMLSYALVVFVAAPLAALTGWRMSSWF
+PTEAKGLNKAFPMEVARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDA
+WGLVVFLVSVAVTAAAWFFLKPAFTAPVASRFGTVGR
+>GCF_003691675.1_02253
+MPKQRMAGYVPLKGAPAETEPAPAPGQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMVGYVPFAREGEWFTELAAVGGPTAPE
+TAAQEVVAEPATAEPAAAEPADAEPAVAAPVAAAPAAEPAPTAPDTRSAPPASTAQPPRA
+APGAATGTPARAAETDAAESAAPSRLRKALPAVAGVVVLALLAVLAGRGLRSLDPVADFI
+ATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLF
+SARGNTPKKFSLTIWMHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHAVSAGI
+QYLSLDWPTENGWVHYNALQMLSYSLVVFVAAPLAALTGWRMSSWFPTKATGLNKAFPME
+VARKVHFPVMVFFVAFILVHVFLVAFTGLLTNLNHMYTSRGGATDAWGLVVFLVSVAVTA
+AAWFFLKPAFTAPVASRFGTVGR
+>GCF_005280335.1_00131
+MARRRRRPGGRSGLGHPAGAPAAAPAPIAASASPTQSPRPAEPAAAQPRLAEQDVAAAVA
+RPAAAAPVAVESDLVPLGQRRRMGGYVPLAREGEWFAELAAADAAPAGETAEPTVLEAAH
+DDAAPAAEAAVTEPAAPTTTAAAAAATTAAAQAPAAPAQPAAAAAAPTAPDTRSAPPASA
+AQPPRAEPAAASGRPARATKKTDAAEEAPAPSRLRKALPLVAGVVVLALVAVLAARWLRT
+LDPVADFIAAYDGHPALAEGTPVGMPPWLGWQHFLNMFLMVLIIRTGLQIRNETRPPANF
+TPKKDGAFSARGNTPKKFSLTIWTHQALDALWLLNGVVFVVLLFVTGQWARIVPTDPYVF
+HHAFSAGIQYLSLDWPTENGWVHYNALQMLSYTLVVFVAAPLAALTGWRMSSWFPTEAKG
+LNRAFPMEAARKVHFPVMLFFVLFILTHVFLVFFTGALKNLNHMYTSRGDATDAWGLVVF
+LVSVAVTAAAWFLLRPSFTAPAASKFGTVGR
+>GCF_020097155.1_00096
+MPQRMQGYTEFRGEPWPPRDRVPQAPAPTTTPAVAADERRPGRRMVGYTAFRGEPWPPVR
+EAAQPAPAPAAAASPAEVTEAAAAAVPLEATAPAGIAVPGRRMAGYTAFRGEPWPPARVG
+AAPQAPEPAPMATVEPAVATGPTPTVEPVAAGAPETTPKPAPSTGRRVAAAVGGVVVLGL
+LAVLGARWLLTLPEVAAFVARYPGVPRHPEVTPVGIPAWLAWQHFLNLFLLVLVVRTGLQ
+VRHETRPPATFTPHQPGPFAPRSATGGTYSLTVWIHQALDALWLLNGLVFVVLLFATGHW
+MRLIPTDPQTPQHMVSTALQYLSLQWPEHDGWLHYNALQMVTYAGVVFVLAPLAALTGFR
+MSSWWPSRNTALSRGFPMELARRLHYPTMLAFVLFVVVHVVLVLFSGVLHELNAMFLARN
+AADAWGLAAFLVGCAVIAAGWVLLKPAIVAPVAERFGRVSR
+>GCF_023573625.1_00241
+MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPFAREGEWFTELAAVGGPTAPE
+MVAQEVVAEPATAEPAAAEPADAEPAVAAPVAAAPAAEPAPTAPDTRSAPPASTAQPPRA
+VPGAATGTPARAAETDAAESAAPSRLRKALPAVAGVVVLALLAVLAGRWLRSLDPVADFI
+ATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLF
+SARGNTPKKFSLTIWTHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHALSAGI
+QYLSLDWPTENGWVHYNALQMLSYALVVFVAAPLAALTGWRMSSWFPTEAKGLNKAFPME
+VARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDAWGLVVFLVSVAVTA
+AAWFFLKPAFTAPVASRFGTVGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000331.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8594e8a29a17c2fe0568d0c2a7d4e192668dcbfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000331.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00241
+MICRVATGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AAVTAGDEDGPLLECWTRPLAWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA
+EFVAAGRLPRGAETRVPMPGLLAARPESLPTADPDVRPAVDAAATAGARFAPKPELANPS
+GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVD
+VDLVPVGADGVPVADKPMVQVQVTFRAARS
+>GCF_003691675.1_02254
+MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AVAAGDEDGPLLECWTRPLSWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMAE
+FVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPSG
+AVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVDV
+DLVPVGADGVPVADKPMVQVQVTFRATRS
+>GCF_005280335.1_00128
+MRWHGDRAAASGVTALTNILGHPIICDAAGRGRSASVLTVQNSLRPAADSPTGPRAHASG
+RTEQLFGIRRHAAMPERDGALNPAAFEAGPWCLDLDGRPTGAAATVIMDNATAVAVHHAA
+PGVETVVTTELQINVLAPLPAFDAAAITEGRAEGPLLECWTRPLSWDAGGGVGRAWLEDA
+EGRRIVEATGWFQAVPTGAPEHRAAFTAAADLPRGPETRVPMPGLLAARPETLPPAARAG
+RPAVTAAVAPGARFAPKPELANPSGAVHGGAMTLRAVVAAQAAMPDRELYDVQAVRVVFT
+RPGHGEMVALTRVRHAGRSLRLVDVDLVPVGEDGAPVAEKPMVQVQVTFRAAR
+>GCF_020097155.1_00095
+MDEITLNPDADARWRGPRRLLLGRPEQLAGLRRRETAEIQGDTLHPGDWEVGPWVRDLDG
+RPTGAAACVAADNLTAVALHWAAAEAYDAMVTTQLQVNVLRPLPVFDPADPADRPRLRML
+GTPLSTDALGGCARGVIVDDDGTAYVEATGWFQATPGPMSLALEAFREHAALPVAEADRA
+DLPAVTAVVADSVPAPRPGERPAVSQEMTAGLRFRAEPLLDNPGGMTHGGIQCLRAVLAA
+QAALPDRLEYDVQAVQVVFARPGLGEQVALTRVRHAGRSLRIVEVELVGVDPETGAPQAG
+RPSILAQVSFRAAQG
+>GCF_023573625.1_00242
+MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AAVTAGDEDGPLLECWTRPLAWDAGGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA
+EFVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPS
+GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVHVVFVRPGHGEMVALTRVRHAGRSLRLVD
+VDLVPAGADGVPVADKPMVQVQVTFRAARS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000332.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000332.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41fe2a7bb3074ef8249762b4a016fc25341b9ec6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000332.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00244
+MSDAQSTATTAPAAARDGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW
+AADPAVRGVLIRGAGEKGLCAGGDVVSLRASLLAGRFAEAEEFFRDEYAMNERIAAYPKP
+YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH
+LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD
+EVLARFAVAEDAQPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE
+AIRTKSPTAVAVAHEAQRRLAARGADLTVADALRQEFTIATHLMREPDMAEGIRALLVDK
+DKDPTWSPARLEDVSTEDVAGHFEPVSGVDPLQLG
+>GCF_003691675.1_02256
+MSDAQSTATTAPAAARDGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW
+AADPAVRGVLIRGAGEKGLCAGGDVVSLRASLLAGRFAEAEEFFRDEYAMNERIAAYPKP
+YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH
+LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD
+EALARFAVAEDARPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE
+AIRTKSPTAVAVAHEAQRRLAARGADLTVADALRQEFTIATHLMREPDMAEGIRALLVDK
+DKDPTWSPARLEDVSAEDVAGHFEPVPGVDPLQLG
+>GCF_005280335.1_00125
+MSDAQTTTTAGSAPQAGEGGDVLLEVRDGLARITLNRPRALNALTHVMVQEIDAALVAWA
+ADPAVRGVLIRGAGEKGLCAGGDVVSLHASLTGGRFEEAAQFFRDEYRMNHRISAYPKPY
+VAFMDGIVLGGGMGVSVHGSHRVATERTRAGMPETAIGFTPDVGGSYHLARAPFHAGRHL
+AATSAHASGADAVALGLADAFVESARLDELEQAMADALGSLEAPSGDAGRDGVRDEAAFA
+AADEVLARFAMAEGERPDSALAAGREWIEDAYGRQTAAEVLAALDERAAGGGEHADAARS
+AAEAIRAKSPTAVAVAHEAQNRLAAHGQDLTVAEALRQEFTVGAHLMRAPDMPEGIRALL
+VDKDKDPKWSPARLEDVTADAVATHFEPVEGVARLELS
+>GCF_020097155.1_00094
+MSEQTSTPQAAAEDEVLFEAADGVGVITLNRPKALNALSHGMVVAVREQLAAWEEDPAVR
+AVVVRGAGERGLCAGGDVVSLHGMITTGRAAEAMGYFEDEYAMNHAISVYPKPYVAFMDG
+FVLGGGVGVSAHGSHRVVTERTRIGMPETGIGFTPDVGGSWLLARAPRNLGRHLGLTSAF
+ATGADALELGFGDVLVDSGDLDAIVAELRAEVGSAGDDADAAHAAVDAVLARHARPASEA
+PLLADAEWLEPAYAHDRVEDVFAALEATAADHADEGVRTRAAEAAETVRAKSPTAVKVTL
+EALRRLGDRAGGTGRREGVAAALEQEHTLASHLTRGHDMAEGIRAQLVDKDRNPQWSPAT
+VEEVSDEAVAAHFGPGEDAPLRLR
+>GCF_023573625.1_00244
+MSDAQTTATTAPAAAQEGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW
+AADPAVRGVLIRGAGEKGLCAGGDVVSLRSSLLAGRFAEAEEFFRDEYAMNERIAAYPKP
+YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH
+LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD
+EVLARFAVAEDARPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE
+AIRTKSPTAVAVAHEAQRRLAARGADLAVADALRQEFTIGTHLMREPDMAEGIRALLVDK
+DKDPTWSPARLEDVSAEDVAGHFEPVPGVDPLELG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000333.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000333.fa
new file mode 100644
index 0000000000000000000000000000000000000000..857752a136e4bd6310415ffe9c55f88bda9a2577
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000333.fa
@@ -0,0 +1,43 @@
+>GCF_002008305.4_00246
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYAEVLPLLEVMGARIVHCGAAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPVNRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA
+>GCF_003691675.1_02258
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYAEVLPLLEVMGARIVHCGAAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPANRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA
+>GCF_005280335.1_00123
+MSEKTATTTTAPVIPHFVHGERVDGSSGRHSDVYHPATGQVEGRVPLASVEEIDAALASS
+EKGFAAWSALNPQRRGRILLKWVDLINENVDELATLLSQEHGKTVPDAKGDIQRGVEVVE
+FAAGAPHLLKGEFSSNAGSGIDVHSIRQPLGIAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKTAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAGRMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPV
+GEETADRLVALLSERIRRLKVGPSLDESSDFGPVVSKDAKERIEGYIAAGAAAARRPGRG
+RPRRRRRGPRGRLLRGRHPLRPRHRGHEHLPRGDLRPGALRGPRRGLRGGAHPRQRARVR
+QRRGHLHPRRRRRPRLRHPRGDRHGGRQRADPRPDRLLHLRRLEGLRLRRPEPARHRRPE
+VLHQDQDHHHALALGRARGRQLRDARRLLTAVHPLPQEDPMTTVLFLGLGHMGGPMAANL
+AAAGHRVLGFDLVPEALEKARMAGIETVTDTAAAAAEADVVLTMLPNGRLVLDVYRGREG
+APGLLDAARPGTVFLDCSTIDVAEAREAAQAAEAAGMRAADAPVSGGQVGAEAGTLAFMV
+GAADEVYAEVLPLLEVMGGRIVHCGGSGLGQAAKICNNMVLGVTQIAVAEAFVLGERLGL
+EHQALYDVMSKASGQCWALTTNCPVPGPVPGSPANRDFQPGFAGALMAKDLGLALAALDE
+QGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHTDRSEA
+>GCF_020097155.1_00092
+MSQSQTPSASLPGTVAFIGLGNMGGPMAANLVAAGVTVRGFDLVPAAVEAARATGVEIAD
+DAASAVPGADVVITMLPNGALVRGVYEGTADAPGLLGAADPDTLFLDCSTISTSEAQEVA
+ALAEAAGHRAADAPVSGGVVGAQAGTLAFMVGGSVEVFEEIRPLLEVMGSRIVHCGGNGL
+GQAAKVCNNMLLAISQIGVAEAFVLGERLGLEHQVLFDVMSEATGRCWSLTANCPVPGPV
+PTSPANRDFEGGFAGALMAKDLGLALKALDEQHVGAEMGRLAQRTYAAYADGEGARKDFS
+GIIETVREAGKDTAA
+>GCF_023573625.1_00246
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYTEVLPLLEVMGARIVHCGGAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPANRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000336.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000336.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7975538d4715b8adf2d4cb52560fc74be3ac6669
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000336.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_00251
+MTAIADRPVPAPGAPAVTPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTDTPGYEATKISGKMGLRIMQNADITLDVRLPA
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV
+>GCF_003691675.1_02263
+MTALADRPLPATGAPAVPPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTETPGYEATKISGKMGLRIMQNADITLDVRLPT
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV
+>GCF_005280335.1_00119
+MTPHADLPHVDLLRLRDGLDPAERTRLEEVEEHLQTAVRPRLAPYWDAEEFAFDLLPGLA
+GLGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMIAHLGSDAHRDRWQA
+RLESFDALGAFCLTEPEHGSDVAGGLATTATLDGDEWVIRGAKRWIGAGMIADVALVWAR
+DTADGEIKGFVVPTDTPGYEATKITGKMGLRIMQNADITLDVRLPADAQLPGAATFDAAR
+DLLRDSRMWVGWQGFGAQMGLLDSLRSYALEREQFGRPLAKFQLIQSAIAEVAGNLAATS
+GMMLQVDALRQEGRMEMMHAAMAKATSTRLARASAALARDALGGNGLLTEYEVSKMMGDV
+EAIYSYEGSYGMNTLIVGRALTGVSAFV
+>GCF_020097155.1_00087
+MTPSPTPSPASAEPAASPATGVLTVAAAVHPGHAAAPAAAVTDGLPDVDLFDLRSLLSAE
+ERAHLERIEAHLEEHVRPHLAEPWNTETLPMEMLPGLASVGLGELDFLGASRLFQNLVHV
+AIARVDLSFSALVGIHNELNIGSIERFGTEEQKQRWVPALRRFEALGAFCLTEPDHGSDI
+AGGVETTATPDGDGWILRGTKRWIGAGTVAAVALVWAKDVSDGEVKCFLVPTDAPGFSAS
+KITGKTGLRIMQNADMVFDDVRLGPEALLPGAGSFDATREMLRDSRAWVGWQGVGVQQGI
+LRTLREYALTRTQFGRPLAKFQLIQAAIAQVAGNLAAATGLMMQVQRLQDDGTLKMVHAA
+AAKATSTRLARESAALARDAMGGNGIVASYEMARFMGDVEAIYTYEGTQSINALLVGRAL
+TGVSAFV
+>GCF_023573625.1_00251
+MTALADRPLPATGAPAVPPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTDTPGYEATKISGKMGLRIMQNADITLDVRLPA
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000344.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000344.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70d65c8851ec7a2f8ca6ad2e4caa1097b592279a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000344.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00265
+MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF
+TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID
+>GCF_003691675.1_02278
+MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF
+TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID
+>GCF_005280335.1_00098
+MDRMILINLKYTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYLLIEGF
+TDEGAKAHVESPHFQEGIDAMRPLLASTPQIISEHVDAEGFGPMGELQID
+>GCF_020097155.1_00069
+MILINLKFTVKPELADQWMDAVAKYIADVRSEPGNMFFEWYKPVEGGDNEFFLLEGFTDE
+GAQAHVASPHFQEGIDAMRPLLQSTPQIISEQIGAEGFGPMGEIQID
+>GCF_023573625.1_00263
+MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF
+TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000347.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000347.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a345d90c9afa50eb6561088c8f5b022f580c24b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000347.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00268
+MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGQADLLRDGVPVDGLPEISRVAAGLAMMELSRLDGSIATMTGVQGGLAMR
+SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW
+IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
+>GCF_003691675.1_02281
+MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGQADLLRDGVPVDGLPDVSRVAAGLAMMELSRLDGSIATMTGVQGGLAMR
+SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW
+IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
+>GCF_005280335.1_00095
+MTENLPTAEPEYDVAAPLDTDFYLALGDVSDDEKEVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGAADLLRDGVPVDGLPEVSRVAAGLAMMELSRLDGSIATVAGVQGGLAMR
+SIQLCGSDEQRAELLPAMSRGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLRGHKKW
+IGNGAAGGVSVVWARSAEDEQVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGQAVGCYEAAVQYAGQRIQFGRPLAAAQT
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASLAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
+>GCF_020097155.1_00066
+MTETLPTAEPDYSTITGPLDTDAYAVFAELPDEDLALARAARAFLTPEVQKRLQEAWDTG
+EYPTELIAGLAEADLLRDGVAVEGKPAQSRLACGLAAMETSRIDGSLATVVGVQGGLAMR
+SIEMCGSDEQKAKYLPAMDRGELFGAFALTEPTHGSDSVSLQTTATKVEGGWRISGHKKW
+IGNGAAGGITVTWARSAEDGQVKGFIVQQDAEGYSAEVIRGKMSLRAIHQAHITYDDVFV
+PDEDVMPGAQSFKNTAAVLFATRLGVAWAAVGHALGCYEAAVQYAKQRVQFGRPLAESQI
+VQERLARMLSELTQVQLLVLRAARLEDAGKLTGPQASLAKYSATRTARSIAANARDLLGG
+NGILLENEVGKHFADIEAIHTYEGTETVQALIVGRDITGVGAFA
+>GCF_023573625.1_00266
+MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGQADLLRDGVPVDGLPDVSRVAAGLAMMELSRLDGSIATMTGVQGGLAMR
+SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW
+IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000349.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000349.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c485138686a450d10c9c821279eaa121322348a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000349.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00270
+MPDTPQPPAVPAHPDHFGFEVTHRLETPGHDGAPLGRTGVITTPHGRIQTPAFIPVATQA
+TVKAVLPESMKDLGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG
+>GCF_003691675.1_02285
+MPDTPQPPAVPAHPDHFGFEVTHRLETGGADGAPLGRTGVITTPHGRIQTPAFIPVATQA
+SVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG
+>GCF_005280335.1_00087
+MPDTSPGPAPSSSSSGAPAHPSHFGFEVTHRLEAGGVDGAPLGRTGVISTPHGQIQTPAF
+IPVATQATVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTD
+SGGFQVMSLGSGFKKVIDMKGPSAPDGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRH
+RFTPEVSVGIQHRLGADVMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVR
+AARPYQALFGVIQGAQYEDLRRKACRDLAAMRADFPSAGELDGVTSGFDGYGVGGALEKE
+NLGTIVGWCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDG
+RFNLPGAKYRRDFGPLDPACDCYTCAHYSRAYIRHLFKAKEMVAHTLISIHNERFTVSLV
+DRIRAALQDGTYAELKEETLGRYYAPKG
+>GCF_020097155.1_00064
+MPETSAPGTAGPTSSSAVTSDPAHPDHLGFEVRERLDAPGADGIALGRTGVLRTPHGEIQ
+TPAFIPVATQATVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGP
+TFTDSGGFQVMSLGSGFKKVIDMKGPAAPEGQGADDAVAPGKERLANVDDDGVWFKSHLT
+GDRHRFTPERSLQIQHNLGADVMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARL
+TAERAGRPYQGLFGVIQGAQYEDLRRKACRDLSGMTAEFAAAGERPATAHGFDGYGIGGA
+IEKENLGTIVGWCAQELPEDRPRHLLGISEPDDLFRAVENGADTFDCVSPTRVARTGAFY
+TRDGRYNLPGATYKRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLISIHNERFT
+VSLVDRIRASIQAGTFAELKAETLGRYYAPKG
+>GCF_023573625.1_00268
+MPDTPQPPAVPAHPDHFGFEVTHRLETGGADGAPLGRTGVITTPHGRIQTPAFIPVATQA
+SVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000350.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000350.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ca1127cb6477e70ba4097921f71c660b707deb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000350.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00275
+MTTPTGAIPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV
+ATHGLDWEAELADVAAVILPGSPFTGSDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG
+CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA
+LPPGAVLLAAGTDCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT
+VAGLAAVDPEHPRRILANFRTLFG
+>GCF_003691675.1_02290
+MTTPTGAIPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV
+ATHGLDWEAELADVAAVILPGSPFTGTDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG
+CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA
+LPPGAVLLAAGADCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT
+VAGLAAVDPEHPRRILANFRTLFG
+>GCF_005280335.1_00080
+MSTPSAPQPAPSADAPPSGRPFLLIQTRPEDEAARAEEEAVRRLGGFAEHQLAALRLDRT
+LDADPDARQDWAALVAGHAGVILSGSPYTSSVPQETKDELQVAVELELGRMLDAVLDADA
+PFLGCCYGVGTLGAHAGGTVDGTHAEPAGPTDVTLTEAGAADPLLEGLPPRFTAYVGHKE
+GLTVPPPGAVVLATGEACPTQMFRLGRRQYATQFHPELDQVGLVERLRIYLHHGYVDPED
+AEDTFARIESTPAPVPPRILENFRRVFG
+>GCF_020097155.1_00063
+MTETTAPAADAAAPRPFLLVQTRPEEDAAAAEAESVRRLGGYDDATLRVLRLDRRVLDAE
+GEAHAGAVDWEAELADVAGVILPGSPFTGSDPEESKSDLQVAVEAELGRLMALVLARQTP
+FLGCCYGVGTLGRAAGGVVDTTYRELPGPIDVALTSEGLRDPLLEGMPAEFAAYVGHKEA
+VRELPPGAVLLATGQACPVQMFRVGEHLYATQFHPELDQAGLLERLEIYADHGYFAAHEA
+DDMFAAIRAREAPIPPRILERFRAIYG
+>GCF_023573625.1_00273
+MTTPTGAVPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV
+ATHGLDWEAELADVAAVVLPGSPFTGSDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG
+CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA
+LPPGAVLLAAGADCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT
+VAGLAAVDPEHPRRILANFRTLFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000351.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000351.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69739aab5595d05db84a99514ad224cb056f79fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000351.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00277
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFGQLLYLRARGGSETLTDADLDSRIARELGALRTLADELEAKAATRR
+>GCF_003691675.1_02292
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR
+>GCF_005280335.1_00076
+MAPMTGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRQEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH
+GLNLRSGSQLEDLFGMAERLYLLHEDVEGTLAALGLLTNLPWDGAVGRWKSIQAGLALAS
+QILRDEGEHIVAANLGKRLHEADEVPSEPGRAARVLEVRQRQLNEPQLYDREISRALQAR
+DAEAEYRWRRARFAQLLYLRGRGGSETLTDADLDSRIARELGTLRGLARDLDAKAAARS
+>GCF_020097155.1_00061
+MSDGGAEVAPIAGGYLRHLKAQDVRPGDSFLTRRGEPAPAVASTRVVRDDFGTPALVIAT
+LVGGREVKIAHGSVIRVRTDRPEEVKAAADTAFSPVDAGSPESRIVAVGQRHLDDAELTA
+TAARLSHGLNLRSGAQLEDVFGMAERMYLLHEDVEGTLTTLGLLTNLPWDGAVGRWKSIQ
+AALGLAALILREDGDHITAANLGSRLKEADEVPSEPGRAARVLEVRQRQLDEPQLYDREI
+SRALQARDAEAEFRWRRARFAQLLYLRGRGGSQTLTDQDLDSRIHRELGTLRQLAKRLAA
+QAARA
+>GCF_023573625.1_00276
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRAARVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000354.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000354.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f90cc52e52c84f0ddafb1343b04c9154cf1abba9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000354.fa
@@ -0,0 +1,74 @@
+>GCF_002008305.4_00281
+MQDASSESRAALERLRAASAPRPDDAETRAPAARPRRALAAPGEISRRDLRRHERALRSG
+RSETAAERRVREDHRADVHRAMDRLRTPGAPAEQRPRRDLSEILDRLGSPDLARFADPLV
+GTVERILPAPGRDPEKAAEAARRRTAAEERRRARLRAGRAAEHERPVAEAAAAAQARDAA
+RARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEEKARAAAEAEA
+RRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAERRRQAAEAERR
+RLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAHTVLHAERALAQARL
+LEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADRPLLSDPEERL
+TDEELFARARVALPEWRRRQRLSTKAQAVRAEATAHSSAGPVTGALPLIPGYTPAPPEEP
+AGSPTAADRRGQALLTVVWALFVLSGAWGLGLAGRVPGLGALDAGAYPLTADGRHGPGAS
+VFGLSPLHPAIWPVLWLLTGMYVLRQWGRGQGASPRHRRIRGAIAGALLALALWFPLAVL
+APGGFDVVPWLLALVLMLRVVRRLGARPAARRVARVAEDGALGVLLGTLLAGAPTAVGAA
+LHAWGVHVGWFPTELLALLVLVALLLAALRLVLGGRGRMGVALGMAWTLLCLALPRLLPS
+PLGAQQSVWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA
+>GCF_003691675.1_02296
+MQDASSESRAALERLRDASAPRPDDDATRAPAERPRRALAAPGEISRRDLRRHERALRSG
+RPETAAERRVREDRRADVHRAMDRLRTPGAPAQQRPRRDLSEILDRLGSPDLARFTDPLV
+GTVERILPAPGRDPEKAAEAARRRTAAEERRRARLRAGRERAAEAARRRAAEHERPVAEA
+AAAAQARDAARARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEE
+KARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAER
+RRQAAEAERRRLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAYTVLH
+AERALAQARLLEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADR
+PLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVRAEATAHSSAGPVTGALPLIP
+GYTPAPPEEPAGSPTAADRRGQALLTVVWALFVLSGAWGLGLAGRVPGLGALDAGAYPLT
+ADGRHGPGASVFGLSPLHPAIWPVLWLLTGMYVLRQWGRGQGASPRHRRIRGAIAGALLA
+LALWFPLAVLAPGGFDVVPWLLALVLMLRVVRRLGARPAARRVARVAEDGALGVLLGTLL
+AGAPTAVGAALHAWGVHVGWFPTELLALLVLVALLLAALRLVLGGRGRMGVALGMAWTLL
+CLALPRLLPSPLGAQQSAWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA
+>GCF_005280335.1_00072
+MQDPSSESHAALERLRGAPKPVPAPEEAAGAPRTPDQDDDGAATAEDPVPAAARTPADDP
+APAPSPSPPQDAETAPAPDASPASDADAPADVEADVEAPRPARRATPPRPRRPRPDLPPR
+PAPPRARPAHRLSPRRPMRGACARAAARTSTRRWSGRAPPAPPRSSAPRRDLSDILDRLG
+SPDLARFTAPLVGTVERILPAPGADPQKAAQAARRREEAEARRRARLQSGRERAAESARR
+RAAEHDRLAAEAAEREAALRDDDARSEARRADEEAAAAKEACRQERLRERRTAGRAAAEE
+RARLAAEAVEADRERERREAEEAAAAAAREEAALQARLQEEARARRERAEQEERLAQERA
+AEEARLAQAARIARRRREEERERQRREAERRRRLAQEAKARAAADQEKRRQQEQERRRRE
+AKVAEERARVQAERRAREEAELAERERRRLEAEAEAERRRQAQEAERRRREAERAEAERR
+ARAEEAERRRREAEEAARRAAEARRLHAERTRAHTVLHAERALAQARLLEDRARDAERRA
+AEEEARRLREHQDRESRALYRAARELEGPEVIPAASQRPLLARPEEGLTDEELVARARQA
+LPEWRHRQRLATKARAVGAETAAGRSAGPPTGPVPLIPGYTPAAPEEPAGPATVRDRRGQ
+LVLTLAWAAFVLAGVWGLGLFRFVPGLDALDAGPYPAAGDGRHGSGATVFSLFPLHPVIW
+PVLWLLTGLHVARQWGPGQGAAPRHRRTRGPMAGTLLALALWFPLTVLVPWGLESVLWLV
+ALALMLGAVRRLGARPAAGRLARLAEDGAPGALLGTLLAGAPTALAATLHAWGVHVGRFP
+TELVAALVLLTLLPGAVRLVLGGRGRMGVAVGMAWTLLCLALPRLLPSPLGAQQSAWVGF
+AAAFGALLLLTAAAVRRSWVRQIERDAARRPPPAVA
+>GCF_020097155.1_00058
+MTSQDDDAPRPAPPAPRHAARPRRALAEPGRLAPEQLERHTRRLRGEPLPPETPEEAAAR
+AGRRHDLAAALDRLPAESAPAAPRPRADLSDLLDRIGTPDLARFADPLLGTVGRILPSGP
+SPERAAAAARRRAEHEGRRRAERAAGRARAAEAARRRAEETARREAEAAERARAARTVEE
+SRAEAVRAAEDAAREAERHRAERLRERREAARAAAADKARRVAEAAERARVEEEALLAVE
+ADAQAREVAAAQAEPDALARERRERADQEERRRRAALLARRRRDEERRRRRREAERARRE
+AEEQRERAARAERSAAEAARRRQAEEAAEAERRQMAVEAARARAEAERLAQEAARERRRR
+IAAARALPRTVAARHIAAGTAAEDRRRQAAARASEEAARVLAAHHDRETRALMAAARELD
+GPDVVPPAHLRPLLADPAEGLDDAALLERARAALPQWRRTGRLLTKADAVRAQTAHGAAD
+GTGPATGAFPIVPGYVPPSGPPEPRAPATREDRRHQLELTGAWLLFVLASAWGLGLFRLV
+PGLRVVDQGSYTAAHGGRYAFTTSVLSLFPLHPAVWPVLWLALGVYVAHQWGPGQGAAAR
+QRQTRRSVAGALALTALWFPLAVLVPWGLEFMVWLAALALMIRVMRGLTAVPARTRAAQT
+CTDGVLGGFLGLLLAAAPTTLASPVAATGVFWGWFPSALVAAALLWAVVLTGARLALQDR
+GRLGLALGMAWTLLCLALPRLLPSPLGAWQSAWVGLSAVAGGLGVLLLVVVRRTWVREIE
+EQAAAAPQGVPAGRVNGR
+>GCF_023573625.1_00280
+MQDASSESRAALERLRGASAPRPDDDATRAPAARPRRALAAPGEISRRDLRRHERALRSG
+RPETAAERRVREDRRADVHRAMDRLRTPGAPAEQRPRRDLSEILDRLGSPDLARFADPLV
+GTVERILPAPGRDPEKAAEAARRRAAAEERRRARLRAGRERAAEVARRRAAEHERLAAEA
+AAAAQARDAARARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEE
+KARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAER
+RRQAAEAERRRLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAHTVLH
+AERALAQARLLEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADR
+PLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVQAEATAHSSAGPVTGALPLIP
+GYTPAPPEEPAGSPTRADRRGQTLLTVAWALFVLSGAWGLGLAGRVPGLGALDAGAYPLT
+ADGRHGPGASVFGLSPLHPAIWPVLWLLTGMYVLRQWGPGQGASPRHRRIRGAVAGTLLA
+LALWFPLAVLAPGGLDVVPWLLALVLMLRVVRRLGARPAARRLARVAEDGALGVLLGTLL
+AGAPTAVGAALHAWGVHVDWFPTELLALLVLMALLLAALRLVLGGRGRLGVALGMAWTLL
+CLALPRLLPSPLGAQQSAWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000356.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa545d12e30e894e651fddf5abe62ad6587a4b1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000356.fa
@@ -0,0 +1,47 @@
+>GCF_002008305.4_00284
+MADPFPKDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDLAAEGWPLIT
+NPHQAPPAWVAPDARVSGSLLSPGCRIAGEVSDSVVGPGVVVAAGATVRGSLLLGDCEVP
+AGAVLDTVVVDVGGAVPAREVTGRAAPAEEVVVLTPQDRGPAEDETTGSGRPGRSD
+>GCF_003691675.1_02306
+MADPFPTDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLT
+NPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSVVVEAGAVVRGSILLGECTVP
+SGAVLDTVIADVGAAIPAEGATGRAEPADEVVVLEPGERGPASSDETTGSGAPVRD
+>GCF_005280335.1_00069
+MPEGDSLVRLAHRLRPVLAGRALTHADLRVPQHATADLTGWTVVEVEPRGKYLLMRLTPP
+AGRPAARPLTLVSHLKMEGRWLVSALDARWGAPAWQVRAVLETADHRVLGAQLGMLTLVP
+TDREDTVLGHLGPDLLDPAWDGSEEAAAALLAEGTRRLTARPERPVGLALLDQRTTCGIG
+NIYRCESLLLAGIDPHRPVGAVPDVPGLLTIARDLLRANVPPAAPFLGWPRTTTGVRANP
+DRPYGIEVVVADRGFPPGLPAAVGSGTAADPAADPGADRTASGPALGRPPARPPADPGAA
+GRRRTGCTGTTAPPACAAAGACARRTSAPPRTTRGSCGGARPASGEPRPNRGPGGGAPYA
+ERRPSPQGRSARPPTPRRTRVADPFPDDPRSAVVALILAGGRGSRLAPLTDARSKPAVPF
+AGQYRLIDVALTTVAHSGLQDAWIVEQYRPFTLNQHVAGGRPWDLDGTRHGLRVLPPAQG
+RDEEGFAQGNGHAIHQQLAPLRRFGAKTVVIMSADHLYRMDLRPVLERHRERDAELTVVT
+TQVAEGASRFGVVSSDADGRVTAYDYKPDEPATDVVATEVFVADVDALTEVIESLLDSAS
+EEQVDDDDPAGAQLGDYGETIIPALVERGRVHEFRHEGYWKDVGTIDAYYQAHMALLRGD
+GLDLDDPRWPLISNFHPRPPAFIHPEAEVNGSMLCPGSRVRGTVTESVIGPGVVVEAGAT
+VHRSVLLGSATVPAGARLDAVIADVGARIPEGATGQTKPGPGNITVLTPDDRSTAEGDET
+TGHA
+>GCF_020097155.1_00049
+MADPFPKDPAGSTVALVLAGGRGSRLDPLTAARSKPAVPFAGQYRLIDVVLSNLAHSGLK
+DVWIAEQYRPFTLNQHLAGGRPWDLDGTRHGLRILPPAEGREEEGFSAGNGHALAQQVPI
+LRSFGAERVVVLSADHLYQLDLRPVLAAHADSGAELTMVTTVTDEDPSRFGVVQADEDGA
+VTAYDYKPEDPEGRLVATEVFVFDVAALHEVVAELVAREKAAGEHADGEEDEDGDPVASS
+LGDYGETIIPAFVERGRVREHRLEGYWRDIGTLDAFYRAHMELLDGAGLDLAAPGWPLLT
+NPPAAPPARVGPRAEVSNALLSPGCVVKGTVEDSVLGPGVVVERGAHVRRSVLFGECIVP
+RGARLDAVIADVGAHIPAEEVGRSRPGPGNLTVLTPATRDPDSEDETTGGAAAKDG
+>GCF_023573625.1_00290
+MADPFPKDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHTRSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLT
+NPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSVVVEAGAVVRGSILLGECTVP
+SGAVLDTVIADVGAAIPAEGATGRAEPADEVVVLEPGERGPASSDETTGSGAPVRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000359.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000359.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ab8fa6329262e382f68d88d8418025bbf58c3a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000359.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00291
+MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHQVQVRAGVRSEESAALLRGFFAAQRD
+>GCF_003691675.1_02314
+MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHRVQVRAGVRSEESAALLRGFFAAQRD
+>GCF_005280335.1_00063
+MGLALDAARAAGEAGDVPIGAVLVAGDGTVLAAVGNEREQHHDPTAHAEVLALRRGARAL
+AEAGEADGWRLSDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHAVQVRAGVRAEESAALLRGFFAVQRG
+>GCF_020097155.1_00042
+MGLALDAARTAGEAGDVPIGAVLVDGDGRVLAAVGNEREQHHDPTAHAEVLALRRGAAAL
+AARGDADGWRLAECTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHTVQVRAGVRGDECAALLVDFFAARRPGG
+>GCF_023573625.1_00298
+MGLALRAARVAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVIRDP
+RFNHQVQVRAGVRAEESAALLRGFFAAQRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000360.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000360.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b1e5ea54fc6f307b88836109a96654cc91886d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000360.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_00292
+MDGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE
+>GCF_003691675.1_02315
+MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE
+
+>GCF_005280335.1_00062
+MRVHLVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVEIQTPVAT
+TTGLRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTYAERLPAD
+LSGRHVFVLDPMLATGGTLIESIRFLYERGAARVTCICLLGAPEGIARLEESLGDVEVDL
+YLAAQDERLDENAYIVPGLGDAGDRLYGLAE
+>GCF_020097155.1_00041
+MRLHVVDHPLVAHKLTVLRDERTPSMIFRQLTEELVMLLAYEATRGVAVTEVEVKTPVAT
+TVGTTLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTYAERLPAD
+LTGRHVFVLDPMLATGGTLIEAIRFLYERGAERVTCLCLLGAPEGVARLEEALGDVDVEL
+YLAAVDERLNEKSYIVPGLGDAGDRLYGLAE
+>GCF_023573625.1_00299
+MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000361.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000361.fa
new file mode 100644
index 0000000000000000000000000000000000000000..863bee06b44dc5e280d93a2eb4820d442214425b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000361.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00293
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
+>GCF_003691675.1_00001
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
+>GCF_005280335.1_00061
+MGQSAGYVHISVRNAQRRADGMSRRGQARADLRLAGGTDAPAAQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGSESHAAVALAPSGA
+EGRDLEVVRQVLGDPTVQGGAHPDLAQAPAPVSTREPGVLIDLSRREVQLDGESLNLTYK
+EFELLNYLVENGERTVGREELLEALWHNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
+>GCF_020097155.1_00040
+MGETAGYVHISVRNAQRRANVSRARRGDLRLAGGTSHEPTPPQTAPTPVLAPSGIPGPQA
+VARENEARGFVIYVGMDELMASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGAA
+GRDLEVVRQVLGDPTVQGAARPDLAQAPAPVSTRQPGVLIDLSRREVQLDGEALNLTFKE
+FELLNYLVENGERTVGREELLDALWKNSDEVPNERTIDVHIRRLRAKLGRLANTVRTVRG
+QGYRFYRHPEVVVWAAPEYSI
+>GCF_023573625.1_00300
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000362.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000362.fa
new file mode 100644
index 0000000000000000000000000000000000000000..894b5099d16f290338dbbc3c522ca8186910ba6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000362.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00294
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHGLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR
+>GCF_003691675.1_00002
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHDLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR
+>GCF_005280335.1_00060
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLRENGLVPDAIVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYHADAAKALAIVNETEETTRSLLVVGHMPWVQN
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWVELDGRDAALTHFVVPGR
+>GCF_020097155.1_00039
+MSPADAKTLVLLRHAKADWPAGVDDHDRPLAPRGHAQAPAAGDWLLEHGIAPEAAVVSDA
+LRTRQTWVWVAQRLGERAPTAYLDRRLYEADAARALAVVNETEETVRSLIVVGHMPWLQN
+LGMRLMSLDSDQDAALEMAEHLPTLGLQVFRVDTPWAELDGRDAALTHFAVPGR
+>GCF_023573625.1_00301
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPTAGDWLREHDLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000364.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000364.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5b002bded5e44c5aefa0981080ea0c1f3b04bdd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000364.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00298
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADRIQVPYNHVIKAVAELRRRGTIQVARGR
+LGGARITEAGLDQRVGELVRDLSPRAEVLDCAGHETGVPCPFAADCRLREALARAREAFM
+AELDLLTVRDLVRPGRAGATGPVSLGLPAMGSHAATV
+>GCF_003691675.1_00006
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADEIHVPYNHVIKAVAELRRRGTIEVLRGR
+HGGAMIAAAGLDQRVGELVRTLSSRDEVIDCAGRDSGVACPYAGDCRLRGALHRAREAFL
+AELDTLRIRDLVSAGPVGGPVLLGLPEIPVTH
+>GCF_005280335.1_00056
+MKLNAYTDVCLRVLMTLAGDEGERLTSQQIADRIQVPYNHVIKAVAELRRRGAIDVARGR
+LGGATIAEAGLELRVGALVRDLAGWDEVIDCTGRESGVACPLAGDCRLRGALHRAREAFL
+AELDAVRVRDLVAAGPAAGPVLLGLPEIPLPADPRPRRRTCPAGA
+>GCF_020097155.1_00034
+MKLTAFTDVCLRVLMTLGRDAGAKMTSQEIADRIGVPYNHVVKAVGELRRRGLVDVARGR
+AGGAVITEAGLDQRVGELVRALSGRPEVVDCEGLESGTPCPLLEACSLRGALARAREAFF
+AELDRQRVRDLVSLPAEFLGLRRLPGA
+>GCF_023573625.1_00305
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADRIQVPYNHVIKAVAELRRRGTIEVLRGR
+HGGAMIAAAGLDQRVGELVRSLSSRDEVIDCTGRDSGVACPYAGDCRLRGALHRAREAFL
+AELDTVQIRDLVSAGPVGGPVLLGLPEIPVAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000365.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000365.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f02e3f22fca683b951e35825248f17b52c9e064
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000365.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_00299
+MDATSHPDAGPRLPETSVPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR
+RALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS
+ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWG
+HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP
+LARASLRLGVLRMPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVA
+YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVG
+RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPAV
+RIKRTALELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT
+TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM
+WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV
+DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN
+SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ
+GVLPLVLAQAG
+>GCF_003691675.1_00007
+MDATSHPDAGPRLPETSAPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR
+RALVVQRTGWGKSAVYFVASLLLRARDAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS
+ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPGLVARMGLLVVDEAHCISDWG
+HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP
+LARASLRLGVLRMPSPAARLAWLLDHLADLPGSGIVYALTVSAAEDTARALREAGHEVVA
+YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVG
+RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPAV
+RIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT
+TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM
+WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV
+DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN
+SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ
+GVLPLVLAQAG
+>GCF_005280335.1_00055
+MDTTQHPDAGPLPSESTAPIGPYGSGAAAPGAAAAREPELHAEALAVLRRLVDRPDAQFK
+DGQFEAIEALVAHRRRALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQV
+AAAARAGVRAVSVSSANATQWDEVRARLAADEVDVLLISPERLTNPRFREEQLPDLVARM
+GLLVVDEAHCISDWGHDFRPDYRRIRDLIGLLPSTGPRAVPVLATTATANARVVGDVVEQ
+LGVDSAQDVFVLRGSLARASLRLGVLRMPSPAARLAWLLDHLEDLPGSGIVYALTVSAAE
+DTARALREAGHEAVAYTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVH
+FGAPSSPVAYYQQVGRAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLQALA
+QHGGALSVAALEPAVRIKRTALELLLKVLAVDGAVERVGGGWRATGREWVYDAQRYARVA
+EARRAEERLMLDYQTTDTCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDTSARERAE
+AALRRTGVPIEPRRMWPSGMDRLGVPVKGRMAPEIQAEEGRALARLTDLGWGTVLRELLD
+KEDAPVPEDVLQGAVGVLAGWGWQTRPIAVVAMPSRTRPLLVGSFAEGIARIGRLPFLGS
+LEHARGGPTAGPGGNSAYRLGSVHGRFEVPEAMAHLLRTASDAGRHGPVLLVDDLVDSRW
+SLAEASRVLREAGAQGVLPLVLAQAG
+>GCF_020097155.1_00033
+MSTSPQDPARPAAVADPALYAEALGVLRALVGRPDAEFKDGQYEAVEALVAHRRRALVVQ
+RTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAASLSSANATEW
+EDVRRSLEADEVDVLLISPERLTNPRFRDEQLPDLVSRMGLLVVDEAHCISDWGHDFRPD
+YRRIRDLIRLLPSSGPRAVPVLATTATANARVVQDVVEQLDVESRQDVFVLRGPLARASL
+RLGVLRLPSPAARLAWLLQHLGELPGSGIVYALTVSAAEDTARALREAGHEVVAYTGRTD
+PEQRARIEQDLKDNRVKAVIATSALGMGFDKPDLTFVVHLGAPSSPVAYYQQVGRAGRGT
+DHADVLLLPGQEDRAIWEYFATASMPDEVQARAVLEALEESGGAMSVAALEPVVSVKRTA
+LELLLKVLSVDGAVERVGGGWRATGSPWTYDAERYARVAEARRAEERLMLDYQTTQTCRM
+EFLARTLDDPTAAPCGRCDVCAGPWYPTGWDGAAREQADRALRRTGVPLEPRRMWPSGMD
+RLHVPVKGRISPAEQAEEGRALARLTDLGWGSRLRELLAAPDAPVPEEVLQAAVRVLAEW
+GWQERPIAVVAMPSRGRPQLVDSLARGLAGQGRLPFLGPLELVGGGPTAGPGGNSAYRLA
+SVHGRFAVPEGMARMLATAPDAGRHGPVLLVDDLADSRWSLAEAARVLRGTGAQGVLPFV
+LAQNG
+>GCF_023573625.1_00306
+MDATSHPDAGPRLPETSAPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR
+RALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS
+ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWG
+HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP
+LARASLRLGVLHLPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVA
+YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHLGAPGSPVAYYQQVG
+RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPDV
+RIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT
+TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM
+WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV
+DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN
+SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ
+GVLPLVLAQAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000366.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000366.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d97c7bf164391ba36ff9a3da1ea64fd85a86d02d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000366.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00300
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETAGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAITALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPAVGEGVG
+EGQAVHEDFAGVATTVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER
+>GCF_003691675.1_00008
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETAGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAITALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPAVGEGAG
+EGRAVHEDFAGVATTVTRMDGTTIAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER
+>GCF_005280335.1_00054
+MTTSTSSLDLHESFKAYDVRGIVGETITADSVRAVGAAFVDVLGLAGETVLVGGDMRPSS
+PAFMAAFAEGATRRGADVVDLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAKA
+GAVPVSSDTGLYEIRDAAQALLDAGEIPAAEAVGTVTQQDILPAYAEYLRSLVDLSGVRP
+LTVVVDAGNGMAGKTTPAVLGDAALDALPLRIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVVDEKGAPVSPSAITALVARREIARAKGEGEETPVVIH
+NLITSRAVPELVAADGGRAVVTRVGHSFIKAVMAEESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGEQDQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPTVGEGAG
+EGRAVHEDFAGVDTAVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEAIR
+DAVLAIVRAER
+>GCF_020097155.1_00032
+MVTLRPGRIIDRVTTAADAINLRDSFKAYDVRGIVGETITAETVRAVGAAFVDVLGLAGQ
+TVLVGGDMRPSSPEFIEAFAEGATRRGGNVQRIGLISTDMLYYAAGVEQAAGVMFTASHN
+PAAYNGMKMAKAGAVPVSSDTGLYEIRDVAQGYLDAGEIPAADAQGSVTESDILTGYAEY
+LRSLVDLSGIRPLKVVVDAGNGMAGKTTPAVLGGEVLEALPLEITPLFFELDGTFPNHPA
+NPLEPENLRDLQRAVVEHGADIGLAFDGDADRCFVIDEQGEPVSPSAVTALVARREIARA
+KASGEETPVIIHNLITSRAVPELVSADGGRAVQTRVGHSFIKAVMASEGAVFGGEHSAHY
+YFRDFFNADTGMLAAMHVLAALGEQDGPLSTLGAEYEPYVASGEINSQVEDKDAAVAAVL
+ARFAPQAADGGESGTAVEDAVAGTSTSVLRMDGTTVSAADGSWWFNLRPSNTEPFLRYNG
+EAKDRATMETVRDAVLAIVRAPR
+>GCF_023573625.1_00307
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQASGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETTGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAVTALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVEDKDAAVAAVVAQFAPAVGEGVG
+EGQAVHEDFAGVATTVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000367.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000367.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c66aad24cf5ae41b00a26eeff6322b88632813c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000367.fa
@@ -0,0 +1,42 @@
+>GCF_002008305.4_00301
+MPPTTPPPPAGPPAVPPSGPAPAAPGEAAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLALSVVPWSVAGDRWGRRRAMVVSMVSASACALAGVLAPTF
+EAMLRLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY
+LQGALLMGGFVALYNFVGYRLLGPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTAPAR
+>GCF_003691675.1_00009
+MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF
+EAMLGLRLLEGMAHGGVAGLAVALLAEEVVPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLTVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY
+LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALVSAVVVLRGRGTAPAR
+>GCF_005280335.1_00053
+MPPQPPPAGPPAVPPSGPAPLAPGDPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSADL
+GVGAHRAALLVSAGTLGLALSVVPWSMAGDRWGRRRAMVVSMVSASLFALAGVLAPTFEA
+MLGLRLLEGMAHGGVAGLAVALLAEEVAPRAVATAAGTYIAGTTIGGLSGRLIALPVAEA
+FTWRTGMLAVTVVGVACTAAFLAVTPQARRFTPSPTSVARLVRIVRGHLGSAELVAVYLQ
+AALLMGGFVALYNFVGYRLLGPPFSWAPTAAGLVFLAYLAGTWSSPRAGRLAARFGRLPV
+LTGATAAMAAGAALTLVPHPAVLVGALVLTTGAFFAAHSVASAWSGTAAPHGRAQSTSLY
+NLAYYAGSSLFGWLGGVFHESHGWTGTVLMVVALALTALAIAVVVLRGRGTAPARCAGAV
+RGAGRRGIRRISRGRLRRRRWPSGAGRARPRGPRGPAARASRPSAGRSRSRCPARRTPPA
+WSAPRPG
+>GCF_020097155.1_00031
+MPPALPAPLEPGTPLYRRLLLGLFLAGVATFAQLYAPQGLLPLVSSDLGVPSHRAALLVS
+AGTLGLALSVVPWSLAGDRWGRRPVMVASLVSASVLALVGVFMPSIELLMGMRLLEGMAH
+GGVAGLAVTLLAEEVAPRVVPVAAGTYVAGTTLGGLSGRLLAMPVGEWAGWRAGMLAVTA
+AGAACTVAFLFVTPPARRSTPVRLSLARLGRIIGGHLRTPGLVALYLQAALLMGGFVALY
+NYIGYTLLAPPFGWPPTAVGLVFLAYLAGTWSSPRAGRLAVRVGRLKVLTGSTALMAVGV
+VLTLVPSPFVLVPALVVATGAFFAAHSVASGWAGTAAPTGRAQSTSLYNLAYYAGSSLFG
+WLGGVFHEGVGWAGTVFMVAGLAAVALVVALVVLRGREDAGPPPPSAVAEGAAA
+>GCF_023573625.1_00308
+MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF
+EAMLGLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSAAALVRIVRGHLSSPELVVVY
+LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTAPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000368.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1cf43677542733ecf3c933d049b67fccd0ddee6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000368.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00303
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPAQEPDATSAGA
+AGPVPADHEEPHRDDTAPAETPGPERPGQDSSGRGEPDAQTPDREPSDAVAEDDARQDTD
+HASAAPRPTATPADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESVRLSSRDLPPWLRD
+QLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMREHRGEG
+>GCF_003691675.1_00011
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATSAGV
+AGPVPGGHGEPHRDDAAPADTPGPKRPGQDSSGRGEPDAQTPDRETSDAVAEDDARQDSD
+HASAAPRPTAPSADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESVRLSSRDLPPWLRD
+QLAAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERRGEG
+>GCF_005280335.1_00051
+MEYLVPVLAVVLIGALAFAVSRWMSAARDRQTAGPRTPSGRPLEIGPERARQAAALLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRSLKDAVMDVQSLAVHPQVYSVPATEQEAPEEAE
+VRDPRTRPTPPEPARDEAADGERQGTERADVVEEGADDPAADDEPRPEAESDLSAEEGRV
+DDGAASGTEPRPGTSEPARADELTALTVPADWSAAPAEEEPPFEVEVMRGMDSVRLSSQD
+LPPWLRDQLSAMVRDGNLESAAVQLSSHSQLSVPEAYELLRRMRERRGED
+>GCF_020097155.1_00030
+MEYLVPILAVVVIGGITLLVARRLSGRSQAPTRSATGTGADTVEASPERARTAARRLDEA
+THRAVYGHIAQGRPFEAVRDYRRATGRGVRDAILDIQSLTLHPQVWSLPVQAEPADDASP
+AAADMPSGPPRGPSDGRGRDGESSARPRLRRAEPSEAGPAPDAEPAPGGDAAADPEADGA
+TSRRPGRQAPEELTTLTVPEGWTADPAPEEPPFEVEVMRGEESVRLASQDLPPWLRDQLS
+AMVRDGNLESAAVQLSSHSSLSVPEAFELLRRMKERREGRG
+>GCF_023573625.1_00310
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATSAGV
+AGPVPDDHGEPHRDDAAPAETPGPKRPGQDSSGRGEPDAQTPDREPSDAVAEDDAQQDTD
+HASAAPRPTATPADELTTLTVPAEWTAAPAEEELPFEVEVMRGTDSVRLSSQDLPPWLRD
+QLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERRGEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000369.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000369.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6f2df0ad7c67f88fa4a64de010c1cb378c740f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000369.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00305
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+ITADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSYSVEHPAADHDGDVRR
+DDVRTDAGTAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRRDVTDADSVVVKDEHLNV
+GTERRASGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTY
+EETPVVNKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
+>GCF_003691675.1_00020
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSAADHDGDVRRDDVRTD
+AGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVTDADSVVVKDEHLNVGTERRA
+SGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTYEETPVV
+NKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
+>GCF_005280335.1_00032
+MDRNMLDQLQNANVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFDKAFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSNVDHDRDVRHDDGLRA
+DAGTAGVAGTAGVAGVADRREDTVVDGDRRDVVDGDRRDLVDADRRDVVDGDRDSMVVKD
+EHLQVGTERQATGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDI
+EVTTYEETPVVNKTVEAEKVSLGKRQVQDTETVSEELRHEDVKIDGDATDRDLDGRTDRK
+DRI
+>GCF_020097155.1_00028
+MDRNALDQLQNGHVFSTDGEKIGSVGQVYLDDVTNEPTFVTVKTGLFGAKETFVPLQQAQ
+TTTDGITVPFTKDFVKDAPNVDADGSLTPEEEQRIYEYYSMDYSAVDTHDRRDVRDAAAA
+GTAGGVVTDRERRDVVDADRRDVVDNDRRDLVDGDADSVVVKDEKLNVGTERRATGRVRL
+RKQSYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDIEVTTYEETPVVNKTVEA
+EKVSLGKRTVQDTETVSEELTHEDVKIDGDDVDGRRR
+>GCF_023573625.1_00312
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSAADHDGDVRRDDVRTD
+AGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVTDADSVVVKDEHLNVGTERRA
+SGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTYEETPVV
+NKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000370.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000370.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e121053ca2e85a0098ee11bb2a95cdb79bc285d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000370.fa
@@ -0,0 +1,61 @@
+>GCF_002008305.4_00306
+MSEPLVADRRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVAEVVEHRAEATALHPRPDGGARLELRDPDGSVSVLDADA
+VVLCLGHQPAELSPGQMRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPTGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALTARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWIAEGRIAEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLEPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAAAAVLAG
+>GCF_003691675.1_00021
+MSEPLVAERRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVVEVVEHRAEATALHPRPDGGARLELRDADGAVSALDADA
+VVLCLGHQPAELSPGQNRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPSGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALAARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+AELMEQTCVEAALGEESPFMMAVGALHAGRLRIKAWVAEGRITEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLGPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAATAVLAG
+>GCF_005280335.1_00031
+MPDAQEAVRRLAVVGAGPRGVMLLERLLARLEGSAPGAHPARLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVQRHQYPARAVY
+GRYLRHLYQDVVAGLRARPEVADVVEHRAEVTALHPTPAGGARLELRDADGAASELAADA
+VVLCLGHQPAELSPGQARMAAAARGRDDLHYQGPQIPSDVDWDTVEPGARVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALAYEPSGREPRLHLMSRRGVPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALSARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYTAPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWVAEGRIAEDSRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPVPVVDAEERAFSVRSPQVGAADSLGPAVVEGE
+WLVEAMMPPNRVQAASSPLIRGMLDDGVAAAGTWEDEEGVRVPAPGFDVTGRPHRLRAAD
+GAVHEDVYVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAVAQAVLAG
+>GCF_020097155.1_00027
+MSPPSISEPTRAIAVVGAGPRGVMVLDRLLARLEAASEPRPTGSLAVHVVDPFPPGPGRV
+WRPDQDPLLLMNTPAFFPTACAADNPGLAPSSVSLSFDQWRLARPDRAAGLERTDYPPRA
+VYGRYLEDVVAAVLDALRARPEVVAVTVHAAQAVALRAAYEGGPVAAPESPSAWRLTLRP
+VDGTPPRELQADVVVLCLGHQDAEPSAAQRRLGEAADASPALHYRGPHLPAELDVDGIAP
+GATVLVRGMGLNAFDLQARLSEGRGGRFEPTGGEPGRALRYVPSGREPVLHLLSRRGLPY
+LPKAAVDAFVPRGVRMSYLTDTEAEALVARHGQLDLAEHLWPLLHRDVVRAYYATLARVH
+PERLGGPADAGRFVRELVGMFESAGRGAPVTARHGQELLHAFAPGMRFLDIRSWAAPFQG
+AVFDDAAAYQEAVAGVLEQACGEAAAGEDSPFMQAVGTLHAGRLRIKAWIAQGLLTDASR
+IRDVQGWFEPLVEGLASGPPLVRVEQMLALHRAGLLSWAGPGPQVEADAEAGVFRARSPQ
+VGADDAVAPAVTEAAWLVEAMMPPSRVEAAATPLVRQMLADGVAAVGRWEDEDGALRSSS
+GFDVTARPHRLRGADGTVREGVLVLGLQLSGVQWGTAIAAEAGADVRDRALFLADADAAA
+RVALGG
+>GCF_023573625.1_00313
+MSEPLVAERRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVVEVVEHRAEATALHPRPDGGARLELRDADGAVSALDADA
+VVLCLGHQPAELSPGQNRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPSGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALAARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWIAEGRIAEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLGPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAATAVLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000371.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000371.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2559a98ccf24bdc878b3412122c359f046810b24
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000371.fa
@@ -0,0 +1,84 @@
+>GCF_002008305.4_00307
+MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE
+LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA
+DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG
+APSANSDPKSLTRTNGVDTDDNSADFTVTGQVTPTNAAATGGEPTPEPEPQPTPSERITI
+AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY
+SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAADGVLPVAEPGAVAPTPVEFPLEEADRE
+ALEGMVLAPQGDWTVTDNYSLNQYGSLGVVPGTKPLDNPTSVARPGAEAQAVAAANAQQL
+IVLDDGASTNFMRSPGNQNPLPYLDADQPVRVGAGLEFSTGVILDWRFDAWSFQPLGHLT
+DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCGAYRDRAGTP
+VTTNGCLPRGAYTPEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE
+ALNAQAGEQRWAYVASPSARPALADEDVIRSAFIYQPAEVTPLGESVILDDQTNFDNARE
+PMAQLFRAADGTAEGAAGTEFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA
+LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYVSQGALTGEYSYAFGGAVGS
+LDGIYASPSAAAAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL
+QLDAPVTEPTPEPEPEPTPGETCDGVTDPRGVPGKPANSVREWLRCIGATPGHGGDHPGK
+GHGGDHPGKGRGPVRP
+>GCF_003691675.1_00022
+MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE
+LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA
+DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG
+APSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAATGGEPTPEPEPQPTPAERITI
+AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY
+SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAAGGVLPVAEPGAVAPTPVEFPLEEADRE
+ALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTPLDNPTSVARPGAEAQAVAAANAQQL
+IVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQPLGHLT
+DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGTP
+VTTNGCLPRGAYTSEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE
+ALNAQAGEQRWAYVASPATRPALADEDVIRSAFIYQPAEVTPVGESVILDDQTNFDNARE
+PMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA
+LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGS
+LDGIYASPSAATAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL
+QLDAPVTEPTPEPEPSPGETCDGVTDPRGVPGKPANSVREWLRCVGATPGHGGDHPGKGH
+GPEHPGKGRGPVRP
+>GCF_005280335.1_00030
+MTQRTFRLSRPAVALAALTLLAPAVVAGPAHAAPTGDGLVINEVYTNGGSANAVFTHKFV
+ELYNPTDTPISLDGWSLQYRSATGTAAPNGVVALSGTVPAKGHFLIQGGSNGTTGAALPR
+PDLNAGGAFNPAGARGTVVLSDQAGALTALPVGSVTTGQAEGVADLLGYGTSNTFETAAA
+GAPSSNSDPKSLTRTDGVDTDDNAADFTVTAQVTPTSSTGEAPVDPIPDPEPDPEPAPAL
+TIAQIQGDGAATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGSAEDATPGASDGLF
+VYSPDTVGSVALGDHVQVTGEAAEHYGLTQVRVGAAGVTPVAEPAAVAPTAVDFPLSEAD
+REALEGMLLAPTGEWTVTDNYDLNQYGSLGIVPGTEPLPNPTSVAAPGAEAQAVAADNAS
+RLIVLDDGASTNFMRSPGNENPLPYLDADRPVRVGAGLDFTTGVILDYRFDAWSFQPLGH
+LTDATAAAVQPVAVEDTRPEEASPEAVGGNVSVGSFNVLNYFTALGQDFPGCRAYTDRFG
+EPVTTNGCLPRGAYTPEAFARQQEKIAAAIDGLDASVVALEEIENSAKFDLDRDRALAHL
+VDALNAQAGEQKWAYVASPADRPALSEEDVIRNAFVYQPAEVTPVGESVILRDEVNFDNA
+REPLAQHFRAADGTEAGVAGTDFVAVTNHFKSKGGSGAAGDNADSGDGQGAYNGDRTRQA
+QALVAFAEQVADDAGTDRVLLLGDFNAYEKEDPIRVLEEAGYVSQGALTGEYSYTFDGAV
+GSLDGVYASPAASAVVTGQDIWMINANESVALEYSRHDYVAEDLYAPDQWRSSDHNPLLV
+GLQLDAPVVEPEPQPGAGHPGKGKGLDKGAGHPGKGKGLDKGAGHPGHGRVPEAARP
+>GCF_020097155.1_00026
+MPTPRLRLVRTAATLAAATLLAPAVLALPAQASPAGDSLVINEAYTNGGSAGALFTHKFV
+ELYNPTDQPISLDGWSLQYRSATGTTAPSTTVALSGTVPAKGHFLIQGGSNGATGAALPT
+PDLTTSFNPAGTKGTIVLADQAGTVAGLPTGSVVTDQVAGVADVLGYGATNTFETAASGA
+PAANSDPKSIARTGGADTDDNAADFTVAADVTPQNAAGGGTAPVDPVDPVDPTPAPAPSV
+TVAEIQGTGATSPLEGRRVSTTGVVTAVYSTGGYDGFYIQTAGTGGAEDATPGASDGVFV
+YAPAEVGSVTLGQTVTVTGDVAEYYGLTQVKAEAGGVRQAAEAGAPVTARELAFPLTEAE
+KEAHEGELLAPAGAWTVTDNYDVNQYGSLGLAPGTSPLPNPTSVALPGADAQAVAADNAQ
+RLIVLDDGASTNFFRSPGNQNALPYIDADAPARVGSAVDFRTPVILDYRYGAWSFQPLGH
+LTDANKAEVQPVDIADTRPAEAVREDLGGNVTVGSFNVLNYFTTLGEDVPGCGYYADKDG
+APVSTKGCLPRGAYTEEAFLEQQAKIATAINGMDTSVVALEEIENSEKFGLDRDHALAHL
+VDALNAQAGYAKWAYVASPTVRPALADEDVIRSAFIYQPAEVTPVGESVILDDQVNFANA
+REPMAQAFRVADGSAGGVVGTEFVAITNHFKSKGGSGATGDNVDTGDGQGAYNGDRTRMA
+QALVAFAEQMKVQAGTDRVLLMGDFNSYEKEDPIRVLEAAGYISQGAKTGEYSYTFDGAV
+GSLDGIYASPAADATVTGQDIWMINANESVAFEYSRDNYVGEEFYAPDQWRSSDHNPVLV
+GLQLDAPAAPVVPTPGTRPTPPADQCALITSPRGAKASAGFSASEWMRCAGVHPGKGRGR
+G
+>GCF_023573625.1_00314
+MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE
+LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA
+DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG
+APSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAATGGEPTPEPEPQPTPAERITI
+AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY
+SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAAGGVLPVAEPGAVAPTPVEFPLEEADRE
+ALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTPLDNPTSVARPGAEAQAVAAANAQQL
+IVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQPLGHLT
+DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGNP
+VTTNGCLPRGAYTSEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE
+ALNAQAGEQRWAYVASPATRPALADEDVIRSAFIYQPAEVTPVGESVILDDQTNFDNARE
+PMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA
+LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGS
+LDGIYASPSAATAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL
+QLDAPVTEPTPEPEPSPGETCDGVTDPRGVPGKPANSVREWLRCVGATPGHGGDHPGKGH
+GPEHPGKGRGPVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000372.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000372.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e389132d3dcf8ed8b302180beccd075a75ed15f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000372.fa
@@ -0,0 +1,72 @@
+>GCF_002008305.4_00308
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKDADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAQAWLTAAGLPR
+>GCF_003691675.1_00023
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR
+>GCF_005280335.1_00029
+MSSLFRRHAVATAACTVLVLAPASAAPALAVETVAADETTISLLSFNDFHGALSSDFSGT
+QFADTVEDYRTAFEAQHGERSVLLTSAGDLIGGSASVSNVQQDDPTIDVMNALGLSALAA
+GNHEFDRGLDDLQDRVIPRAEFPVLAANFVDPDTLEPILASHAIFDVNGVSVAVIGAVPN
+ELYATTTGAGLQGNTVLDMVEAVNGVAAELEASGAADVIVASYHEGAAGAGDLAAELGKR
+EVFRSMVEDTHPAVDVIFNGHTHQLYQYETAGDGVARPVLQAGASGSNLAAVELTVDAAG
+EVTAVASRLLDRSTQDPAEAAAESAVTAEVYAIEQEAVAVFEDMQSQVVADLDGSLTTDY
+QKRLDEGGTWRAGGTRSAETTLGNWVADATKQTALNADPEVDLGVVNPGGLRSEILVDAF
+TGGGTFSPKPADLIGKLTLGELLDVAPFGNSISYFDIPGSSIELALEQNWRDDVRTFTLG
+WSENLTWTYDESRPQGEKVTGVWIDGEPLEQDAIYTVATQSFLADDTWVALGDPTAAPDG
+YTAFATGREDFVDLGVLDTQAISDYARLQASAEGAVGPDFAKKGVPVSGAPETVAAGEEI
+VLTLGDLVIDSDDAPAAAEVAVAFEAADGTVTELGSVTVPAGSEEVTLSGIAAPAEAGAG
+ELRMTVRYADGTETIVRHALEVTASEAPVEPTEPTDPTVPADPSEPADPADPTVPADPSE
+PADPADPSDPTDPAAPVEGDDDGDDRDEEHTVPSTVETGDASAWWLAGFGALLGAALLRG
+RRALGLTASSTPAGR
+>GCF_020097155.1_00025
+MSSIFSRRTAATLACTTLVLAPAAAPALAADASGERTISVLSFNDFHGALSEDFKGTQFA
+DTVEDYRTAFEAQHGEGSTLLTSAGDLIGGSASVSNVQQDNPTIDVMNALGLASLTAGNH
+EFDRGLDDLQGRVADRADFPVLSANFVDPNTKAPVLTSHKVFDVDGVRVAVIGASPNELY
+ATTTGAGLQGNLVVDMVDAVNAVATGIEAADEADVIIASYHDGAAGAAADLSAELGNRAT
+FDAMVERTVPAVDVIFNGHTHQLYQYQTDNGGVPRPIMQAAASGADLAAVELTVDAAGEV
+TAVTPRMLPRSTQDPAEAAAESPVTARVYEIEQQAVDVFTDMQSQVIADLSGSITTDYAT
+RIAAGMGWKAGGTRTAETTLGNWVADSLKHSVSAAEPGVDLGVVNPGGIRSELLVDQTNA
+GGVFSPKPEQLVGKLTMGEVMDVAPFGNTLTYFDLPGSSIKEALEQNWRDGERTFTLGWS
+SNLTWTYDDARAQGDKVTGVWIDGEPLQADRMYTVAAQSFLADDTWVKLGDPSKAPDGYT
+AFATGRQGFVDLGVLDTTAVLSWARAQDAADGAAHPDYAKKGVPVTGAPASVEGGQDVVL
+TLGDLVIDSDGAPAATAVDVAFQGADGAVTELGTVEVPAGQESVTLSGITAPQTAGAGEL
+VMTVRYADGTTAVVRHALEVTASAAPVDPSTPAEPTQPGEPSDPAEPTTPGEPTPSAQPT
+APVEPTAPVEPSAPAEPTAPVEPTAPAESPEPTPTAQPSTPAEPTAPTPSAPAEDGGEHA
+VPGKVQTGDQAIWLVAALGALGAGALVAVRRRAAAR
+>GCF_023573625.1_00315
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSGDYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELAAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLTRSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000373.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000373.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb6633f35840ee3a2e7f742032a526f1cba3d485
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000373.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00311
+MRGPFARFRQERADDRELGTGLWRRAHDRLGRAMDRYWQVLAGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGAGL
+>GCF_003691675.1_00026
+MRGPFARFRQERADDRELGTGLWRRAHDRLSRALDRYWQVLEGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGAGL
+>GCF_005280335.1_00026
+MRGPFARFRQSCSDDRELGTGLWRRAHDRFVRAMDRYWQVLEGDRGPDLLRTEQRNGVVH
+AGNVLAERLPAVRALCVRLHRDHAGDGEHIPPEAADVHRELSRAAHELAATAQALAMHRL
+GQGSSDSVGRHAERTLAHLDRAEELAARL
+>GCF_020097155.1_00022
+MIRGPFARFRQGRSDDRELGTGLWRRSHDRYVRALDRYWQVLEDGRSAGGFTPEERNGLV
+HAGNVLAERVPAVRALAARLHAAHPGDGEQHIPPVTAPVHRELSRASHELAAAAQAVAMF
+RRGVSGSEAVSRHAQRTLDHLDRAEGLAADL
+>GCF_023573625.1_00318
+MRGPFARFRQERADDRELGTGLWRRAHDRLGRALDRYWQVLEGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGARL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000374.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000374.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40bd1ab2efe3348bf3d9fdb55e69d85339d865df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000374.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00313
+MSLPHAPRTPAPPAAASSAVPLRLAVVDMSGTSIVEHGLQDTAFARSLDQHGVPAGTPEH
+DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEATFDALLAEHGVRAVPGAEEALI
+RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD
+LEDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADHVLLAAGSDRVVPGLADVPDLV
+VRTR
+>GCF_003691675.1_00028
+MSLPHAPRTPAPPAAASSAAPLRLAVVDMSGTSIVEHGLQDTAFARTLDQHGVPAGTPEH
+DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEAAFDALLAEHGVQAVPGAEEALV
+RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD
+LDDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADDVLLAAGADRVVPGLADVPDLV
+VRTR
+>GCF_005280335.1_00024
+MSLPPRPPPRGRAPRADGPPAPPLRLAVVDMSGTSIVERGLQDAAFAHALETHGLAADAP
+AHADAVRVFRARRATSRTAVFAQVFPDRPAAAAAARTFEEAFDSLLAEHGVQPVPGAEEA
+LLRLRALGLRVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPFPDMILTALLG
+LDLDDVRGVLVVGDTAEDMTAGRRAGAGLVAGVRTGRDADAALLAAGAHHVVDGLADVPA
+LVGAGG
+>GCF_020097155.1_00020
+MSLSTAVPALSVGTPVPLRLAVVDMSGTSVVEGGLQDRAFAEVVAARGLAEGSPEHERAA
+RLFRERRGTSRTAVFQALFEGRTAALEATRAFEAAFDRLLAEHGVTAVPGAEGALVRLRE
+AGLDLCLITGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMVLTALLALDHDDV
+RSVLTVGDTAADILAGRRAGAGLVVGVRSGQDTGGVLAGAGADQVVDSLAQVPDLVATLR
+G
+>GCF_023573625.1_00320
+MSLPHAPRTPAPPAAASSAVPLRLAVVDMSGTSIVEHGLQDTAFARTLDQHGVPAGTPEH
+DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEATFDALLGQHGVQAVPGAEEALV
+RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD
+LDDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADDVLLAAGADRVVPGLADVPDLV
+VRTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000377.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000377.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c1e7cc6a38910dc88d1942b52825395fb8106c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000377.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00316
+MHVALLFDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG
+LLGVLAGGGMGMFGLVAACVACVYLAGPRQDMGPALRR
+>GCF_003691675.1_00031
+MHFALLVDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG
+LLGVLAGGGMGMFGLVAACVACVYLAGPRQDMGPALRR
+>GCF_005280335.1_00021
+MHLALTFDQWLFRILAIVGLVLEVWAFLDALRRSPGDFARIGGRDKSFWMILTGVAAAVG
+VLGVLSGGGMGMFGLLAACVACVYLAGPRQEMGPATRR
+>GCF_020097155.1_00017
+MHLAIVAGNWLFYALAVVAFLLELWAFADAARTSQETFLRTGGRTKGFWLALTGAAAAVG
+LVGVLLGPTGGFGILGLAAVCVASVYLAGPRDDLRFYGGRRGR
+>GCF_023573625.1_00323
+MHFALLVDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG
+LLGVLAGGGMGMFGLVAACVACVYLAGPRQDMGPALRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000379.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000379.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc15c4efa0fe0460fafde0daebc30769677abd79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000379.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00319
+MRELYRADLERLGRDLTEIARLVHRAVMDAQAALEAADVHGAERVISEDARIDQLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEPVRTV
+FTAMCDAAVEVAQEVVLLLETQDLAHGDRIDALNEDVNALHVSVFRAIAAPDWSATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS
+>GCF_003691675.1_00034
+MRELYRADLERLGRDLTEIARLVHRAMMDAQAALEAADVHGAERVISEDARIDQLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEQVRTV
+ITAMCDAAVEVAEEVLLLLETQDLAHGDRIDALNEDVNALHLSVFRAIAAPDWSATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS
+>GCF_005280335.1_00018
+MRELYRADLERLGRDLTEIARLVHRAMIDAQEALESADVHGAERVISEDARIDRLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPAPVRPV
+FTAMCDAAVDVAEETVLLLETQDLAHADRIHAVNEDVNALHASVFRFIAASDWTATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWAYHRGSETSGP
+>GCF_020097155.1_00014
+MRELYRADLERLERDLVGTARLVHRAVLDARAALDAADVHLAEQVISEDARIDLMQEGLD
+EQAVRLLSLQAPVASDLRTVLATLRMSASLERMGDLARHIAQLTRLRYPEHVIPCDMRPL
+FGSMTDAAVEVAQEVVLLLETQDLAHADRIHALNQVVNDHHVSVFRAIAAPSWGSPPATT
+TDVTLASRYLERFTDHGLAVAAKARYLVTGESTRREGSAPA
+>GCF_023573625.1_00326
+MRELYRADLERLGRDLTEIARLVHRAMMDAQAALEAADVHGAERVISEDARIDQLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEQVRTV
+ITAMCDAAVEVAEEVVLLLETQDLAHGDRIDALNEDVNALHLSVFRAIAAPDWSATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000382.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000382.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd01539bdef41039f7b4bbfd283ca433a8508277
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000382.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00322
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH
+>GCF_003691675.1_00037
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH
+>GCF_005280335.1_00015
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIEYDASDGINGEEKDFLSYRNLA
+LVGDGDSGPARLIGTLENLSDQAQTYTFQAEGGGSATVQVPAGETFKLEDDANQTVLERQ
+DAWVGELLPVTVSGNGGQTELEVPLLGATQDHYRDLLPEGVSPSDEELGSHLDEETHDYG
+GEH
+>GCF_020097155.1_00011
+MKSVASRPARRRLAAGALALTAVLGATGCSAVSPVATGIQYSASDGVNATQTGFVEVRNL
+GMVGEGASGPARLIGSLKNDSGADKTYTIAVQDGGQITVPVKAGETVKLEEQQLEVERSV
+WPGQNAQATVSADGTQLQLGVPVLSATQEQYKEYLPAGQSADTEHLDEQTATYGEGEGEQ
+H
+>GCF_023573625.1_00329
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000385.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000385.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab8d7eddd42d138fefdd8833f1232e75fcdb89c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000385.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00325
+MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILERSAASHEAGFEASDLYPAREPWWALAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARLWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD
+>GCF_003691675.1_00040
+MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILERSAASYEAGFEASDLYPAREPWWGLAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD
+>GCF_005280335.1_00012
+MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASHEEGFEPSALYPAREPWWALAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLVERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKEGEPATAVWTSPWGAGRPGWHLECSAMATKYLGAQFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVAYGGEKMSKSVGNTISPEEMLGM
+ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFTARARTAGAVPPAVDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAAQDLESAAARLTEVEAMTAVLGLDDV
+PEGDGDGTGPAADALDSLVRSQIEARAQARAEKDWAAADRIRDALAAAGVVVEDGADGAT
+WRLAD
+>GCF_020097155.1_00008
+MAQRFYDTRSAEIRDFVPLVPGQASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASQEPGFEPSEMYPADEPWWALAFRFENAFDAAYLALGVR
+RPTYEPRATGHVPEMLALIERLIERGHAYPAADGSGDVYFDVRSWDRYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKEGEPVTAVWSSPWGAGRPGWHLECSAMSTKYLGGEFD
+VHGGGLDLRFPHHENELAQSAAAGDPFARFWLHNGLVTYQGEKMSKSVGNTISPQEMLAM
+ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFVQRAAAALGAPELTAPLAEHV
+PAAFRAAMEDDLAVPQALAVLHEAVRAGNSALAAGDDAAARARLAEVAAMTAVLGLDDVP
+EASAGGSGPEAAALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGAQGATW
+HLAG
+>GCF_023573625.1_00332
+MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASHEAGFEASDLYPAREPWWALAYRFERAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLIERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGAEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRTAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDLLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000386.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000386.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e36e3319fa2af59d1e67735b948080129f36634d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000386.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00326
+MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE
+QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI
+ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN
+TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQIVSIP
+IDSTMESLNASMAVGISLYEISVQRAGGR
+>GCF_003691675.1_00042
+MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE
+QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI
+ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN
+TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQIVSIP
+IDSTMESLNASMAVGISLYEISVQRAGGR
+>GCF_005280335.1_00009
+MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGKGPTPKAEDRVYHKAYRAKQLSERSAA
+KRGGPVRPSRPKLTDETVSGRNPVVEALRAGIPAKALHVAVRIEMDDRVKEALRLCLEQG
+VPVMENTKPELDRLSGEAIHQGLVLQIPPYEYADAMTLATDALEKHEKGHLRTPPLLIAL
+DGITDPRNLGAIIRSGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLNTT
+LVELHRAGYFVLGLDGGGDVSLPGLSLATEPLVLVVGAEGKGLSRMVREHCQQIVSIPIN
+SDMESLNASMAVGISLYEISVQRAGGR
+>GCF_020097155.1_00007
+MSTAPRSGGSRAPKGKKGPQKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KHGGGRVPVRDQVRGRVKLTDETVSGRNPVVEALRAGIPAKALHVATRIEVDDRVKEALR
+LCAENKVPVMENTRPELDRMSGEAVHQGLVLQIPPYQYADALTLGREAMEAQEKGHLRTP
+PLLIALDGITDPRNLGAIIRSASAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQA
+GNLNTTLVELHRMGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQI
+VSIPIQSEMESLNASMAVGISLYEIAVGRAGGRPVAS
+>GCF_023573625.1_00333
+MSTAPRSGGSRKPKGKKGPVKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE
+QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI
+ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN
+TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRLVREHCQQIVSIP
+IDSTMESLNASMAVGISLYEISVQRAGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000387.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000387.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9130fcf3e134f9714e32d8607d021807d261c908
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000387.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_00330
+MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV
+RATVRLLDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT
+VKIAAGIDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASAES
+AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF
+ATAADRLPAVARMGFQVVYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA
+AHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN
+PPKKYQDIYPLNFDNDPDGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR
+AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYFTWRNTAEELAEYLQEISHETPAFYRP
+NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE
+KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS
+ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVAEATLDLDLEALRLRPEDRDASGAVE
+VEDLLTGQRWRWGRTPYVRLDPHVEPAHVLRIVRNG
+>GCF_003691675.1_00046
+MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV
+RATVRLLDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT
+VKIAAGIDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASSES
+AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF
+GTAADRLPAVARMGFQVVYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA
+VHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN
+PPKKYQDIYPLNFDNDPDGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR
+AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYFTWRNTAEELAEYLQEISHETPAFYRP
+NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE
+KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS
+ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVVEATLDLDLEALRLRPEDRDASGAVE
+VEDLLTGQRWRWGRTPYVRLDPNVEPAHVLRVVRNG
+>GCF_005280335.1_00005
+MSNSKQAAQSTPVPDVRLQTVTGRIPVTGVQPVVQDGRFPAKAVVGEDIPVRATVFGEGH
+DAVRATVRLLDPSGAEVQRVHMRPGRPGLDEFLATLRPSETGVHHFVVEGWHDPVGTWLH
+AATVKLAAGVDVELMLAEGAALFRAAAEDAERSAQDRAAFEETARVLADEGLVPAQRLAG
+AESAELAAVLGARPLREHVTSSELLPLDVQRELAGRGGWYEFFPRSEGARFDEAAGTWSS
+GTFTTAARRLPAVARMGFQVVYLPPIHPIGTAHRKGPNNTLTAGPQDPGSPWAIGAAEGG
+HDAVHPDLGTIADFEDFVAAAADEGLEVALDLALQCSPDHPWVAEHPEWFTTRVDGTIAY
+AENPPKKYQDIYPLNFDNDPEGLAQAVLEVVQGWVGRGVHIFRVDNPHTKPLWFWEWLIA
+RVRAEEPRVVFLAEAFTRPAMMHALGTVGFQQSYGYFTWRNTAAELAEYLEEISHETPAF
+YRPNFFVNTPDILTEYLQHGGPGAFRIRAVVAALANPLWGVYAGYELFEHVARPGAEESI
+DNEKYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALRDLQNLTLHRSTHQDLLVFSK
+TRTARPEGEHRDAEAVTDAGAHEDTVITVVTVNPHHVAEATLDLDLSALRLRPEDLDESG
+SFEVEDLLTGQRWRWGRTPYVRLDPHVEPAHVLRVVRHG
+>GCF_020097155.1_00006
+MSTSKPRPAAHPAPPAPALPDVRRTTLTGRIPVSNVQPTVEEGRFPAKAIVGEDVPVRAN
+VYREGHDAVRATVRLLGPDGAEVQRVHMRPGRPGLDEAVATLRPSEPGVHHFVVEGWDDP
+VGTWRHNASVKLAAGVDVELMLDEGAALFRAAAQDPERGAADRAVFEEAVRGLEDASLAP
+VQRFAVTQSAEVSAVLDARPVRRWVTSSELYPLDVQRPLAGRGAWYEFFPRSEGARYDEA
+AGLWHSGTFRTAAERLPAVAAMGFQVVYLPPIHPIGVAHRKGPNNTLTAGPQDPGSPWAI
+GGEAGGHDAIHPGLGTFEDFDAFQERVRELGMELALDLALQCSPDHPWVTEHPEWFTHRV
+DGSIAYAENPPKKYQDIYPLNFDDDADGLARAVLDVVLGWVRRGVHIFRVDNPHTKPLWF
+WEWLIREVRAVEPEVVFLAEAFTRPAMMHGLGRVGFQQSYGYFTWRNTREELEEYLEEIT
+AETAGFYRPNFFVNTPDILTDYLQHGGPGAFKARAVIAATSNPLYGVYAGFELFEHVARP
+GAEEYIDNEKYEFRPRDWAGEEAAGRSLAPYLTRLNRIRAEHPALQDLQNLTLHSATDPE
+LLVFSKTRSALPEGDHRDAAAVTDAGSAEDTVVVVVACDPHRVAEATLRLDAEALRVRPE
+DRDEEGRFEVEELLTGARWRWDEQPYVRLDPAVEPAHVLRVVRRG
+>GCF_023573625.1_00337
+MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV
+RATVRLFDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT
+VKIAAGVDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASAES
+AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF
+ATAAGRLPAVARMGFQVAYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA
+VHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN
+PPKKYQDIYPLNFDNDPGGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR
+AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYYTWRNTAEELAEYLQEISHETPAFYRP
+NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE
+KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS
+ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVVEATLDLDLEALRLRPEDRDASGAVE
+VEDLLTGQRWQWGRTPYVRLDPHVEPAHVLRIVRNG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000389.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000389.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a285d34e2ddb040370335a147a949fe285381f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000389.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_00335
+MSWWPFPRPSASPSPDDDGAPAAAELEEAVAALRQLLRAERHRLRPDSWALAWEMVEQAA
+EYAPAWTRLQRTRPVETQELVLALTGRLEPLLCDFLALPDSEKPTHADAVHARLREQGTE
+HGRLRRRLTRALTARLRAGEEL
+>GCF_003691675.1_00051
+MSWWPFLRSSASPSPDDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEHAA
+EYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLALPDSEKPAHADAVHARLREQSTE
+HGRLRRRLTRALTARLRAGEEL
+>GCF_005280335.1_02680
+MAWWPFRGPSGAPRDDDASTAGRASLEAAVHSLRALMTAERHRLRPDSRDLAWTITERAA
+EYGPAWDRVSAQRPAEAQELLLLLSHRLEPALRDFLDLPDSQKPRHADELHGRLSELQTE
+AQRLGRRLTRALSSRLRARGEL
+>GCF_020097155.1_02492
+MAWWARRRLSSSGPAPLGKPPLVAAEELRRLTDELSEILQRESARIRPDAAAVLRSFLNR
+SRALLPAWDRTAPARSAEALAAYELLRDRVLPGLQDWLCLPDHLKPVHADDLLADAQAWE
+GDLSHHAARLTQVLTARGRAVRELDERQ
+
+>GCF_023573625.1_00342
+MSWWPFLHSSASPSPDDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEHAA
+EYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLAIPDSEKPAHADAVHARLREQSTE
+HGRLRRRLTRALTARLRAGEEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000390.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000390.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aac0a9fe54f8830ddb92f52d52c185fb4b519524
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000390.fa
@@ -0,0 +1,17 @@
+>GCF_002008305.4_00337
+MTEQTPSLEHPQVRKNAERYEIVVDEAGTVAGYTVAIDYDTGDGPTQRIFPHTKVDHGYE
+GRGLASTLVREALKDTVAAGRRIVPVCPYVKDWVNEHDDVAGEVDPAGPEHLQFLESRQD
+>GCF_003691675.1_00053
+MTEQTPSLEHPQVRKNAERYEIVVDDAGTVAGFTVAIDDDTADGPAQRIFPHTKVDHQYE
+GRGLASTLVREALKDTVAAGRRIVPVCPYVKDWVDEHDDVAGEVDPARPEHMQFLESRQD
+>GCF_005280335.1_02676
+MTENTPTLDAPQVRKVGEKYEIVVDGDGTVAGYTLAIDYEGTDGVAQRIFPHTKMAEEYG
+GRGLASVLVREALKDSVAAGFRIVPVCPYVKQWTQKHDDVAGDVDQARPEHLQFLEEHAR
+RRSEG
+>GCF_020097155.1_02488
+MTEQTSSLDHPQVRKNAEKYEIVVDADGTVAGYTLAIDYTAEDGTAEDGTEQRIFPHTKL
+EDAYEGKGLASTLVREALRDTEAAGRRIVPVCPYVKQWADKHADEVEGQVDQPRPEHLQF
+LEKHAQERKQG
+>GCF_023573625.1_00344
+MTEQTPSLEHPQVRKNGERYEIVVDDAGTVAGFTVAIDDDTADGPAQRIFPHTKVDHEYE
+GRGLASNLVREALKDTVAAGRRIVPVCPYVKDWVDEHDDVAGEVDPARAEHLQFLESRQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000391.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000391.fa
new file mode 100644
index 0000000000000000000000000000000000000000..831cf5dc1ab099cba990347770781e84c4d9e5b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000391.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00338
+MTAADTPAPRQDPLAFFLDKAVPEAWHAVGPLASAARGAAEQAGLDRQLVELVNLRVSQL
+NGCVFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAIVMNLTNRISILSHHPVRRRDG
+>GCF_003691675.1_00054
+MTAADTPAPRQDPLAFFLDKAVPEAWHAVGPLASAARAAAEQAGLDRQLVELVNLRVSQL
+NGCGFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAMVMNLTNRISILSHHPVRRRDD
+>GCF_005280335.1_02674
+MSAAENPATRKDPLAFYLDKAVPDAWKAVGGLAAAVRTAAEEAGLDRQLVELVNLRVSQI
+NGCGFCLDLHAREGAKAGLNAQRMALLPAWREAEAVYSEQERAALELAEAVTELPEQEQL
+HYVQASTAAALTDAQYAAVQWAAMVMNLTNRISILSHHPVRRRED
+>GCF_020097155.1_02486
+MSSPHDDAAPARKDPLAFYLDKAVPEAWVAVGGLAAAARRAAVEAGLDEQLMELVNLRVS
+AINGCAYCLDVHTRKGVGAGLSDQRRGLLSAWREAPEVYTELERAALELAEAVTELPEQE
+QQQYVQLSTHGVLTDAQYAAVQWLAIVMNVTNRISILSHHPVRRHDS
+>GCF_023573625.1_00345
+MTAADTPAPRQDPLAFYLDKAVPEAWHAVGPLASAARDAAEQAGLDRQLVELVNLRVSQL
+NGCVFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAIVMNLTNRISILSHHPVRRRDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000392.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000392.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44a59395ba36d440fd69b5e0e50ae37f88c076c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000392.fa
@@ -0,0 +1,48 @@
+>GCF_002008305.4_00339
+MAAAPQAHAVAWDRVELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDD
+RASQAFNGRVLERARAEHPDWLSADGQKWADGLVIVALDPDNRLIGVYVGEDRMLSTDQL
+RDVREAGHEAARAARWTDTVVEVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAVL
+ASRRRRRRRTADLLTEARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRGFRRQAL
+DASAELDRLEALPERSLHRTEHARAAEDVRDRARELDRLDDAVAAANTFLNRHPGWPSAW
+DQQTAPLRADLDAVGTLASSVGSAGPVRSAVAALESFRAEAQGRLEALGADLQDERLTPA
+AALDELDALRRRLTGLVSALADAEVAAFGKDEAERELLRDELRTHRGPARSARGSILDSA
+LPTDAYWTVVAFTTGHQAGERSVQDHRQAQSSSSGTGYGSSAGSFSGAGSSGRF
+>GCF_003691675.1_00055
+MTRPTHRTARRTLAAVALSAAALTGPAAAATVVALPVTAGVTGAVVATAPQAHAVAWDQV
+ELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDDRASQAFNGRVLERAR
+AEHPDWISADGQKWADGLVIVALDPDNRLIGVYVGEDRTLSTDRLREVREAGHEAARAAR
+WTDTVVDVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAALASRRRRRRRTADLLA
+EARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRTFRRQALDASAELDRLEALPER
+SLHRTEHARAAEDVRDRARELDRLDDAVAAANTFFNRHPGWPAAWDQQTAPLRADLDAVG
+TLASSVGSAGAVRSAVAALESFRTEAQDRLEALGADLQDERLTPAAALDELDALRRRLTG
+LVSALADAEVAAFGKDEAERELLRDELRTHRGPVRSARGSILDSALPADAYWTVVAFTTG
+RQAGERSVQDHRQAQSSSSGTGYGSSGGSFSGAGSSGRF
+>GCF_005280335.1_02673
+MDEAGVVDPERLRRGLAEVEFREPTRVAVVTERGPDLSGLDDDRAAQAFNGRVLERARAE
+HPDWLSADGQTWADGLVIVALDPDNRMLGLYVGEDRSLSTDQLQDVREDGYEAARAAKWT
+DALVDVTDSAAELIGRPWWQHPGLWVGAGAVGLVGAGTGAAVMADRRKKQARTQADLESA
+RGHLTAVTLELDATEVNASTVPTDSPHAATLLERFRGFRERTLDATAEQQRLEAVPEKDL
+HRRKHREAAAALRAQTAELDGLDDAIGAANALLNRHPGWPAAWDLQTAPLREDLDAVAEL
+RDAVTDTPSVQAAVAALESFRAEASGRLDALGGDLEAERVTPAAALDELDGLRGRLTSLV
+GSVAEAEITAFSDDDEERRILREKLRSRRGTHRAARGSILDCTLPSDAYWTVVAFNAGHR
+AGERSVQERREAASSPSSSGTGYGSSGGSFSGTGSSGRF
+>GCF_020097155.1_02485
+MPEPTAPRPSRLARAPRARLLARAARPLAAAAVAGAALAGAAAPAGVAATAAAVPVAAGA
+VVAAPAAHALEWSRVDLADQAGIIDPAQLERDLAGIEFRAPTRVAVFTERGPDIRGLDEE
+RKAQAFNGRVLEFARAQRPGWISADGQKWADGLVIVAVDPDNRMLGVYQGEDRKLESGGQ
+SAVREAGTDAARDARWTDAVVDMVDEAATRIGRPWNEDPVVWLGLGGGALGVLGAGAGIT
+AAVVGPRRSRARRSAEHLEEARHHLTSVTLDWETTELNASTVPLGSRHGARLMERYRGFH
+RSALDATARLEELEAAPVKDRSAQSFVDRAGGVRDDVAALDALDDAIADANALLNRLPGW
+EDAWDRQVAPLREDLHRVPALHDRLGDVDGTAVPLAALDSFRDEARTELERLGTGLTAQT
+VAPDDAIDALERLRRRLTVRIEELARAVAQAQDGRKKQRLMQESLDGQRAVPRDRRGSIL
+DAGDGWRTYWTVTAFDAGVDAGDSAVASYESSSSGTGYGSSGGSFSGSGSSGSF
+>GCF_023573625.1_00346
+MTRPTHRIARRTLTAVALSAAALTGPAASATVVALPVTAGVTGAVVAAAPQAHAVAWDQV
+ELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDDRASQAFNGRVLERAR
+AEHPDWLSADGQKWADGLVIVALDPDNRLIGVYVGEDRMLSTDRLREVREAGHEAARAAR
+WTDTVVDVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAALASRRRRRRRTADLLA
+EARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRNFRRQTLDASAELDRLEALPER
+SLHRTEHARAAEDVRDRARELDRLDDAVAAANTFLNRHPGWPAAWDQQTAPLRADLDAVG
+TLASSVGSAGPVRSAVAALESFRTEAQDRLEALGADLQDERLTPAAALDELDALRRRLTG
+LVSALADAEVAAFGEDEAERELLRDELRSHRGPARSARGSILDSALPADAYWTVVAFTTG
+HQAGERSVQDHRQAQSSSSGTGYGSSGGSFSGAGSSGRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000393.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000393.fa
new file mode 100644
index 0000000000000000000000000000000000000000..524ad33a069d67f6ad5bfe8edd0d69e29987bf84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000393.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00340
+MSSSEAAAPAHALPRVVGILGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQ
+RHLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLALAGPATRAVVDLTNTWGDE
+PVPAWLDDDAAPGTTRIAERWAAAGLRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTE
+PADATADPAAVAAARDTVIALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAAL
+LADAPTG
+>GCF_003691675.1_00056
+MSSSEAAAPADALPRVVGVLGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQ
+RHLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLTLAGPATRAVVDMTNTWGDE
+PVPAWLDDDGAPGTTRIAERWAAAGLRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTE
+PADATADSAAVAAARDTVIALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAAL
+LADAPIG
+>GCF_005280335.1_02629
+MSSSEPAAPAALPRAVGILGAGRAGTGVARAIARIPRLSPGLPEVRALVAGTRRPSAVQR
+HLTVYAPAAQAVAAEELAARAEVIVVAVPREDLDDVDPLALAGPGVRAVVDMTNTWGEEL
+LPAWLEAGPDDAPGTARIAARWAAAGLEVPVVRALSEVSHHDLDVHGRAAAPRRALAVGT
+VPAADASDPGAVVAARDAVAALVTAMGFDAVPYEGLERAAVLEPGGAGFGVAHDARELAA
+LLGAGPRG
+>GCF_020097155.1_02484
+MPHDAAPRPDQPAAFESLPASVGILGAGRAGTALARAIARIRVLHPGTAAPRVVLAATRS
+PAAVRRHLAIHAPGAEAAHPGDLATDTELTVVAVPREELDEVDPAWLAGPRTLAVVDMTN
+TWGDELVPDWLAAAAAPGLPTMPGSAAIAAHWAEAGLTAPVVRAFSEVSHHELDRDGRAQ
+PPLRALGVGADSPGPARAAVAALVTAMGFEPVEYAPLARAAALEPGTRAFTRPLPADELA
+RELA
+>GCF_023573625.1_00347
+MSSSEAAPADALPRVVGILGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQR
+HLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLALAGPATRAVVDLTNTWGDEP
+VPDWLDGDGSPGTARIAARWAAAGVRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTEP
+ADTAADPAAVAAARDTVVALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAALL
+ADAPTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000394.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000394.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01cac661a14527c9f0397d965535fbb2e2656839
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000394.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00341
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLITLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
+>GCF_003691675.1_00057
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEERRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFAQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFSADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLVTLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
+>GCF_005280335.1_02628
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPECRDVGEYLTAEPQEQRE
+MVESALRAAQEDRSLLLDTSTLVYDTLIPFPTKVFCVGLNYTNHIEETGQNQPEHPTLFA
+KFTQSLTGALDPVEVPEEDHLVDYEGELCIVIGEPGRRIAVEDAKEHIAGYAVANDVSMR
+GWQGRTSEWLQGKVWEASTPVGPWLVTPDELTADARIITRVNGVERQDDRIADVVFSPEE
+LVAYVSQMITLNPGDLIMTGTPAGVAVARKGADGRRPWLQAGDVVEVEITGLGRQRNELV
+>GCF_020097155.1_02480
+MKLATFRQPDSDASYPGATFAAVLTSFHPQDPQVAVRAVALPECRDVGEFLTAEPQEQKD
+MVREALEAAKEDHGLLLDVSTLVYDTLVPFPTKVFCVGLNYADHIRETGQEKPEHPTLFA
+KFAQSLTGALDPIEVPEEDHRVDYEGELCVVIGEPGRRIAVEDAKDHIAGYAVANDVSMR
+GFQGRTPEWLQGKVWEASTPVGPWLVTADEFPKDARIVTRVNGEVRQDGKVKDVVFSPAE
+LVSYVSQLVTLNPGDLIMTGTPAGVAVARRDGDGRRPWLRADDVVEVEITGLGRQRNELV
+>GCF_023573625.1_00348
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVADAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLITLNPGDLILTGTPAGVALACRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000395.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000395.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05017ada762a5eefe3bdc5427417da9575951139
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000395.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00342
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVLPPPPDADPGVGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHETDPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGVSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLMEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGAVGEVAAELGGSREAVVLAWLLRL
+PWDVRPVIGTQDPERVAACAEAAAAAEAMDSAQWHRLWTAARGAGLP
+>GCF_003691675.1_00058
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVLPPPPDADPGVGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHEADPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGVSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLVEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGVVGEVAAELGVSREAVVLAWLLRL
+PWGVRPVIGTQDPERVAACAEAASVAEAMDSAQWHRLWTAVRGAGLP
+>GCF_005280335.1_02627
+MAWGAAPAPAPAPGEGPALLASAGPEHAEAARERARGALRAGIDAGVDLLDTADIYGAGV
+SEETVGALLHELPYEERSALKVQTKCGIVLDEVDADGRPMVRYDSSPEYVRARLEGSLAR
+LGELRVDTLVIHRPDVLTPVADTVRAFLDAREEGLVGKLGVSNLGVGRTLEFQRELAAQS
+ADGTGLACVQVELGLHHRTLVESVILANHPGAAADADVADLGRVCAAEGIELQAWGSLGQ
+GRFSSGDDGAAGVVGEIARELDTSREAVVLAWLLRLPWGVRPVIGSQDPGRIAACADAAA
+AAEAMDSAQWHRLWTAARGAPLP
+>GCF_020097155.1_02479
+MTAQDTAPQTPAASPLILGTMGWGDVERARGALRAGLEAGIGLLDTADIYGAGASEETVG
+ALLAELDPAERTRLRVQTKSGIVLHEPGPDGTPAVRYDNSPAYLHERLALSLERLGLDRV
+DTLVVHRPDVLTPVSDTVRAFLDAREAGRVDALGVSNMGTRRVLEYQHALREVSADGTGL
+ACVQVELGLHHRMLVESVVLANHPAAAPDGGAGDLGEVCAGEGIEIQAWGPLGQGRFTRG
+SDGTVPADPAEQAALAAAGGAPAVVARVARELEVSREAVVLAWLLRLPWGVRPVVGTQDP
+ARIASCAQAADAAARMDGAQWHRLWTAARGETLP
+>GCF_023573625.1_00349
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVPPPPPDADPGAGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHETDPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGLSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLVEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGVVGEVAAELGVSREAVVLAWLLRL
+PWGVRPVIGTQDPERVAACAEAASVAEAMDSAQWHRLWTAARGRPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000397.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..540bc641f7af3628de972cb2c48ee10eb13ca27c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000397.fa
@@ -0,0 +1,75 @@
+>GCF_002008305.4_00344
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDAVARAAHEAGMGVLVDIVPNHVGVATPQANPAWWDVLTHGPEA
+AHAAWFDVDWAAGGGSLLIPVLGDGPDGDADAELNRLVVDEGRLRYWDNVYPLAPGSLEA
+AEAETGLRAAEVFAEADPAKESTAERARLARAVHDRQHYRLVGWRRGDAELNYRRFFTVT
+TLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYL
+VVEKILEPGEALPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRA
+KHDVATGSLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAVLE
+GALADAAEAEPALAAVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRWAN
+LNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDR
+WAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSW
+TDQDPEFEARLAALAAAVTSPEGPARGVLQAVADRIAEPGLVVQLGHKLVQLAAPGVPDV
+YQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAAVLRTRRD
+RPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWED
+AVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP
+>GCF_003691675.1_00060
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDMVARAAHEAGMGVLVDIVPNHVGVATPRANPAWWDVLTHGPEA
+AHAAWFDVDWAAGGGSLLIPVLGDGPDGDADAELNRLVVDEGRLRYWDNVYPLAPGSLEA
+AEAETGLRAAEVFAEADPASEPTAEQARLARAVHERQHYRLVGWRRGDAELNYRRFFTVT
+TLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYL
+VVEKILEPGEALPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRA
+KHDVATGSLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAVLE
+GALADAAAAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRWAN
+LNEVGGDPSHVALSLADFHSAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDR
+WAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSW
+TEQDPEFEARLAALAAAVTSPEGPARGVLQAVADRLAEPGLVVQLGHKLVQLAAPGVPDV
+YQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAAVLRARRD
+RPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWED
+AVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP
+>GCF_005280335.1_02625
+MSTSTERPVPSSTYRLQVGPDLPLESVAGLVPYLRRLGVGWLYLSPILEAEPGSDHGYDV
+VDPTRLDAARGGAEGLEAVARAAREAGLGVLVDIVPNHVGVATPEANPAWWDLLAHGSEA
+AHAPWFDVDWTAGEGRVLLPVLGDGPDGEAEAELDRLVVETGDDGGRLRHWDTRYPLAPG
+SLAAAEEETGLRAADVFAGAEPAHEPTPERARLARAVHARQHYRLIGWRRGDAELNYRRF
+FTVTTLAGVRVEDPEVFDAVHAEPARWVREGLVQGLRVDHPDGLADPAGYVRRLRSHVLP
+EGYLVVEKILEPGEELPADWDVDGTTGYDALGEVERVFMHPVAAGGPNEDERRRRDWDEV
+VAEAKRDVATGSLVAETARLVREVRGVHALGAHADEDVAAAFAAVLSRLPVYRTYLPVGL
+AVLERALADAGEAEPALAPVLADLGPELADPDSPVARRFQQTSGMVMAKGVEDRSFYRWT
+RWANLNEVGGDPAHVQLSLDAFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAE
+EPDRWAGELAGLRALHPLGDEGAERLLWESIVGVWPTDGTAPSTERILGFLQKASREAAL
+STTWTDQDPEFEGRLEDLARAVTAPDSPARGAVQAVADRIAEPGLVVQLGHKLVQLAAPG
+VPDVYQGTELPVPSLVDPDNRRPVDFHARADLLDRLDAGHVPGLDDADAAKLAVVAAVLR
+ARRDRPELFTRHRRLDVSGPAAEHAVAFDRGGALAVATRWPVHLAAAGGWGETVVTLPPG
+RWEDAVTGRPVHPDARGAVRLDELLSTLPVALLVPARAEEATP
+>GCF_020097155.1_02477
+MSHTDAVSAPASTYRLQVGPDLPLDSVAGLVPYLRRLGVDWLYLSPILAADPGSDHGYDV
+VDPARVDPARGGPEALAALAAAAHEAGMRLLVDVVPNHLGVATPLANPAWADLLAHGPEA
+AHAAWFDVDWEAGDGRVLLPVLGDGPEGDPRGAEAGLDQLIVDPSAGEHGVLRHWDTAYP
+LAPGSLAAAEEETGLRAAEVFAGADPAAPTDDAARLGRAVHDRQHYRLVHWRRGDAELNY
+RRFFTVTTLAGLRVEDPEVFDATHVEIGRWVSEGLVHGLRIDHPDGLTDPGAYLRALRER
+VLPEGYLVVEKILEPGEDLPAAWPVDGTTGYDALGELERVFMPADPDGPAADDAARAAWE
+ALIAEAKRDVATGSLAAETARLVREARAAVVLGAHSDEALTEAFADVLASLDVYRTYLPV
+GAERLAAAVARARAAHPEPADVLDDVARVLADPDSPVARRFQQTSGMVMAKGVEDRSFYR
+WTRWANLNEVGGDPAHLDLPLAGFHALQRARQASWPTTMTALTTHDTKRSEDVRARITAL
+AEEPASWEDALARLRTAHPLDAPGLEELVWESIVGVWPTDGTAPEADRLEEFLLKSAREG
+QEHTSWTAQDDAYEGRLRALAADVVAPDSAARAVVQEIADRIAEPGLTVQLGRKLVQLAA
+PGVPDVYQGTEIPFPTLVDPDNRRAVDFEARADLLDRLDAGHAPTLDEPEAAKLLVVSRA
+LRARRDRPELFHGYRPLDVDGPAAAHLIAFSRGGALALATRLPLTLAAAGGWRETVVSLP
+PGRWRCAVTGRAVTPDARGAVRVDDVLSQLPVALLLPEEETA
+>GCF_023573625.1_00351
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDMVARAAHEAGMGVLVDIVPNHVGVATPPANPAWWDVLTHGPEA
+AHAAWFDVDWAAGDGSLLIPVLGDGPDGNADAELDRLVVDAEGGRLRYWDNVYPLAPGSL
+EAAETETGLRAAEVFAAADSAKEPTAEQARLARAVHDRQHYRLVGWRRGDAELNYRRFFT
+VTTLAGVRVEEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEG
+YLVVEKILEPGETLPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVV
+RAKHDVATGPLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAV
+LEGALADAAEAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRW
+ANLNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEP
+DRWAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTTPEEERILGFLQKASREAALAT
+TWTDQDPEFEARLAALAAAVTSPEGPARGVLQAVADRIAEPGLVVQLGHKLVQLAAPGVP
+DVYQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAGVLRAR
+RDRPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGQTVVTVPAGRW
+EDAVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000398.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000398.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f8782b5b3647da36afbf43ce620a2fd94d3e509
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000398.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00346
+MDTVETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
+>GCF_003691675.1_00062
+MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
+>GCF_005280335.1_02623
+MSERIVTVDTVETPSPDDRLTVTGAPSGDASEDPATALLALPWSTALEDWPEDVLAALPR
+GISRHVVRFARVGGGVVAVKETTEDLAFREYRLLRRLEGSPAPSVVPVAVVTGRTDGRGE
+PLPAALVTRYLHFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVL
+FRRDAGGFAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPA
+ATPELFVDAYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMML
+AAPVEVHAGYHRRRLTRLTGLQVQENQARRLLVDIEAARRAWDPFLDLEGAAHRWVVEVF
+DPVVRSVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRVRRDED
+AVALHPTTTMLRTVPPADED
+>GCF_020097155.1_02475
+MDEHEQPRTDPADRLTVTAAPSGDASEDPATSLLALPWERPLEDWPAEVLAALPRGISRH
+VVRFARMGAGVVAVKETTEELAFREYRLLRELEDRPSPSVVPVAVVTGRTREDGTALPAA
+LVTRHLRFSLPYRAVFSERMERRTLVRLMDALALLLVELHLEGFFWGDVSLSNVLFRRDA
+GGFAAHLVDAETGELRERLSTGQREHDLDVARVNIGGELLDLHASGLADPDVDAIATPDL
+FVESYRQLWQQLTEPTVFPRGEPWRMDRRFRRLTELGFEVEEYSLRAADAPGMMVAQPTD
+VNSGYHRRRLERLTGLHVQENQARRLLVDIEAARRSWDPFMDMDHAAHRWVIEVFDPVVR
+SVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLDEAVDSYVETVLRARRDEDALALH
+PTTTMLRAVPAPEADPEG
+>GCF_023573625.1_00353
+MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000399.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000399.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc3f3942d30d753ab9393b3ec471f6924353759b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000399.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00347
+MARNTSGSHTSATDARARARQIQEEQRRKDRRRRTGVIWGSVLAAVLVIGLVVAFALTRN
+GDDAAAAGPIPAAANEQGGIELTSATGLAEGAGEREVDPSEIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYADFNCVHCADFESSNAEQIEQWLEQGEVTVEYRMVDFLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVAALFAAYDEHQGKGLDNAALTQLAQEQGVDISSCVEDG
+TFRSAVEHTTRQARVAGVAGTPTVFVDGKNWALDGEDKTFTDWAGAKIAD
+>GCF_003691675.1_00063
+MARNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNRN
+GDDAAAAGPIPAVANEQGGIELTSATDLAEGAGEREVDPSKIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASCVEDG
+TFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG
+>GCF_005280335.1_02622
+MARNTSGSHTSATDARARARQIQEQQRKKDGRRRTAVIWGSVLAAILVIGLIVAFALNRG
+GDEPAAAGPIPAAANEQGGIELTSATTLAEGAGAREVDASTVEVPEQGAAQQPETIPAAE
+APAEGEPSEIVLYADFNCVYCADFETSNAAQIEQWLEAGEVTVEYRMVDFRSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVTALFGTYQEHGGKGIDNAALTQLAQDNGADIASCVEDG
+TFRSAVEHTTRQAQAAGVGGTPTVFMDGENWAIGGPDQSFQEWAQSKISG
+>GCF_020097155.1_02474
+MASRNPAPSEVDARARARQMQVDQQKKARRRRTATIWGAVLAAVLVIGLIVGFVVKGNQG
+TEISATGPVPGVVNEEGGVEMTSATALADSGKSERQVDSSSVAVPETATAPEELTTIPAA
+GEPADGEPAQIVVYADFNCVHCAEFESQNSEQLQSWLRDGKATVEYRMVNFLSAPNNKNY
+SARSANAAYCVAAAKPEAYNEFTTGLFMAWEGHGGKGLSDDELIQRADALGVDIEGCLKD
+NTYRPAVEWATNKAKAASVAGTPTVFVNGKNWSTDGGDKSFVDWAKPMVEG
+>GCF_023573625.1_00354
+MARNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNRN
+GDDAATAGPIPAVANEQGGIELTSATDLAEGAGEREVDPSKIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASCVEDG
+TFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000400.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000400.fa
new file mode 100644
index 0000000000000000000000000000000000000000..275304e3096de9355a149822c0ca82a21b4485e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000400.fa
@@ -0,0 +1,56 @@
+>GCF_002008305.4_00349
+MQSSTPRSTRRIGALVAGAVLAGGTLTSSPALAAPSGAAPAAPAASPTVASPLAAAQVED
+PNADGYDSFIVTYKETAANAHAKGRANAWGKAAKEAGVSVKELRETALGSRVVTVDRKLD
+QAESAKFMADLKASGAVEAVEPDAILTATGLSPVDALYSQQWGFTGTHGMRVPGAWDRTT
+GSGATVAVIDTGITSHPDLDRNVVPGYDFISDSAAARDGGGRDSNPRDEGDWYAAGECGT
+AGASDSSWHGTHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGKCGGSLSDIADAVVWAAG
+GTVAGVPANPNPADVINMSLGGSGMCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVRP
+ANCQNTIVVAASTSQGARASFSNYGSAVDVTAPGANIISTVNNGATTPTTAGHAAYNGTS
+MATPHVAGLAALLLAAQPSLTPAQVESTLRSTARSMPVTCSAGCGAGLADASAAVSSLGG
+AQTEPGPAPVASLIVNGGFESGSTGWTGTPTGFVRTDAAKAASGQAFAQLNGVGRRNTTT
+VEQKVTVPASGATLTYALQVDTAETTASRSYDLLDVQVVTGATGTYTVASHSNLDKGGYA
+TRTVDLSRFAGTTVTLRFRGTEDSSAATTFRIDEVAVTAR
+>GCF_003691675.1_00065
+MQSSTPRSTRRRIGALVAGAVLAGGTLTSSPALAAPSGGAPAAPAASPTAASPLAAAQAE
+DPNADGYDSFIVTYKETAANAHAKGRANAWGKAAKEAGVSVKELRETALGSRVITADRKL
+DQAESAKFMADLKASGAVEAVEPDALLTATGLSPVDALYSQQWGFTGSHGMRVPGAWDRT
+TGSGATVAVIDTGITSHPDLDRNVVPGYDFISDSAAARDGGGRDSNPRDEGDWYAAGECG
+TAGASDSSWHGSHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGRCGGSLSDIADAVVWAA
+GGTVAGVPANPNPADVINMSLGGSGVCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVR
+PANCRNTIVVAASTPQGARASFSNYGSAVDVTAPGANIISTVNNGATTPTTAGHAAYNGT
+SMATPHVAGLAGLLLATKPSLTPANVESTLTSTARSMPVTCSAGCGAGLADAARAVSSLG
+GSS
+>GCF_005280335.1_02612
+MKSSVQHSTRRRVGALLAGAVLAGGALTSSPAFAAPAEGARAEQAPRPVAAAPLATVDAA
+DPNADGYDSFIVTYKETAQNNNGKGRALAWGKAAKAAGVSVKELRETALGSHVVQADRKL
+DQSESARFMADLKASGAVEDVEPNAIMTATGLSPADALYSQQWGFTGTNGMRVPGAWDYN
+TGSGVTVAVLDTGITSHPDLDRNVVAGYDFISSSAAARDGNGRDSNPRDEGDWYAAGECG
+ASQPGNSSWHGTHVAGTVAAVTDTQGVVGVAPNAKIQPVRVLGKCGGSLADIADAIVWAS
+GGSVTGVPANANPADVINMSLGGSGTCGTTYQNAINAAVNRGVPVVVAAGNENQPAANAR
+PANCSNVITVAASTSQGARSSFSNYGSAVDVTAPGSSIISTINRGLTTPTTAGHASYNGT
+SMATPHVAGLTALMLAQQPGITPAQVESTLKSTARSMPVACSAGCGAGLVDATRAVAALG
+GGSTTPTPTGVIVNGGFESGATGWTGTPSDFVGNTAGYARSGSNYGVLNGYGRSNTGTVE
+QRVTVPASGASLSYWLQVGSDETTTRSQYDTLAVQVVDGSQTTTVKSHSNLEKGTSYAQH
+TVDLSAYKGKTVTLRFRGVEDYSNSTVFRIDDVAVTAK
+>GCF_020097155.1_02471
+MTALTSPSARRRVGSLLAAAVLAGTALTAAPTLAAAERPAEPARTSPAAAAPLADPNADG
+YDSFIVTYRETAANSTAQGRAKAWGRAAREAGVSVKELRETALGSRVIATDEKLTQEESA
+AFMADLRASGAVEAVEPNVIMTRAALSPADPYYADQWGFTGVNGMRVPGAWDVSTGTGAI
+VGVIDTGQTDHADLNANTVPGYDFISDATTARDGGGRDADPRDEGDWYLAGECGQSRASN
+SSWHGSHVAGTVAAVANTQGVVGVAPGAKVQHARVLGKCGGTLADIADAIVWSSGGSVPG
+VPANPTPVDVINMSLGGQGTCGTTYQNAINAAVGRGVPVVVAAGNENQSAANARPANCQN
+TITVAATDVNGNRASYSNYGSAVDVAAPGSGIISTVNAGTTTPTAGAYAQYNGTSMATPH
+VAGTVALMLAEDATLTPAEVESSLKTNSRPIPGVCAEGCGAGLVDAAKTLASLRGGTTDP
+HPVTPVPGAEKLVNGGFESGLTGWTATGRVAASSTAGLSATGSLHAALNGKGGTSTATLT
+QKAVLPAGAAATLSYAVRVDSAETTTARQWDKLTVSVSDGATTTTLRTHSNLDKGRGYLA
+QAADLSAYAGKTVTISFSGTEDGSGATTFRIDDVSVKAG
+>GCF_023573625.1_00356
+MQSSPPRSTRRRIGALVAGAVLAGGTLTSSPALAAPSGDAPAAPAATPTAASPLAAAQVE
+DPNADGYDSFIVTYKETAATAHAKGRANAWGKAAKEAGVSVKELRETALGSRVIKADRKL
+DQAESAKFMADLKASGAVEAVEPDAILTATGLSPVDALYSQQWGFTGTHGMRVPGAWDRT
+TGSGVTVAVIDTGITSHPDLDRNVVPGYDFISDGRAARDGGGRDSNPRDEGDWYAAGECG
+TAGASDSSWHGTHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGKCGGSLSDIADAVVWAA
+GGTVAGVPANPNPADVINMSLGGSGMCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVR
+PANCRNTIVVAASTSQGARASFSNYGSVVDVTAPGANIISTVNNGATTPTTAGHAAYNGT
+SMATPHVAGLAALLLAEQPSLTPAQVESTLTSTARSMPVTCYAGCGAGLADATRAVSSLG
+GSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000401.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000401.fa
new file mode 100644
index 0000000000000000000000000000000000000000..616f3e4e4618dd3a6aa7a215ed6254a0b28a25d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000401.fa
@@ -0,0 +1,59 @@
+>GCF_002008305.4_00351
+MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES
+AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL
+SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL
+PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV
+ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH
+RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG
+MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL
+PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT
+LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAV
+AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN
+AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
+>GCF_003691675.1_00067
+MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES
+AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL
+SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL
+PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV
+ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH
+RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG
+MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL
+PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT
+LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGVGFGAYLAAQQVGVSDRLVPAV
+AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN
+AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRR
+>GCF_005280335.1_02610
+MLAPADADGALPAPDVLPEPDVTVPDPVVPVGPPEKRGRRRGRKAREVFVENLPTQALVL
+ADRLHSSPYGRRMRSTLQQRREAETHALEARTTLDFALKLGETMFSFGAASLDVETSIIV
+VTQAYGILETEVDLTNQSISLNYAPDSSRGESPYTLQRVVRSSSVNFEGLVAVHRLVEEI
+ADGRLDRAEAQRRLVEIRHQPKPFPPVFEILFAGVFVACFIPFIGGNWTGSLLGMISTWL
+VFWLKIQADRARFPEIFSTMFGAIVATVIALAAFALELPVNPAVVIAGGIMMLLPTARFV
+TAVQDAINGFPVTAAGRFLSALLVFTGVMAGIMVAVALGDLAGLEHLDLAEAGTLQHPPL
+LLLALVTAAGMSDAVVEQSRWPQILACGLVSGAGYGVFLAAQQLGIGDRLVPAAAATAVG
+FLGRLVAQRIAAPALVIVLPSMLFLLPGLMMFRSVYGFTVETGSTLLGLAGLFNAAVIVV
+AIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
+>GCF_020097155.1_02469
+MGAEPRRGPAQGTGPLGPDRNPRKDPVRSVDPLAPQDGSPEDGGVPQGARRAGTRPDAAG
+SAPAEPAVHVALLPVLRPADARTPAGASDGDAPAGDGVDLAAAPAREPGPEDVLPPVLAP
+VAAPTVPVETLPTPEPAPAPEEEPTPAADAPLTAPPLSEPVPTSVLAPAEGDAPTAQEAA
+AAVPDVVVPDPLKQHGPEEPRGRRRRRRTREDHRAVFEEVLPTQAIVLVDRLQASPYGKR
+MRSTLRQRRDTEAAALEARTTLDFALKLGETMFGFGATSLDVETSIIVVTQAYGIHETEV
+DLTNQAISLNYAPDSSRGEVPYTLQRVVRTYSTNFEGLVAVHRLVEEISDGTLERAEAQR
+RLVEIRRRPKPYPPAVEILLAGVFVACFIPFIGGTWQGSLLGMVSTWFVFWLHTRTSVFL
+PEIYSVMIGAFLATLIALGAYALHVPVNPAIVVAGGIMMLLPTSRFVTAVQDAINGFPVT
+AAGRFISAMLVFIGIMAGIMVAVGLTDMLGIARLDLAATQSTAYPTTLLLALVVAATACD
+AVVERSGWRTLLASCAVTAAAFAAHTVVAGLGVSAQLLPAAAAAMVGFAGRIVALRVGAP
+PIVVVVPAILFLLPGFAVFRGLYEFTVESASTMAGLAGIVNALVIIVGIGAGAVFGDTLA
+RPVTERLSPARSTPGPEGHTR
+>GCF_023573625.1_00358
+MEQEGTQEPARFDPRIAEPPAVPTLIPVLRPAGAEDAAAVGDLAIDPEDPGLLDLDPAES
+AHPAAAAVAVEPTEPLPPVVRPAAADPEPEPEEPAEPEAETLPEPAADAPLTEPPLSEQV
+PTSVLAPADADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENLPTQA
+LVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDVETSI
+IVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVHRLVE
+EIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALGMVST
+WLVFWLKVQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLLPTAR
+FVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLLGFEQLDLAEAGTLSYP
+PLLLLGLVMAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAVAAAA
+VGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFNAAVI
+VVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000402.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000402.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b9ff2d612d4dcb7325474a1c6fb78554abfaa66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000402.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00352
+MEFIAPLDPGWEAALAPQAAAFEQVGERLRARRAGGEQVLPAPEHILRAFRQSFADVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGITPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLTAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
+>GCF_003691675.1_00068
+MEFIAPLDPGWEAALAPQAAAFEQVGEALRARRAAGEQVLPAPEHILRAFRQPFADVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGITPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLAAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
+>GCF_005280335.1_02609
+MELIAPLDPGWEAALAPQAAALEQVGAALTQRRAAGEQVLPAPEHILRVFRRPFEDVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLVNIHRELQDDLGIAPPAHGDLSAWADQGV
+MLLNRALTVRAGAPGSHRGLGWEQITEAAVRALCERGTPLVGLLWGADARRMAPLLTQAG
+AGVVESPHPSPLSAHRGFLGSRPFSRVNRLLEEAGAEPVDWRLPD
+>GCF_020097155.1_02468
+MDLISPLDPGWAAALADQEEALVRVGAELTARRAAGEHVLPAPEHILRAFRQPFADVKVL
+IVGQDPYPTPGHPIGLCFACDRHVRPLPRSLANIHRELHDDLGVPPAAHGDLSAWTDQGV
+LLLNRVLTVRAGAAGSHRGIGWEQITEAAVRALVARGTPLVGLLWGNDARRLAPLLTAGG
+AGVVESAHPSPLSASRGFFGSRPFSRVNALLEAAGASPVDWRLPD
+>GCF_023573625.1_00359
+MEFIAPLDPGWEAALAPQAAAFEQVGERLRARRAAGEQVLPAPEHILRAFRQPFADVRVV
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGIAPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLTAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000403.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000403.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d6fe2d33ad3944b44a8da365c21775e53eb9a52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000403.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00353
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLSPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
+>GCF_003691675.1_00069
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLPPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
+>GCF_005280335.1_02608
+MPTSAPEPRRDALTPQERAVLDLEAATWRHGGAKDHAVRERLGLSPTAYYQVLNGLLDRE
+AALAYRPLLVARLLRKRGTRSRARRAPADPAPSTPASRQEN
+>GCF_020097155.1_02467
+MPDADPRPAAPADGPEPTPQDELTELEEAVLALEAQTWRHGGAKDHAIRERLQITPTAYY
+QVLNGLLERRAALARQPLLVSRLARSRGTRSRARRRPAPENSAPPASPQER
+>GCF_023573625.1_00360
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLPPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000404.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000404.fa
new file mode 100644
index 0000000000000000000000000000000000000000..052f4c6975b0619107acf010a82f7a9f83899847
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000404.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00354
+MAYQPDRFDEVPEYTDQRGAHRESFAVAGATATGGGRRLSPLLWVAGLVLLAGLFVGVVL
+PWLTGDRSEPVAAESSTTAPAAAPSTSASSVSSSASSASASTASATESATPSEDAVEASR
+SAAAAESSRAAQEAAAAEAAESSQAAASSRAAAEAQAAEASRSEAAAQSAEASRAAAEAQ
+AAEASRSEAAAQSAEASRSAAAVQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSA
+AASSSRAAAQSAAVRGTHVTVYNATRTQGLAASYAQRLTGAGYTSVDAKNWSGYGIQSST
+VLYNGSANKAAAEAVGKELGFPVMQTPNLQVNGIAVVVTS
+>GCF_003691675.1_00070
+MAYQPDRFDEVPEYTDQRGAHRESFAAAGATAAGGGRRLSPLLWVAGLVLLAGLFVGVVL
+PWLTGDRSEPVAAESSTTAPAVEPSPSTSTSASSESSSASSASASTASATESATPSEDTA
+EASRSAAAAAAESSRVAQEAAAAEAAESSRAAESSRAAAEAAESSRAAAEAQAAEASRSE
+AAAQSAEASRSAAAVQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAA
+AQSAAVRGTHVTVYNATRSQGLAASYAQRLTSAGYTSVDAKNWSGYGIQSSTVLYNGSAN
+KAAAEAVGKELGFPVMQTPNLQVNGVAVVVTG
+>GCF_005280335.1_02607
+MAYQPDRFDEVPEYTDQRGAHRASFAAPAGAAAAGGGARRFSPLLLVAGLVLLAGLFVGV
+VLPWLTGDRSEPVAAESSASSPAADPSTSSEPASPTEGAATTEPASPSEDAAAAEASRSQ
+AAAQSAAEQSAAEAAAASSRAAEEAAAAEASRSAEAAQAAEASRSAAAAAEASRSAGAAQ
+AAEASRSAEAAQAAEASRSAAAAAEASRSAEAAQAAEASRSAAAAAEASRSAEAAQAAEA
+SRSAAAQAAEASRSAAAQAAAAARSTNVTVYNATRTTGLAASYAQRLRSAGFTSVSAQNW
+GGYGIQSSTVLYNGSGNQAAAEAVAAELGFPVLQTPNLQVNGVAVVVTG
+>GCF_020097155.1_02466
+MAYPADRFDDVPEYTDQSGAHRESFAAAPAAAGAAGATAAGTEAAAGGGILKWLLAAAAA
+VLLVGLFLGLVLPRLNGGDDKPVAGAASSSSSSEPAADASSSSSDAPSSDASSSAGPDSA
+APAAPSSDAGAESAAAPSSDAAVESRAAAESSQAAAESSQAAADAQRSRDDAARAASESA
+QAAADASSADAAARERAASESAQAAADASRAAEASRSAEASRSAEASRSAEASRSAEASR
+SAEASRSAAASRSAAAQESADRAVKSTPVNVYNATRRNGLAASYADRLTGAGYTRVTADN
+WPGFRVTSNTVMYNGADKRAAAEAVGRELGMPVQQVPNLQVPGIAVVVVR
+>GCF_023573625.1_00361
+MAYQPDRFDEVPEYTDQRGAHRESFAAAGATAAGGGRRLSPLLWVAGLVLLAGLFVGVVL
+PWLTGDRSEPVAAESSTTAPAVEPSTSASSESSSASSASASTASATESATPSEDTAEASR
+SAAAAAAESSRVAQEAAAAEAAESSQAAASSRAAAEAQAAEASRSEAAAQSAEASRSAAA
+VQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAAAQSAAVRGTHVTVY
+NATRTQGLAASYAQRLTGAGYTSVDAKNWSGYGIQSSTVLYNGSANKAAAEAVGKELGFP
+VMQTPNLQVNGIAVVVTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000407.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000407.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a49ce3b3cdce96dfef95d1bbd8de1556ab08c07a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000407.fa
@@ -0,0 +1,59 @@
+>GCF_002008305.4_00358
+MRARLDAAAARVRHPRAWLRGAWQGQSLRTKLVVMIAALMLALVAVTAVATAVLFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE
+PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER
+VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD
+RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA
+GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH
+GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERLPARDTDDDAAGPPTGPLALAAP
+SGAGASAADAARSSRLLRAAERFRRASAERRRRASAPAQAPQADPPSPGEDDPAAERDAR
+P
+>GCF_003691675.1_00074
+MRARLDAAAAHVRHPRAWLRGTWQGQSLRTKLVVMIAALMLALVAVTALATAALFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE
+PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER
+VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD
+RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA
+GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH
+GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERPSARDTDDDAAGPPTGPLAQTAP
+SGAGASAADAARRSRLLRAAERFRRASAERRRRVSAPAQAPQADAPSPGGDDPAAGRDAR
+P
+>GCF_005280335.1_02603
+MSGRLDAAAARARLPRAWLSSAWRGQSLRTKLVMMITVLMLALVAVTAIATAALFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRYYGVVWDNDGDRVVQTPVVPGSDE
+PDLPSITPERALEIGSASFEVAGTQDESSRWRVQLYGLSSGDGTMAVALPLEGVRSSVER
+VTSLVVTIGLLGTAGTVIVANLAVQRAFRALNRVERTAAKIAAGDLTQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEVSEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLELAPVDLLILAMDSMMDASVNAPD
+RKVTLVGLDGGRAGSAPIVGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDPLGGPG
+AAGDGEGRTSVIEIRDHGLGVSEEDAARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQ
+HGGSVRLLETEGGGATFSVHLPWAPFEDDDDLEDEDDAGPVSESENAAEVSHTGPLGLVA
+PSGAGASVVDAARRSRLLRAGERFRRASAERRPRAGTPAQAPAEGAASPGEEEPGPAAPD
+RP
+>GCF_020097155.1_02462
+MGPRLGVAAARLRHPRTWLWGWWGARPLRTKLVVMITALMMVLVAVIALVTAVLFRTELL
+RQLDDDLSHNRDEVSIYLTTMSQTGGYYTPQQSILRFYGVVWDTSGRAVVSTPLMPGADG
+PALEGMTPEQVDAQGSASFEVPGTTAGSDGWRVQLYHLRSGEGSLAIALPLHGVRTSVER
+VVTLVVTIGLLGTAVSVVASNLLVERAFRALNRVERTAAKIAAGDLSQRVAYAPPSTEVG
+RLSRSLNAMLAHIETAFRDKEASEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGITRE
+EDVAAAMGRIESEAGRMHRLVEDLLTLARLDEQRPLEHEPVDLLVLGMDSMMDASVNAPD
+RKVSLVGLDGGPAGSAPLMGDENRMRQVVVNLMTNALRYTPEGTPIEIAVGTRDAFGGDS
+GVDGTRHSVIEIRDHGAGVSEEDAARIFERFYRADASRHRETGGTGLGLAIVAAIVAQHG
+GSVRLLETEGGGATFSVHLPWAALEDDADDDLDLEDDDARPGAGVPAGRPPTGGSTAAGS
+AGALETGQRRRLAWAGERFRRASAARRQAQAGTSPAQAARDGA
+>GCF_023573625.1_00365
+MRARLDAAAARVRHPRAWLRGAWQGQSLRTKLVVMIAALMLALVAVTAVATAVLFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE
+PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER
+VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD
+RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA
+GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH
+GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERPSARDTDDDAAGPPTGPLAQTAP
+SGAGASAADAARRSRLLRAAERFRRASAERRRRVSAPAQAPQADAPSPGGDDPAAGRDAR
+P
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000408.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000408.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42df65a2dc347bb95842f7791c5e7d401ebc74d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000408.fa
@@ -0,0 +1,14 @@
+>GCF_002008305.4_00360
+MTSQDSPTRVAGMPRTSTLPAPAPADHRGGRGVVLVLGVAVTAVSALALVALLVAYFLAW
+PASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP
+>GCF_003691675.1_00076
+MTSQDSPTRVAGMPRTSTLPASAPAADPADHRGGRGVVLVLGVAVTAVSALALVALLVAY
+FLAWPASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP
+>GCF_005280335.1_02601
+MLGVTVTAVSFVALLGLLAAYFFSWPAVPALYALAMFGLPVGFSLMLLHVVLGAVRRSRL
+>GCF_020097155.1_02460
+MPSPRTSPQPRPDAAPAPSGARRALRVLLTAGVVLTVVSGLGLLGALAAYFLHATPAFLP
+ALYAVSLFGLPLGFTLMVLHVVLSAVLRARS
+>GCF_023573625.1_00367
+MTSQDSPTRVAGMPRTSTLPASAPAADPADHRGGRGVVLVLGVAVTAVSALALVALLVAY
+FLAWPASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000410.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a77ca6697d0ce88a06a60448ed2186ba790772a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000410.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00362
+MTTHDDAPRVDHRSPDAEPAEERTAVPPARGRAPRRDELLAADVDTARAGLAGLAAPDEV
+GEHVDVLVDDDRLLTHRFACRLPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLVAP
+PWVPYAERVNEEERERLKAVAEGRVPGAPAPDAEGDGTPEAAARG
+>GCF_003691675.1_00078
+MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD
+EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLV
+APPWVPYAERVNEEERERLKAVAEGRVPGAPAPEAEGDGTLGAAALG
+>GCF_005280335.1_02599
+MTDREDATPVEQEQAAPAAEEAVVKAPPARRRAPRRDDLLAAAVDEARAGLAGLAAPEEV
+GEHVDVLVDDDRLVTHRFESRLPGYAGWLWYATIARAPRSRLVTVCETGLVAGEGALVAP
+PWVPYAERVSEEERERLRAVAEGRVPGAAAPAGQPAPEGDGKG
+>GCF_020097155.1_02458
+MTEHSDTPGQTDTSGQTHTPEQAPAVAPAGPAADAAPAASARAPRRRAPKRDELLAAAVD
+EARAALTELAEEGQVGPHLGVTVDDDRLMTHRFAAEVPGYTGWVWYSTIARAPRAKKVTV
+CETGLEAGEGAVVAPAWVPYADRVSAEERERLAAVAEGRVPDAG
+>GCF_023573625.1_00369
+MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD
+EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGALV
+APPWVPYAERVNEEERERLKAVAEGRVPGAPAPETAPDDRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000412.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000412.fa
new file mode 100644
index 0000000000000000000000000000000000000000..186a96275c352170950448df90cfce9fb21f6336
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000412.fa
@@ -0,0 +1,23 @@
+>GCF_002008305.4_00364
+MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGMDR
+RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL
+ENPTETPYGTPIPPRPEQASAEDWSRDMGLAGTRLSEEAATAGRFRVRGLAEGVQTDPDL
+LAQLAGAGVTPGRVVRAEAARDAGYIRVEGEAEDGAAADGGALELAAATAAHVWVERLDG
+>GCF_003691675.1_00080
+MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGTDR
+RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL
+ENPTETPYGTPIPPRPEQASAEDWSREMGLAGTRLSEEAATAGRFRVRGLAEGVQTDPEL
+LAQLAGAGVTPGRVVRAQAARDAGYIRVEGEAEDGAAADGGALELAEATAAHVWVERLDG
+>GCF_005280335.1_02597
+MGLAGTRLSEEAATPGRFRVRGLAEGVQTDPELLAQLAAAGVTPGRTVTAQAAIDPGYVR
+VEGEAADGAPESGALELAVETAAHVWVERLDA
+>GCF_020097155.1_02456
+MTDLIDTTEMYLRTILELEEEGTVPLRARIVERLEHSGPTVSQTVARMERDGLVHVGSDR
+RLLLTDEGRERAVAVLRKHRLAERLLSDVIGLDWAYVHDEACRWEHVMSDRVEQRLLEVL
+ENPTATPYGTPIPPRPEAQSAGEWSRDLGLAGEPLATAAATPGRFRVGSLSEGVQADPEL
+LAELQDAGVLPGGVLEAQPALEAGYVRVQGEGSAEALELSAGTAAHVWVQRL
+>GCF_023573625.1_00371
+MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGADR
+RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL
+ENPTETPYGTPIPPRPEQASAEDWSRDMGLAGARLSEEAATAGRFRVRGLAEGVQTDPEL
+LAQLAGAGVTPGRVVRAEAARDAGYIRVEGEAEDGAAADGGALELAEATAAHVWVERLDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000413.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000413.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c387d3bc1105f657b7e1b80127a599ee5635b449
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000413.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00365
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK
+ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA
+>GCF_003691675.1_00081
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK
+ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA
+>GCF_005280335.1_02596
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDAHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNALK
+ADRSLESMGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA
+>GCF_020097155.1_02455
+MRTLVLNAGYEPVSVVSDRRALLLVATGKASVLEDGDAPMHSPTRAWGRPLVILLHQYVR
+VPHADAAAVSRKGVLRRDGHRCAYCGAHATTVDHVHPRSRGGQNTWENLVACCLRCNSAK
+ADRSLDALGWRLRVVPTRPCGVQWRLRELERPAPAWEGWLQFAA
+>GCF_023573625.1_00372
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK
+ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000414.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000414.fa
new file mode 100644
index 0000000000000000000000000000000000000000..848b80b363537b8032de69a36451d58071230d37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000414.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_00368
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVHVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRRGPAARED
+>GCF_003691675.1_00084
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVNVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRGRATRAA
+>GCF_005280335.1_02593
+MRGRGPALLDPAPGRQTGTGLGGWSAEVPPLSQKPRKPRKSRPSRASQSGARSGSSAARA
+AGGAERARPTLRDLNIREDLAAAGRQEGSPAIPVSALIVTTLLVGAYLHLLVLQQMTQLT
+GGLAMPDSMLFYGQDHVRALSAVMDDAARGQLNWVHKTAGVIFPIAVALTLAAVGAWRLR
+PAAAKWGALGVGVLFAVVDIAENIAIEQAIAAGGPGTGLAAALTLARWVLLALIALAIVV
+MLWAGRRRREPAARRR
+>GCF_020097155.1_02452
+MSKKQKKSRPARTGSSAAPTAEPRRAGLHDVSPRADLADAAQQEGSPAMLITALIGTTLF
+IGAYFHLLVLQQMTQLTGGLAMPDSMLFYGQDHVAALSAVMDDAARGQLNWVHKTAGVIF
+AVAVALTVAAVGAWRLKPVAAKWGALALGVLFAVVDIWEGLAIEAAIAAGGPGTGLAATL
+TAIRWVLLAVITVAVVVMLWAGRRRRPRT
+>GCF_023573625.1_00375
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVNVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRGRATRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000415.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab42fcdf85893ccdcde56c4c5d7adb9798449734
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000415.fa
@@ -0,0 +1,79 @@
+>GCF_002008305.4_00370
+MADLFSALGRTHLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGVDARPAAPSHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGVTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAG
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAVAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDVQDESRADNLGELVAVVRSFETTHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPETLID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+AVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
+>GCF_003691675.1_00086
+MADLFSALGRTPLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGEDARPAAPAHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGMTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLSGPAD
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAATIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAVAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRSFETTHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPEALID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+AVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
+>GCF_005280335.1_02592
+MPTAVTRAAADPEAWGGDPESWGRDAAPAHTPDSLVAGLNPQQSAAVTHTGAPLLIVAGA
+GSGKTRVLTHRIAWLLATGRARPHEILAITFTNKAAAEMRERVSGLIGPTAQRMWISTFH
+SSAVRLLRNEAANIGLKSTFTIYDSADSLRLVTTIAKLHELDPKRFAPKALLNRISSLKN
+ELVEADDYASTVAEGDPWGRAVAAVYRDYTARLRQANALDFDDLIGMTVHMFEAFPRVLD
+NYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAGEPEGVDTPGGELTVVGDSDQSIYAFRG
+ADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILDAANAVISNNPDRRKKDLWTAEGAGAAI
+VGYAAENESAEAEWIASTIDRLQDEDGIRPADVAVFYRTNAQSRALEERLVTRGIPYRVI
+GGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRILNEPKRGIGDRAEGAVAAWAERNRTTF
+SAALRDAEHAPGMATRSLKAVNGFVQMMDDLAQVAESAGPATVLEAVLEQSGMLAALRES
+EDLQDESRADNLGELVAVVRSFEKTTPDGTLSDFLEQVALVADADQLPTAPDVEGESLAE
+AQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPHARSMTDEKELAEERRLAYVGLTRARRR
+LFLTRAEARSLWGQHQFNPPSQFLGEIPEALIDWEREGAVRSAGSLSLTGAGTSRYAGRF
+GSGGGRPAWRSRDDDGGARPQRLTRGDEPTDLTVPSAVVRGRAPSRVQPQKEIVALSPGD
+RVSHATFGQGRVDAVAGAGDKTVATVTFEDSGAQKRLLLRYAPLTKVED
+>GCF_020097155.1_02451
+MADLFSSLGRDPLFAPRTRPADPETALPGLVPTAVTRAADPEAGAWGAGRDAGAPSAGPL
+TPEGLVEGLNPQQAAAVQHTGSPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEVLAIT
+FTNKAAAEMRERIAGLIGDTARRMWISTFHSSCVRILRNEAANIGLKSTFTIYDSADSLR
+LVTQIAKVQDLDPKRFAPKALLSRISALKNELVDPEDHASRVAEGDPWGRAVAAVYTEYT
+ARLRQANALDFDDLIGMTVHMFEAFPRVLDGYRRRFRHVLVDEYQDTNHAQYRLIRLLSG
+PAGEPEGVDTPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAATIKLEQNYRSTQT
+ILDAANAVIAHNPDRRKKDLWTAEGEGPRIIGYAAENESAEAEWIASTIDRLQDEEGIRP
+ADVAVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNV
+RRILNEPKRGIGDRAEGAVAAWAERNRVPFFTALRDAENAPGMATRSLKAVQGFVQLMDD
+LAQVAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRAFEKGTPGGT
+LTDFLEQVALVADADQLPAAPDVEGEELAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGV
+FPHSRSLTDEKEMAEERRLAYVGITRARRRLHLSRAEARSLWGQHQFNPPSQFLGEIPDE
+LIEWERAGTDRSFGGLTSLAGAGTSRYANRFSGGGSGSARRGSMTGAWGDRAAGGVGGGL
+ASNRPQRLTRGEEAADLTVPSSVVRGRAPSRVQPQKEVVALSAGDRVEHATFGAGRVDAV
+AGTGDKTVATVTFDATGAQKRLLLRYAPLTRVEG
+>GCF_023573625.1_00377
+MADLFSALGRTPLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGEDARPAAPAHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGMTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAG
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAIAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRSFETSHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPEALID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+GVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000416.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000416.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c3480a9c6ab56aa2184bd0629ec2b398cebf274
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000416.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00371
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGIDAETAQKIVTEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAQFRHEDHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEQHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDQVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
+>GCF_003691675.1_00087
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSPLTGIDAETAQKIVTEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAAFRHEGHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDQVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
+>GCF_005280335.1_02591
+MDLYEYQARDLFEAHGVPVLAGIVAQTPEEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSPLTGIDAETAQKIVAEAGFPEELRADVADVIQKLWVVF
+EKEDATLVEVNPLVKTGDGKILALDGKVSLDDNAEFRHEGHAALVDERTEDPLEAKAKAN
+DLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEQHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDAATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
+>GCF_020097155.1_02450
+MDLYEYQARDLFEKHGVPVLQGIVAETPEEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVNKVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGLDQATADTIVAEAGFPEELRADVAAVIVKLGEVF
+KNEDATLVEVNPLVKTGDGTILALDGKVSLDDNAEFRQADHAGLVDKTTEDPLEAKAKAN
+DLNYVKLDGQVGIIGNGAGLVMSTLDVVAYAGENHGGVKPANFLDIGGGANAEVMAAGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDSATKPLVVRLDGNAVEEGRRIL
+QEADHPLVTLAATMDEGADKATELAHSAN
+>GCF_023573625.1_00378
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHRVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGIDAETAQKIVAEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAAFRHEGHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000417.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000417.fa
new file mode 100644
index 0000000000000000000000000000000000000000..451ec294d41c071928b6b225de1dab1b5a03e72c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000417.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00372
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDTAEFFAL
+SQSKTGEDGKPKTRIIGPNCPGVITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILQAQA
+>GCF_003691675.1_00088
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDTAKFFAL
+SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGTGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPIIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILEG
+>GCF_005280335.1_02590
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGSVTEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAKFFAL
+SQSKTGEDGKPKTRIIGPNCPGVITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILQAQA
+>GCF_020097155.1_02449
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDEDGNAVEL
+PVFGSVAEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAEFFAL
+SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LKDFGFSTAIGIGGDPVIGTTHIDALEAFEADPETKAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETADLMRE
+IMKGL
+>GCF_023573625.1_00379
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAEFFAL
+SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILQAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000422.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000422.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b782a9990451c366c6e6e3c91de94a34eec5efe0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000422.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00380
+MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLLAAVVLPRG
+>GCF_003691675.1_00104
+MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLMLAVVLPRG
+>GCF_005280335.1_02575
+MDAAETPEGPEATAYDGGRPAWQHRLLAGGDEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVALSTVLLVLAALLAVGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLMLAVVLPRG
+>GCF_020097155.1_02447
+MDAAETPDGPEAAAYDGGRPAWQHRLLAGGDEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVALSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLMLAVVLPRG
+>GCF_023573625.1_00386
+MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLLAAVVLPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000423.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000423.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48fc10011f4e2e3937908c9717abfde095f42933
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000423.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00381
+MRLHHDPGLQPERTVMSWGRTALALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA
+>GCF_003691675.1_00105
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIARERARPALASVACMVALVVGLAALGITATLLHAA
+>GCF_005280335.1_02574
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLMFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAQSRGIAGEWARPALASVAGMVALVVGLAALGITATLLHAA
+>GCF_020097155.1_02446
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAQADGIAREQARPALASVACMVALVVGLAVLGITATLLHAA
+>GCF_023573625.1_00387
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000424.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000424.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ace9a98483ad47fd61ebb23785b45acb7584865
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000424.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00382
+MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEICETANPDQ
+ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLTVLSDILPTAFHGLV
+EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSTT
+ENLQDAVSDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDITRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPVMRYNRQLMMSILWDRMPYLTE
+MVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR
+>GCF_003691675.1_00106
+MTTENRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEVCETTNPEQ
+ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLAVLSDILPTAFHGLM
+EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSTT
+ENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDVTRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE
+LVNPRVITLDEAPQAYAEFDQGSVEKFVIDPHGMIAR
+>GCF_005280335.1_02573
+MSPRGRSGSRLTQASLETEGNSFMTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG
+VILKIVATNICGSDLHIYRGSFPVPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNV
+ACGRCRNCRAGRTEVCETANPEQACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQ
+AMEKILDLAVLSDILPTAFHGLMAAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG
+DQDASRLELVRKHGCETIDLSVTENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEM
+QPIAAVNQVLDITRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA
+PIMRYNRQLMMSILWDRMPYLTEMVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR
+>GCF_020097155.1_02445
+MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+VPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNVACGRCRNCRAGHTEICETANPEQ
+ACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLAVLSDILPTAFHGLM
+AAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSVT
+ENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEMQPIAAVNQVLDITRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE
+MVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR
+>GCF_023573625.1_00388
+MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEICETANPEQ
+ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPGQEQAMEKILDLAVLSDILPTAFHGLM
+EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSVT
+ENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDITRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE
+MVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000426.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000426.fa
new file mode 100644
index 0000000000000000000000000000000000000000..636511990d6a69085eb54a2924bde6a170ece131
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000426.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00384
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLADAPAVNLGGEGIRERLITPRGSRDLQILRADIAPR
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV
+VLWTLVGHA
+>GCF_003691675.1_00108
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLADAPAVSLGGEGIRERLITPRGSRDLQILRADIAPR
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV
+VLWTLVGHA
+>GCF_005280335.1_02571
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLSDAPAISLGGEGIRERLITPRGRRDLQILRADIAPH
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTLPGREPHSWANPDDRPAI
+VLWTLVGHA
+>GCF_020097155.1_01754
+MKSLPLHPTPTTPQVGRRLRALREQARISLADLAQVTGLSKGFLSRVERDLTSPSVASLV
+AVCQALGTSPGHVLDAPEVTVVRGGEAPAISLGGQGITESLLSPPGLRPLQVIRAEIAPG
+GTGEDELYTVDCEVESVHVVSGRLTLRTVDGAHALAAGDTATFSGQEPHSWQNPDPDSPA
+LVLWILAGRT
+>GCF_023573625.1_00390
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLADAPAVNLGGEGIRERLITPRGSRDLQILRADIAPR
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV
+VLWTLVGHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000428.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000428.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e18575638203667341346dd49fc5f154bae48e80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000428.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00388
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLGRVGHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
+>GCF_003691675.1_00112
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLRRVRHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
+>GCF_005280335.1_02568
+MTPQHHDTADAPSMQRPDPVAEPGDHLMFEHPDGEPVLVLDEDQVWRLLRRVRHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGTHPERNESQTD
+>GCF_020097155.1_02439
+MTEHTTPSMQRPDPAVGPGSMFPHPEGEPVLKLTDEQIWKLMRGVRHARLGLAVGGEPDI
+VPVNVRAVDGVVWFRTAPGSKLAELTVNPRVVVQADGILSDQAWSVLLHGTARRADTAEE
+IAEAESMGIRPWVPTIKDFYVKVEVDSATGRHFLLGEQPERDGAEPTD
+>GCF_023573625.1_00394
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLGRVGHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000434.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000434.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f94b7e6984026880cac3f850949444f54c648247
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000434.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00396
+MRVVVVAESFLPHMNGVTNSILQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLMGYYEKAIAVQERRRVELARRLLTAPALLAARVFG
+>GCF_003691675.1_00120
+MRVVVVAESFLPHMNGVTNSLLQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLMGYYEKAIAVQERRRVELARRLLTAPALLAARVFG
+>GCF_005280335.1_02561
+MVAESFLPHMNGVTHSILQVLRHLRERGDEAIVIAPAASWSAGWTQRAGEGQAPREVEGF
+PVHALPSVPLSGYSSVRVAAGTVGRLRGILTAFGPDVVHIASPFVLGWRAVQAAEELGIP
+SVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNTATLTLAPSSFTVRQLHAAGLRRVHL
+WGRGVDTRRFHPVKRDDALRAELAPHGERLIGFVGRLAHEKQVEDLRVLSDLPGTRLVVI
+GSGPLREQLERRLPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMASGVPV
+VAVGRGGPLDIVDPSRTGWLYPPGELDELRRHVADLAHDDVKRSAFAQAAWASVQGRTWP
+VLCEQLVGCYEKAVAVQDRRRRELARRLLAMPSQLTARVFG
+>GCF_020097155.1_02432
+MRVAVIAESFLPHMNGVTNSILQVLKHLRSRGDEAVVIAPAASWSAGWTQRAGAGQAPSE
+VEGFPVITLPSMPLSGYASVRVAAGTVLRLRSLLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPRYAAKYGAPWLEDVLWNHVTRLHNTATLTLAPSSFTLRQLHHVGVR
+RVHLWGRGVDSTRFHPAKRDEALRAELAPNGERLIGFVGRLAHEKQVADLRVLADLPDTR
+LVIIGSGPLRDQLERRLPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDSSRTGWIYQPGDLGELRARVADLAYDDAKRAAFAEAAWASMQG
+RTWPVLCEQLVGYYEKAIHVQRRRRGELSRRLLGAPGAVASRAYRVFG
+>GCF_023573625.1_00402
+MRVVVVAESFLPHMNGVTNSILQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLVGYYEKAIAVQERRRVELARRLLTAPSLLAARVFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000436.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000436.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e076d28f3fb927bef0b1a24fcb4cdc9766cc93b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000436.fa
@@ -0,0 +1,19 @@
+>GCF_002008305.4_00398
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCGASALTV
+RAQQACADEFTRQVEERTGVPQLRP
+>GCF_003691675.1_00122
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCGASALTV
+RAQQACADEFTRQVEERTGVPQLRP
+>GCF_005280335.1_02559
+MVLSLSLVLPWKLAALVLGLVALVLGVRVWLTSRGERRAGLPRAVAAGGMALALFGTTTA
+ALPLLAWDATVELERCTSSALTVRAQQACADAFTRAVEERTGVPQLRP
+>GCF_020097155.1_02430
+MSALPPVPPSAPDRRPADAAARARVGRLLVAQSAALLAMLGAFTLVLPFKVLTLAAALAA
+LVLGVLVFTASRRTAQSLVPRAAAGAGMALALMGLTVGVFPLLLWNETAGFERCTASAVT
+VRAQQTCADDFTATVERRTGVAQLGG
+>GCF_023573625.1_00404
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCSASALTV
+RAQQACADEFTRQVEERTGVPQLRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000438.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000438.fa
new file mode 100644
index 0000000000000000000000000000000000000000..103b36726d570d7a8113cc74268d9bddf2833b6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000438.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00400
+MSSATPPRPSADGAHPGPAPDVVAPDAALPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGMGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSSGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLTFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD
+>GCF_003691675.1_00124
+MSSATPPRPSADGAHPGPTPDVVSPDAALPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGVGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSGGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLAFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD
+>GCF_005280335.1_02557
+MQGRIFLIGGLGFMFDAWDVALNGVMIPLLREEWALAPADAAWIGTANLIGMAVGAFLWG
+TIADRIGRKAAFAWTLAIFSVFTLAGALTDSLLWFAVFRFVAGVGLGGTIPVDYALVGEF
+TPRRLRGRVLAAMDGWWPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIP
+ESPLFLMSRGREAEARKVIDRMVEATGAERREYVMPPVEQERAGGVLAQLAAVWRFSPRI
+TAVTWALFVAIMVVYYIALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATVLIEV
+TGRRWLLGVSAVVASALLVWLASVLGVPSAVLPLVLAFGFVVQIAIPVLYTYVSELYPTT
+LRASGFGWASAASRVGAGLGPLFFVGTLVPAMGLPAAFAVTGGLVLLACVAMLALAPETR
+GRALEVSAD
+>GCF_020097155.1_02427
+MPPTGSHAASAAPTGEQVVQELPWRWPVQGRIFLIGGLGFMFDAWDVTLNGVMIPLLTEE
+WGLSKADAAWIGTANLIGMAVGAFLWGTVADQIGRKAAFTWTLLIFSVFTLAGALTDSLL
+WFAVFRFMAGIGLGGTVPVDYALVGEFTPRRLRGHVLTAMDGWWPIGAALCGVVSAWLVG
+TWSDWRLPLLAMVLPALLVFLVRLGIPESPLYLMSRGREREARAVIDRMVERTGAEPRPY
+VMPAADSRAHGGLLAQLAAVWRFSPRITATAWLLFVAVMLIYYIALQWLPTFLIEAGFAQ
+SRAFITTSGMAAAGLVGVAVSAVLVEATGRRRLLAVSGVVASGLLVWLASVLGVPGAALP
+LVLAYGFVIQIAVPVLYTYVSELYPTTLRASGFGWASAASRVGAGLGPLFFVGTLVPALG
+LPGAFGVTAGLVVVAVLVMFAWAPETRGRALEVAED
+>GCF_023573625.1_00406
+MSSATPPHPSADGAHPGPTSDVVAPDATLPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGMGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLMAMVLPALLVFVVRLGIPESPLFLMSRGRETQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSGGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLTFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000439.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bce206a793db57c57573f9bea84182ae4e075bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000439.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00401
+MLEDTRTPSKERPLVTSAQPTTTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVST
+GSTAQRIAAAGVPVTEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEV
+EPFDLVVVNLYPFVDTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEV
+VQAAQSGGFDLRARRRLAALAFAHTAAYDNAVAAWTAAHFGEDTHADEIPVFPPYAGFSL
+ERAQILRYGENPHQPAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVP
+AVAIVKHANPCGVAVTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQAKDVF
+TEVVVAPSFEPEALEILTAKKNLRLLSLPEGFVRDAVEAKQVSGGMLLQITDAVDADGDD
+PATWTLAAGPAADEATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLA
+VERANTLGAAQTGGQDVSTAGGAENVSGDGAPERARGAVAASDAFFPFADGLQILLDAGV
+RAVVQPGGSVRDEEVVAAAEAAGVTLYLTGARHFFHG
+>GCF_003691675.1_00125
+MTSAQPIPTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFGEDTDADEIPVFPPYAGFSLERAQILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVPAVAIVKHANPCGVA
+VTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQVKDVFTEVVVAPAFEPEAL
+EILSAKKNLRLLSLPEGFLRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGPAADE
+AVLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGSVAASDAFFPFADGLQILIDAGVKAVVQPGGSVRDEE
+VVAAAEAAGVTLYLTGARHFFHG
+>GCF_005280335.1_02556
+MTSAQPTTTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVAQLRDLEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFAEDTEQDDVPIFPPYAGFSLERAEILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPAPAVAIVKHANPCGVA
+VTDEGADVAQAHAKAHACDPVSAFGGVIAANRPVTAVMAAQVKDVFTEVVVAPSFEPEAL
+QILTAKKNLRLLALPEGFVRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGAAADE
+ATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVTTSEVTTAGGAENVSGEGAPERARGAVAASDAFFPFADGLQILIDAGVRAVVQPGGS
+VRDEEVVAAAEAAGVTLYLTGARHFFHG
+>GCF_020097155.1_02425
+MSSAPSVTTVLDEVPLKRALISVYDKTGLEELATGLHAAGVQLVSTGSTAQRIAAAGVPV
+TEVSEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVAQLADLDVEPFDLVVVNLYPFV
+ETVRSGADEDAVVEQIDIGGPSMVRAAAKNHASVAVVVDPARYVDVVAAAQAGGFDLRTR
+RRLASLAFAHTAAYDNAVAAWTAAHFGEDAEDEDAPVFPPYAGFSLERAATLRYGENPHQ
+PAALYVDHEAAPGIAQAELLHGKAMSYNNYVDADAAVRAAFDHAVPAVAIVKHANPCGVA
+VAGEGEDVAVAHAKAHACDPVSAFGGVIAANRPVTRAMAEQVAPIFTEVVVAPSFDEDAL
+EVLTAKKNLRLLALPEGFARDAVEAKQVSGGMLMQIADAVDADGDDPRTWTLAAGEAADE
+ATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGAVAASDAFFPFADGLQILVDAGVKAVVQPGGSVRDQE
+VVDAANAAGITMYLTGARHFFHG
+>GCF_023573625.1_00407
+MTSAQSIPTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFGEDTDADEIPVFPPYAGFSLERAQILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVPAVAIVKHANPCGLA
+VTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQVKDVFTEVVVAPAFEPEAL
+EILSAKKNLRLLSLPEGFLRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGPAADE
+AVLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGSVAASDAFFPFADGLQILIDAGVKAVVQPGGSVRDEE
+VVAAAEAAGVSLYLTGARHFFHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000442.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000442.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98541393245268bb8ac77b2787306daa60438734
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000442.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00405
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKRAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFTDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARVRALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGLGGPVATSGGES
+HDGSPWLSWIGADDIAGAFAHAVIDDGVTGPVNAVAPEPVTAREFATVLGRVLHRPAVIP
+VPDAGPRLLLGEEGRVETVAADQKVVADRLVASGYDMRDPELEGALRHVLGR
+>GCF_003691675.1_00128
+MTEITVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKKAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFSDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARARALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAETSGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGVGGPVATSGGES
+HDGSPWLSWIGADDIAGAFAHAVLDDGVTGPVNAVAPEPVTAREFATVLGRVLRRPAVIP
+VPEAGPRLLLGEEGRVETVAADQKVLADRLVASGYEMRDPELEGALRHVLGR
+>GCF_005280335.1_02551
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPSDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGEDLLGRVPGVGAAASRRAHEAF
+EAELSRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VVRLVRSPKKAGALDAALWDPGRETVDEDALAGADVVVNLAGEPIAGRFTDEHKEAVHDS
+RVRGTRTLVDALARITAREGDDARARALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGVGGPIASSGGES
+HDGSPWLSWIGADDIAGAFAHAVLDDGVTGPVNAVAPEPVTAKEFATVLGRVLRRPAVIP
+VPEAGPRLLLGEEGRVETVAADQKVVADRLVASGYDMRDPELEGALRHVLGR
+>GCF_020097155.1_02419
+MTETRVFEHRTLLRHPRRTVFDWLAAPGALQRMNPPFASELAAGPSDGLREGSQTRLRIG
+APGSLGLFAGAVDGALRAALPAAVSRRIPAALSPRLPWRARHTAYEEGRMFRDEMASGPL
+SAWRHTHSVEDAAPGEADTAEGEPGAVVVDRVEYALPGVGTAGRLPVVGRPAADAAHRVF
+EAELRRQFEFRGRVMAEDLDFHAGHPGPLVGGPARTVLVTGAGGLVGTQLCALLTGGGHR
+VIRLVRSPAQAEAEDAVLWDPAGGTVDTAALRAADVVVNLAGEPLAGRFTEKHRRAVHDS
+RVDGTRTLVDAIARLPEAERPTVLVNGSAVGWYGADAGAGPDGRGLTEDLPAGDDFLAGV
+VADWEAQARRAEELGLRVVRVRTGIVLSPTGGMLAQLLPLFLAGAGGPVATRGGRSHDGS
+PWISWIGVDDIAGVFAHAALAEGVVGAVNGTAPEPVTAKEFARVLGTVLHRPAAVPVPEF
+GPRLLLGEQGAAELVRADQKASAELVLDSGYAFRDAALEGALRRLLGR
+>GCF_023573625.1_00411
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADMADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKKAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFSDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARVRALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGLGGPVATSGGES
+HDGSPWLSWIGADDIAEAFAHAVLDDGVTGPVNAVAPEPVTAKEFATVLGRVLRRPALIP
+VPEAGPRLLLGEEGRVETVAADQKVLADRLVASGYQMRDPELEGALRHVLGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000443.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000443.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b548b673ce5ad905bf6c6ad9001e5b8a54f9b6e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000443.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_00406
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAVPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALSQLIRETGALQD
+>GCF_003691675.1_00129
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLMVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVFVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMAAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTTRVLTAQVMVALQEGFPQLALALWEALARDAF
+TALGQLIRETGALQD
+>GCF_005280335.1_02550
+MTTPVQKHLDRLTSAHTGEGDVPDGLGVAMLMVDGHRYVSGSMTSVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSDTTDENALGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVLELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEIRELMAAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSQHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALSQLIRETGALQD
+>GCF_020097155.1_02418
+MKSPVQDRLDRLTAAHTPGTAADADATSDAGTGLALSVATVGGDHYSAGELVAVPLAGLA
+GPVVHALALEDLGVERVGEAVGTVPRPDLRTRLELEPGTGRPLTPLQDAGTMALAALVKG
+RGGRDRAARLLQQLAGLIGRETAPTDAAVRAADRAQHRARAAAWLLRSVGVLEADPDGLL
+ADVATLRAAPVTVADLALLAGTLAAHGVHPVSGERVLAEETVRAVLSALDACGMDTVDGA
+WALDVGQPGWSSARAGTVIAVVPGHMGIAVQGPADPDDADAPSPAALAALRTLVRDFELH
+PSQAAGSPRAAFRTHYRVDQAPSGSVRSAEVLELLSAHGDTAHVLELGGHVGFSQVDALA
+HVARNLPAALETIIVDVRSVSSTSHAAAVLAAQWFAYALHHGLDVVVVDRDTAAVDQVMA
+TAEASGVTLPDPLHDADDADPGHQDLGPAFRFFDSRSRAVQWAEQRLLARHAPHLLPASE
+EEAAMAPLLQHLSSEDARLLESMMDERVYEDGQIIRRAGQPFGGIYVITSGRVELTGQGT
+GGRRVRRTVLTPGMTFGEMALGQPGRQPSTVRARGRVTTRVLTAQVMYALQEGFPSLALT
+LWEALARDAYTALGQLIRETGALQD
+>GCF_023573625.1_00412
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSAMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSNTTDENGLGAAAMTALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAALAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALGQLIRETGALQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000444.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000444.fa
new file mode 100644
index 0000000000000000000000000000000000000000..017bf9fea118ba1d4240bd682a0d42aa79154dc8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000444.fa
@@ -0,0 +1,81 @@
+>GCF_002008305.4_00410
+MVPMPTPVDPVTVPSALSAALGRLSAGLTFAAALPDLEAALDARGAAVVEAPPGTGKTTV
+VPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADSHPGADPDARARLADA
+AVGYAVRGDAVGGGASAVEFVTPGLLLRRLLADPGLDGVGAVVLDEVHERDLDTDVLFAL
+LADLRQLRPELALVAMSATVDAAALAARWARGMGEAPLPVVSTPAVLHPLREEHAPFRGH
+RLTAEGRVDRAFLDHVAATAARAHAKALEADPTVDALVFLPGVAEVETVAGRVAALAPDT
+EVRVLHGRQEPADQDAALAGRTDPAVPRVVVATAVAESSLTVPGVRLVVDSGLAREPRRD
+RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAP
+VALAFAAWGAPGGRGLTLPEDPPADAMAAAERTLASLGAVDADGRITPHGAVLAELPLDP
+PLGHALLRAAPLTGPRPAAEATAALALDLRAPGADLEALVAALRDGRHPEAGRWHREADR
+LERLARRHAHHAPETREPDEPGPEAATAPRHSAGLVAALAFPAWIARRAGEEGAYLLASG
+TRAALPRDAVGGLAGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRSLVERAGAGLRRTE
+DTAEWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRDALAADGLARFDPRGRAERL
+RRRVHLLHRVLGAPWPDLSDTALPDLDTLVDGLAADLAAGRPLARLDAEALLRGALPWPE
+AGRLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVL
+HLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAVAEPTARTNRRAL
+>GCF_003691675.1_00130
+MDPMPTPVDPVAVPSALSTALGRLSAGLTFAAALPELGSALDARGAAVVEAPPGTGKTTV
+VPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADAQPGADPDARARLADA
+AVGYAVRGDAAGGGASAVEFVTPGLLLRRLLADPGLDGVDAVVLDEVHERDLDTDVLFAL
+LADLRQLRPELALVAMSATVDAAALAARWARGMGEAPLPVVSTPAVLHPLREEHAPFRGH
+RLTAEGRVDRAFLDHVAATAARAHAEALEADPTVDALVFLPGVAEVEAVAGRVAALAPDT
+EVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRD
+RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAP
+VALAFTAWGAPGGRGLTLPEDPPADAMAAAERTLASLDAVDADGRITPHGAVLAELPLDP
+PLGHALLRAALWTGPRPAAEATAALALDLRAPGADLEALVASVRDGRHPEAGRWRREADR
+LERLARRHAHHSLETRAPGEPGPEATAAARRHPAGLVAALAFPAWIARRAGEAGAYLLAS
+GTRAALPRDAAGGGLAGQEWLAVAEVARVAGDAAGTGAAIRATAPIDRTLAELAGAGLRR
+TEDTADWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRTE
+RLRRRVHLLHRVLGAPWPDLSDAALPGLDALVDGLAADLAAGRSLARLDAEALLRGALPW
+PEAGRLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPV
+VLHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRAR
+>GCF_005280335.1_02549
+MPAPSPHSSRPASVDTAVAPALSAALERLGSGLTFVAALPDLEAALDARGAAVVEAPPGT
+GKTTVVPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRSAVLDAADRTSAPDALADAA
+VGYAVRGDAVGGGASAVEFVTPGLLLRRLLADPGLDGVDAVVLDEVHERDLDTDVLFALL
+ADLRQLRPELALVAMSATVDAAALAARWARGMGEEAPLPVVSTPAVLHPLREEHAPFRGR
+RLTAEGRVDRAFLDHVAATAARAHAAALDADPTVDALVFVPGVAEVEAVAGRVAARAPDT
+EVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRD
+RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGAAPAAPTPALAVVDLAP
+VALAFAAWGAPGGRGLTLPKDPPADAMAAAERTLASLGAVDTDGRITPHGAVLAELPLDP
+PLGHALLRAAPLTGPRPAAEATAALALDLRASGADLEALVAALRDGRHPESRRWRREADR
+LERLARRHAHRAPETREPDGPGPEAATARRHPAGLVAALASPAWIARRAGEAGAYLLASG
+TRAALPRNAVVGGLAGQEWLAVAEVARAAGDAAGTGAAIRAAAPIDRPLAELAGAGLRRT
+EDTADWRGDRLTGRRVDRMGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRAER
+LRRRVHLLHRVLGAPWPDLSDTALPGLDALVDGLAADLAAGRSLAHVDAEALLRGALPWP
+EAGRLDELAPERLPVPSGRGVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGRELVV
+LHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRVR
+>GCF_020097155.1_02417
+MSTSSASHSTPDLRAALAAASARLGADLAFSASLPALEAALDARAGAVVHAPPGTGKTTA
+VPPAVALWLARRAESGGEGGRVLVTQPRRVAVRAAWRRLHGAVADALGPESGPDTGRLPD
+AVVGYAVRGDAVGRGASAVEFVTPGLLLRRLLGDPGLEGVGAVVLDEVHERDLDTDVLFA
+LLADLRQLRPELALTAMSATLDADALAARWATGMGEDPVPVVRTPSVQHPLTVEHAPFGG
+PRTTADGRVDRDFLDHVAATAARAHAEALDADPTVDALVFVPGVAEVEAVAGRVAALAPD
+TEVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRR
+DRGRGITGLATVQASRAAADQRAGRAARLGPGTAVRCHTAAALGAAPAAPTPALAVADLA
+SVVLAFAVWGAPGGDGLVLPEDPPADAMAAAERTLASLDAVDTDGRITPHGTVLAELPLD
+PPLGHALLRAAPLTGPRSAAEATAALALDLRAPGADLEALVAALRDGRHPEAGRWRREAD
+RLERLARRHAHRAPETREPDEPGPAATATARRHPAGLVAALAFPAWIARRAGEEGAYLLA
+SGTRAALPRDAVGGGLAGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRPLAELAGAGLR
+RTEDTAEWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRVALAADGLARFDPSGRA
+ERLRRRVHLLHRVLGAPWPDLSDATLPGLDALVDGLAADLAAGRSLTRLDAEALLRGALP
+WPEAGRLDELAPERLPVPSGRGVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREP
+VVLHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTDRTNRRA
+R
+>GCF_023573625.1_00413
+MPTPVDPVSVPSALSAALGRLSAGLTFAAALPDLEAALDARGAAVVEAPPGTGKTTVVPP
+ALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADAQPGADPDAQARLGDAAVG
+YAVRGDAAGGGASAVEFVTPGLLLRRLLADPGLDGVGAVVLDEVHERDLDTDVLFALLAD
+LRQLRPELALVAMSATVDAAALAARWARGMGEDAPLPVVSTPAVLHPLREEHTPFRGHRL
+TAEGRVDRAFLDHVAATAARAHAEALDADPTVDALVFLPGVAEVEAVAGRVAALAPDTEV
+RVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRDRG
+RGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAPVA
+LAFAAWGAPGGRGLTLPEDPPADAMAAAERTLASLDAVDADGRITPHGAVLAELPLDPPL
+GHALLRAAPWTGPRPAAEATAALALDLRAPGADLEALVAAVRDGRHPEAGRWRREADRLE
+RLARRHAHHAPGEPGPEAAATVRRHPAGLVAALAFPAWIARRAGEAGAYLLASGTRAALP
+RDAAGGDLTGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRTLAELAGAGLRRTEDTADW
+RGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRTERLRRRVH
+LLHRVLGAPWPDLSDAGLPGLDALVDGLAADLAAGRPLTRLDAEALLRGALPWPEAGRLD
+ELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVLHLLSP
+AGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000445.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000445.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bda52d14ace3b7b8bc5555c1d594d4d9a71e3d12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000445.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00411
+MRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA
+NGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ
+AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEAA
+RSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEVTTNLDSEAGRTAARIIS
+TIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG
+WAVYPRTVEGEDAAPPVGGINLGVGAKSEHQDLAWDAISCITTTEHQSQYFVENGNPPAD
+PAAYDAPEVAEKYPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET
+DDFIQEVLRGERLL
+>GCF_003691675.1_00131
+MRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA
+NGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ
+AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEAA
+RSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEVTTNLDSEAGRTAARIIS
+TIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG
+WAVYPRTVEGEDAAPPVGGINLGVGAKSEHQDLAWDAISCITTTEHQSQYFVENGNPPAD
+PAAYDAPEVAEKYPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET
+DDFIQEVLRGERLL
+>GCF_005280335.1_02548
+MRHDTRARQRRRATLAGAVVAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA
+NGRYRIETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ
+AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEVA
+RSQDKDLGVQGARAESMTVWLNALIEGGGEQIIPNAEAPTDEVTTNLDSEAGRTAARIIS
+TIGKEGLGSAGLPTQDENASMLLFQGNNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG
+WAVYPRTVEDKDAAPPVGGINLGVGEKSEYQDLAWDAISCITTTEHQSQYFVENGNPPAD
+PAAYDAPEVAEKFPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET
+DDFIQEVLRGERLL
+>GCF_020097155.1_02416
+MGDDGRHIRLASNEVPLVRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN
+PDDGGQAKIAAQCTDAANGRYRIETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV
+PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAA
+GLDMSKPVTWDQLIEVARSQDKDLGVQGARAESMTVWLNALIEGGGEQIIPNAEAPTDQV
+TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL
+GSVEEGSLPKDLPEDIGWAVYPRTVEDKDAAPPVGGINLGVGAKSEHQDLAWDAISCITT
+TEHQSQYFVENGNPPADPAAYDAPEVAEKFPMADTIRESLELGAPRPQTPYYNEVSTAIQ
+QRYAPPSGVSESTPAETDDFIQEVLRGERLL
+>GCF_023573625.1_00414
+MRDDGRHIRLASIEVPLVRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN
+PDDGGQAKIAAQCTDAANGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV
+PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDEIVTVPFWANTQLLWYRKSVAEAA
+GLDMSQPVTWDQLIEAARSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEV
+TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL
+GSVEEGSLPEDLPEDIGWAVYPRTVEGKDAAPPVGGINLGVGAKSEHQDLAWDAISCITT
+TEHQSQYFVENGNPPADPAAYDAPEVAEKYPMADTIRESLDLGAPRPQTPYYNEVSTAIQ
+QRYAPPSGVTESTPAETDDFIQEVLRGERLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000447.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000447.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c74ecac95bf574f4192c20cc846dc11074758679
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000447.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00414
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFDPDPAVAEMLSSLAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAAEERRRQIEMAAERDA
+AEHEADAPRR
+>GCF_003691675.1_00134
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFEPDPAVAEMLSALAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAGEERRRQIEMAAERDA
+AEHEADAPRR
+>GCF_005280335.1_02545
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDISDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPAEEEIDRKVRN
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKEKDGVHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDQGSTFDATLTHLEWLGHEQYGYIEFDPDPAVAEMLSSLAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPKTGENLTRDPEVGAELTRRAAEERRRQIEVAAERDA
+AADREAADTRR
+>GCF_020097155.1_02413
+MASITLNHIEKTYDDGYHAISDVNLDIEDGEFVILVGPSGSGKSTLLRMIVGLEDISGGD
+LLIDGRRVNEAAPKDRNLAMVFQNYALYPHLSVYENIAFPLRLAKDGKLSEEELDRKVRD
+AARVLELQDHLDRKPANLSGGQRQRVAMGRAIVRDADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPATVKEQGGQYVLSSPIGDIPVPAEKAQRAAGRDIVFMGLRPEFFEDAELVEDA
+KRPHGSEFDATLTHLEWLGHEQYGYIEFEPDPEVAELLSSLAKDLDADELRPVVVTTLSA
+ESAARPGVPTRLWVDTTRVHLFDPKTGENLTRDAEAGAELTRRTAEARRRQIEAAQARDA
+EGR
+>GCF_023573625.1_00417
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFEPDPAVAEMLSALAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAGEERRRQIEMAAERDA
+AEHEADAPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000448.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46fb8a2021b25d94d13a4bcdca13c67c9d7cb378
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000448.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00416
+MAHIITVAGATPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGAGTNLQ
+DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG
+>GCF_003691675.1_00136
+MAHIITVAGATPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGAGTNLQ
+DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG
+>GCF_005280335.1_02544
+MAHIITVAGAGPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGERTNLQ
+DNVVLHADKGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKVNAATYLELSAAHREATAER
+>GCF_020097155.1_02412
+MGHLVTVLGRTPRVDPSAFVARTAVLSGDVELGPRASAFYGVSARGDSAAIRVGEGSNLQ
+DNVVLHADAGFPCTLGAGVSVGHAAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+VVLEGTQVPPGSLVAGVPAKVRRGLTEEERASLTVNARTYLDLAAAHRAAEEAEQAGV
+>GCF_023573625.1_00419
+MAHIITVAGATPRIHESVFLAPTAAITGDVEMAEHSSAFYGASARGDSAPIRVGAGTNLQ
+DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000450.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000450.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8656e54ab1ad49cb908dc82a5c67f1bbfdb8b16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000450.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00419
+MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYSEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVHNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSAQEREDFVETVAGALKGVRQDVQARAFEYWKNVDTAIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
+>GCF_003691675.1_00140
+MTEYQKKTPHATGSTRQNGAPAISDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYTEEGNYDIVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVHNYAFEGQMWYDHTGDRSTYVPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSDQERDDFVETVSGALKGVRQDVQARAFEYWKNVDATIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
+>GCF_005280335.1_02540
+MTENQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLVETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGAKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYTDEGNLDVVGNNTPVFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNTPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNFSNEEAEAMA
+GKNADYHRQDLFESIAKGDYPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFNPGNMVPGVGLSPDRMLLGRSFAYHDAQLYRVGAHVNQLP
+VNRPKNEVHNYAFDGQMWYDHTGSRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRKDDDDFGQAGTLVREVFTDAERDAFVETVAGALDGVREDVQARAFQYWKNVDATIGQR
+IEDEVNKGQGDDIPGAAGGGEARI
+>GCF_020097155.1_02409
+MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYSEEGNYDIVGNNTPVFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISQKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVNNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSDQERDDFVETVAGALKGVRQDVQARAFEYWKNVDATIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
+>GCF_023573625.1_00422
+MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYSEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVHNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSAQEREDFVETVAGALKGVRQDVQARAFEYWKNVDTAIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000453.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000453.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6492c398f5163dea855855471c7cc1ec48224f89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000453.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00422
+MSHTTLHASPGDASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM
+LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY
+SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ
+ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR
+EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA
+LPAPVTTLTRRASLEDVFLILTGRTLVD
+>GCF_003691675.1_00143
+MSHTTLHASPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM
+LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY
+SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ
+ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR
+EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA
+LPAPATTLTRRASLEDVFLILTGRTLVD
+>GCF_005280335.1_02536
+MSHATPASPSPSQSPADAPDAGPAPVIRARGLRKQYGDFHAVKGIDLDVRPGECFGLLGP
+NGAGKSTTMRMLAGTSQRTAGELSILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENI
+LIYGRYFGLPYSYLRPKADELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFL
+LDEPTTGLDPQARHILWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDGGQIMAAGT
+PAALIREHAAREVLEARFGADRNEAAARTVQARAGDGVVHRVEVLPDRVLVYAAHADDLH
+AVVQGLVDDGALPAPVTTLTRRASLEDVFLILTGRTLVD
+>GCF_020097155.1_02406
+MTRTTSSPSPAAPAGGGAAPVILARGLRKQYGDFHAVQGIDLDVRPGECFGLLGPNGAGK
+STTMRMLAGTSQRTGGELRILGIDPEEDGPAVRARLGVVPQQDNLDEDLTARENILIYGR
+YFGLPYSYLRPKAEELLAFAQLTDKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPT
+TGLDPQARHTLWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDAGRIMAAGTPASLI
+REHASREVLEARFGTDRNATAARLLRESLPGLHRLEVLPDRVLLYTEHADTLQQDLDRLV
+AEGHVTAPVTQLTRRASLEDVFLILTGRTLVD
+>GCF_023573625.1_00425
+MRLCCRLVSPTTLHAPPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAG
+KSTTMRMLAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYG
+RYFGLPYSYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEP
+TTGLDPQARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAEL
+IREHASREVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQ
+RLVDEGALPAPATTLTRRASLEDVFLILTGRTLVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000454.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000454.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5413b0a22d584598e177eee4a68e869e8eab3f7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000454.fa
@@ -0,0 +1,49 @@
+>GCF_002008305.4_00424
+MTPRPPHPADPASGAFTPDQRRILTALLMPLFLALMSVSVVNVALPAIESGLDATSADLQ
+WVLAGYTLTFGTVLVAAGRAGDLWGRKNLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLT
+GLGAGVFNPQVIGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWR
+STFLMNVPVGLAAVAMGALWLPPPTRVHGLPPAPGPRGIAALDPVGALLLGAGGVSLMVP
+FIVPGTAWLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRPSFTIGALESTIY
+LATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGA
+LVGLVSLGVLALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGA
+AGGVAQTAQRLGTALGLSVVTGAFFAALAGAAGESAGPPSAAAYAHAASTAMGMVAVCWA
+LTAAVAALDVVRRRRAARAA
+>GCF_003691675.1_00145
+MTPRPPHPADPASGAFTPDQRRILTALLMPLFLALMSVSVVNVALPAIESGLDATSADLQ
+WVLAGYTLTFGTVLVAAGRAGDLWGRKNLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLT
+GLGAGVFNPQVIGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWR
+STFLMNVPVGLAAVAMGALWLPPPTRVHGLPPAPGPRGIAALDPVGALLLGAGGVSLMVP
+FIVPGTAWLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRPSFTIGALESTIY
+LATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGA
+LVGLVSLGVLALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGA
+AGGVAQTAQRLGTALGLSVVTGAFFAALAGAAAESAGPPSAAAYAHAASTAMGMVAVCWA
+LTAVVAALDVVRRRRAVRAA
+>GCF_005280335.1_02533
+MGGPVAATARRPANRRAGPVVVRAYPEAVTPRPRSADGDAAPAAFTPEQRRILTALLMPL
+FLALMSVSVVNVALPAIESGLHATSADLQWVLAGYTLTFGTVLVASGRAGDLWGRKSLFL
+VGIGLYVAGALVSGFAADPLMLNAGRLVTGVGAGVFNPQVVGFIQSNFSGRARGRAYGLF
+GTVIGLGVAVGPMLGGLLLGALGPEWGWRSTFLMNAPVGLAAIVMGVLWLPAPTRVHGLP
+AAPGPRGIAALDPVGALLLGLGAVCLMVPFIVPGTAGLLVLAAALVTAWWLWEKRVKARA
+SATGVQPMVDPALFRRLSFTIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGLVGL
+PGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVLALAFERSAAGAWSPWIVGVGL
+IVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAALAGA
+AAEGAGPPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAVRAA
+>GCF_020097155.1_02403
+MTLPSPAAAESGAFTADQRRILTVLLIPLFLALMSVSVVNVALPSIEGGLGASSADLQWV
+LSGYTLTFGMVLVAAGRAGDLWGRRPLFLAGIALYVLGSLLSGLAPDPLWLNAGRLLTGL
+GAGVFNPQTIGFIQSHFTGRARGRAYGLFGMVVGLGVAVGPLLGGLLLGALGPDWGWRST
+FLMNVPVGVLAIVMATAWLSPDTRVKGAAGRSGGPRGIAALDPVGALLLGGASLCLMVPF
+IAPGTWALLAGAAVLGVGWWLWELRVKRRAAATGVEPMVDPALFRRASFSIGAAESTIFL
+SSMPAVFAVTAVFLQQGMGFSPLASGLATLPGAVVQAVASPWAGSKVPSQGARMVFGGGV
+VGLASLAILALAFERSAAGAWSPWIVGAALAVMAVSQALILTTTQVLMMEDVAGHEAGAA
+GGVAQTAQRMGTALGLSVVMGAFYAALAGAAGPGGAPSAAGFAHAASAAVLMVGACWLVT
+TAIAAADLVRRRRTAR
+>GCF_023573625.1_00427
+MPLFLALMSVSVVNVALPAIESGLDATSADLQWVLAGYTLTFGTVLVAAGRAGDLWGRKS
+LFLAGITLYMLGSLLSGLAGDTLLLNAGRLLTGLGAGVFNPQVIGFIQSNFHGRARGRAY
+GLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWRSTFLMNVPVGLAAVAMGALWLPPPTRVH
+GLPPAPGPRGIAALDPVGALLLGAGGVSLMVPFIVPGTAWLLVLAAALVTAWWLWEKRVK
+ARAWATGVQPMVDPALFRRPSFTIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGL
+VGLPGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVLALAFERSAAGAWSPWIVG
+VGLIVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAAL
+AGAAAESAGSPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAARAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000455.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000455.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2380a12bf399fabb3ebbca65112d2abb3e9319d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000455.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00425
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VSGTVIG
+>GCF_003691675.1_00146
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VSGTVIG
+>GCF_005280335.1_02532
+MSQPLTTGSGETRRGPRAGLRVGSVGFAAMIVILIVAIMFAANQNDVIGWLVVAVAAGWL
+VFALVVFLQMRRGVQAAGRKVDAAMENARADVAALRGQGAAAAPQAAAHAPAGDPMRDTK
+LDHSFKIAQVQVKVVREQLAAGGAMDREMVDRALETIDITAANARDMIKESRGQGGSEGP
+VSGTVIG
+>GCF_020097155.1_02402
+MPQSIPSGSAGTRPARAGLTVGSTGFAVMVAVLLVAIVFAANANDLIGWLVVAIAAGWLV
+FAVVVFLQMRKGVREAGRKVDTAMQNARADVAALRAPQQPAPAAAVPAAAGDPMRDTKLE
+HSFKICQVQARVITQQLDAEGPLDREMVDRALETITITAQNARDMIKESARDAEGPVSGT
+VVS
+>GCF_023573625.1_00428
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVQAAGRKVDTAMQNARADVAALRGRDADAAAPAVAPSAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGESMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000457.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000457.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2f89c58c2b7b5b2088cd4f84ca8976fd04a5eed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000457.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00427
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLAPVRERALALLDDPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR
+>GCF_003691675.1_00148
+MTMKKNSVQDVLAQDAAATAHLPGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILAAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLAPVRERALELLADPAELDRILASGAEKARAVATPVLEDVYAKVGFLPPLR
+>GCF_005280335.1_02530
+MKKNSVQDVLAQDVSATAHLAGASDRHRVLSGMQPSADSLHLGNYLGALTNWVRTQDDFE
+AFFFIPDLHAITVPQDPAALAQRTRVAAAQFIAAGIDPERSTLFVQSQVPEHAQLAWVLT
+CMTGMGEAMRMTQFKDKSAKQGAEAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQHVE
+LTRDLAQRFNHRHGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINVMDDPKR
+TAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAMTDVPVAELEGRYVGRMYGHLKVDV
+ADAVVERLAPVKARTEELLADPAELDRILAAGAAKARAVATPVLEDVYAKVGFLPPLR
+>GCF_020097155.1_02400
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSDRPIPELEAEFEGKMYGHLKV
+AVADAVVERLAPVRERALGLLDDPAELDRILAAGAAKAREVATPVLEDVYARVGFLRPLR
+>GCF_023573625.1_00430
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLVPVRERALALLADPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000458.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7a64628e19153378c24ea14a184dbbb0513cd05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000458.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00428
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAERARRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA
+DERVGTERDGARA
+>GCF_003691675.1_00149
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA
+DERVGTERDGARA
+>GCF_005280335.1_02529
+MHTVQQAAGAHAPAGREPVLETENLVKVYGRGESRFDALKGVTLQIQAGESVAIVGKSGS
+GKSTLMHLLALLDRPSAGVVAMDGRPVQDVSPAEVARLRNETFGFVFQQFFLNPAQTVLE
+NTVLPLKISGVPRAERRERGMAVLERLELADKAGNKATDLSGGQKQRVCIARALVNRPTV
+LFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAARCDRRLVMQDGMIVDE
+TTTAGAQA
+>GCF_020097155.1_02399
+MSTVHTHPPETQASRGEEPVLETENLVKVYGRGASRFDALKGVTLQIHRGESVAVVGKSG
+SGKSTLMHLLALLDVPTSGVVAMDGRPVSQLKAAEVAHLRNERFGFVFQQFFLNADQTVL
+ENVVLPLKIAGVPRHEREARGREVLERLEIADKAKNRANDLSGGQKQRVCIARALINRPT
+VLFADEPTGNLDSATSRSVEEILFGLHRDEGITLVVVTHDDDLAAQCDRRLVMQDGVIVA
+AEGAGRAVAAGTGARA
+>GCF_023573625.1_00431
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDDGITLVVVTHDDDLAAKCDRRVELQDGVVID
+DERVGTEQDGARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000459.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000459.fa
new file mode 100644
index 0000000000000000000000000000000000000000..04075c8fa5b8f8824110d968a148094671397c31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000459.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00429
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYAEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLVGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQEIYDITTEGLPE
+SQRDTYFQATAIVADPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLVGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE
+>GCF_003691675.1_00150
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYTEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLVGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQAIYDITTEGLPE
+SQRNTYFQATAIVEDPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLVGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE
+>GCF_005280335.1_02528
+MKATDLAGTALANTMRAKLRTFLTVVAIVIGAFTLTLTSGLGAGINKFVDNMVEGFGSPD
+QLTVMKQVDPTSFAAGGAPQEYEPDEAAAGEMFGLPLLTAADLDRIRDTEHVTEVETARL
+VEPEYIEGEDGRQWQVPFMGSSFEIGALSLAAGREPAADAAEVTVPQDWVEALGGQTPED
+VLGQTVTLVAADPLGKQDGVEAEVVGVTEPMASGSGSGPVPSGEVETRLHEIQTAGLPEA
+QRDTFFSASVTVADMAANEAAVKAALAEEGYSAQTLEDQLGPIRGIIDAVTWVLNGFALI
+ALLAASFGIINTLLMAVQERTREIGLMKALGMTGRKIFGLFTMEAVVIGLLGSLIGVGLG
+VAVGVVANQVLTEGALSGVTGLVLYAVEPLSLALIVLLIVAIAFLAGTLPAARAARKDPI
+EALRYE
+>GCF_020097155.1_02398
+MKAPDLIRTALGNTARAKLRTFLTVIAIMIGAFTLTLTSGLGAGINKYVDNMVAGFGAPD
+ELTVSKPAGNQMAGMTGGAPTEYEDSAAAGEMYGMPLLTQEDLDRIGATEHVTGVETVRI
+VEVQDLRGADGRRWSVPMMGGTYEIGKLSVKAGREPAADGGAMELTVPTEWVESLGGTAP
+EDVLGQEVTLTTKTPLQQERTVQAEVVGVTERLPSGVGANPVPSAALEQGLHDIQTEGLP
+EEQRNTYFQATAIVEGMPGNEAAVKAALSEQGYQAQTLEDQLGSIRGIISAVTWVLNGFA
+LIALLAASFGIINTLLMAVQERTREIGLMKALGMTSGRIFGLFTLEAVVIGLLGSLLGVG
+LGVAVGVGVNAWLTTGGPLEDVAGLVLYAVDPLALLLIVLLIVAIAFVAGTLPAARAARK
+DPIEALRHE
+>GCF_023573625.1_00432
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYTEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLIGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQEIYDITTEGLPE
+SQRDTYFQATAIVADPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLIGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000460.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000460.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbbe3d33d0a6f19cfc10a7f2da003e35d3af9bb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000460.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_00430
+MTTDRPNPDPNPEQPAVGSRYGTQPYAAPGYGAQPGSPYGIVPEPAAFPALLTLTLTSLA
+LYVLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVGASVTVGTIIVLLIGVALY
+ALVYFNLRGAKNWARILGIVVGILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNIL
+WLVKAFNPQVAAYTRQGRRA
+>GCF_003691675.1_00151
+MTTDRPNPNPEQPAAGSRYGTQPYAAPGHGAQPGSSYGIVPEPAAFPALLTLTLTSLALY
+VLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVGASVTVGTIIVLLIGVALYAL
+VYFNLRGAKNWARILGIVVAILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNILWL
+VKAFNPQVAAYTRQGRRA
+>GCF_005280335.1_02527
+MSNQNPDFTNPAYNPANPPFEGESGQAGQAPQQGQPGQAAQYGQPGPYGQAPQYGQPGQY
+PATGTRYGTQPYGVDGRYGTVPEPRGFRTLLTLTLVSAALWVLSSLPAMFTMDDMMDVVM
+RDAASQPGVTAEDMEMVSSFMRTAGITSIVISLIIGLGLYALVYFNLRGVKNWARILGIV
+FAILGALAIFSGIGFLFSGSTMLILSGALTLAYAVVNIIWVITAFRSDVAEWFRQGRPAA
+A
+>GCF_020097155.1_02397
+MTDQNTPYPQNPQGGQPAPQYGQPGQAAPQYGQPGEGSRFGTQAYGAPGLQYGAPLAEPA
+KFRTLLKLTLASAVVYVLSALPGLFVDQDALVRDQLRAQGMSAEQIDQAMQNAGMFSAMA
+GIGAVVGLLIALGLYALVYFGLRAGKNWARVLGIVLAILGTLSAVFGLFSLGSFPAGVMI
+ASLVLSVLFIAVNVLWLVNAFNKDVAAYTKQGRLPAA
+>GCF_023573625.1_00433
+MTTDRPNPDPNPEQPAAGGPGPYPGQNPAYGQPTAGSRYGTQPYAAPGYGAQPGSPYGIV
+PEPAAFPALLTLTLTSLALYVLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVG
+ASVTVGTIIVLLIGVALYALVYFNLRGAKNWARILGIVVAILGTLSAVGGIFSFVTYPGI
+GGVLASVLSLALVIVNILWLVKAFNPQVAAYTRQGRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000461.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11b938f8ebdf21b395bd9341f5e31f47992c6772
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000461.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00432
+MHPLDDDPHAATDRDPAPDRAALRPLRLFQTVTAVTGALSAAGVAGVLALQSTPGYARAV
+LEARSWGASEVTDADVAAFVTPAGAWPVAAAAVVLLAVVLLAGITRRIRAVRPVGSVLVV
+LGMLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAMWLRVAHRRETRDGFDG
+>GCF_003691675.1_00153
+MMGGMHPLHDDPHETTERDPGPDRAALRPLRLFQTVTAVTGALSAAGVGGVLALQATPGY
+ARAVLEARSWGASEVTDADVAAFLTPAGAGPVAAAAVVVLTLVLLAGITRRIRAVRPVGS
+VLVVLGMLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAVWLRVAHRRETRDAFDV
+>GCF_005280335.1_02525
+MHTPDDAAADADDAAARAALHDRVVRRPLRRLLTLTAVTGALSALGTAGVLALQGAPGYA
+RAVLEARSWGRAAVTDADVASFLTPPWGVPAAVLGVLAVAALLMLGVARRVRAVRPVGTV
+AVGLGLLSAAFWMVDGGRMVAAGGAGPLVLAAVVAMFLACAVWLLTAHLRATRDAFDG
+>GCF_020097155.1_02396
+MRSDDVAPASARPSGLDDPAVRGPIRRYQAMTAGTGLVSAAAVAGVLGLQSDPGYAREVL
+QSRTWGQYEVSAQQVQDFLTPPGGAVLGAVGVLLTAALLVWGAQRLWGATRWLGTALAGV
+GLLSAVFWAVDGGRMAARGASGMAVLVAVGAMAVFCAVWLVTAHSKAVREAFLG
+>GCF_023573625.1_00435
+MHPLDDDPHETTDPAPDLASLRPLRLFQTVTAVTGALSAAGVGGVLALQSTPGYARAVLE
+ARSWGASEVTDADVAAFLTPAGAWPVAAAAVVVLTLVLLAGITRRIRAVRPVGSVLVVLG
+MLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAVWLRVAHRRETRAAFDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000462.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000462.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6f84ea5b73cbc66601b13d6f01a2fbdf599592d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000462.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00433
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKRAILARQF
+>GCF_003691675.1_00154
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKQAILARQF
+>GCF_005280335.1_02524
+MSHAATETEAPVAQDQTQAAGGGMGAIESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGICGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREVMPFLVAEGHEPSKERYQSQADRARYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAIAEVKQAILARQF
+>GCF_020097155.1_02395
+MSHAATETQAPAAPAQQTQGQDGGMGEIESFDITLRVRRFLPESSEESYWDEWRLTMFGT
+DRVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSQPITVE
+PIKGLPVEKDLIVDMEPFFQSYREVMPFLVAKGHEPSKERYQSQADRAIYDDTTKCILCA
+ACTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTE
+ACPRGIQVTKAIAEVKQAILARSF
+>GCF_023573625.1_00436
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKQAILARQF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000463.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000463.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5411f0119a1028dc6a8c20187fc6f68f0e89091
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000463.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00434
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGEIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>GCF_003691675.1_00155
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGGIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGRRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>GCF_005280335.1_02523
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFYNEFYVLDLLLVEEDAVREDGTP
+YKQKRAAGVVSYELATGEIHVFQAKSVVFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNSDGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGVPTNIKAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAQTADFVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGKRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDANFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>GCF_020097155.1_02394
+MQVHKYDVVIVGAGGAGMRAAIESGQRARTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEIMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHDVEFYNEFYVLDLLLVDEDATREDGTP
+YTQKRVAGVVSYELATGEIHVFQAKAVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNAEGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGMPTNVKAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IHAAEYAAQADWVELPEGGELPTVQHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRHRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPNRDDANFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>GCF_023573625.1_00437
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGEIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000467.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000467.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a386052c3d142a33de81277b26173c28a3201a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000467.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00438
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADADLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH
+>GCF_003691675.1_00159
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADPDLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH
+>GCF_005280335.1_02519
+MTTSDSVLSDQRPASLPSVASVVAELEAEVVAFRRDLHRHPELSYEEYRTTDRIMELLTG
+YGFSPVRMESTGAYVDIGEGPVVLALRADIDALPLEEETGLPYVSVNDGVTHACGHDMHT
+AVMAGAALVIGRILRGATADPALRTAGERARGSVRVIFQPAEERLPGGSLSVLRQGILDG
+VPRILAAHCDPAVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGDLLDE
+VVTQVAAPYGVQVQLEHVRGVPPVHNTDAETALIETAARRELGARAIQLTPQSMGGEDFA
+WMTQRVPGSMLRLGTRTPGGPVYDLHRGDFTPDERAIGVGMRVFAAAALQALVGEEGH
+>GCF_020097155.1_02390
+MTTSESVVTGTAPRLAPPSVAPVVQQLEEHVTAFRRDVHRHPELSYEEYRTTDLIVETLA
+EYGLNPVRLEGTGAYVDLGEGPVVLGLRADIDALPVEEETGLPYVSVNDGVAHACGHDMH
+TAVMLGTALTLGRILRGAAPTAELRAVGERARGRVRVIFQPAEERLPGGSLAVIRQGVLE
+GVPRVLAAHCDPHFDVGTIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQI
+AVNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDAGVWEEAGALLD
+EVVTQVASPYGVQVQLEHIRGVPPVDNAEAETALIEDAARRELGAHAIALTPQSMGGEDF
+AWMTQKVPGAMLRLGTRTPGGPTYDLHRGDYAPDERAIGVGMRVFAAAALDVLAGPAR
+>GCF_023573625.1_00441
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADPDLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000468.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000468.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1f6845c8ed0603443e070f8cefaa6bbad15907b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000468.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00439
+MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASDSGAAESEAIATVDGVGSD
+NKDYKACIVSDEGGFDDRSFNQSSYEGLKAAEEAYGITTSEAESNEPSEYTPNVTAMVNG
+DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTDGDFTDNFQKLTYDTAQAAFLAGYLA
+AGTTETGAVATYGGAEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF
+ENVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK
+DGNLILTSVKKNMGQSVTDVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK
+DELKDLEAKIISGELKVGSEYSPEA
+>GCF_003691675.1_00160
+MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASGSGAAESEAIATVDGVGSD
+NKDYKACIVSDEGGFDDRSFNQSSYEGLKAAEKAYGITTSEAESNEPSEFTPNVTAMVNA
+DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTAEGFSDNVQKLTYDTAQAAFLAGYLA
+AGTTETGTVATYGGMEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF
+KNVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK
+DGNLILTSVKKNMGQSVADVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK
+DELKDLEAKIVSGELKVGSEYSPEA
+>GCF_005280335.1_02518
+MGTATPSAEGRRRLLLPAAVLGASALLLTACGQAPEASNSSEPAGSASATGAAAEVGSDN
+SDYTGCIVSDEGGFDDRSFNQSSYEGLKAAEEEFGIEIREAESNSVGEYVPNLNAMLDAD
+CNLVVAVGFQLGDTMKPIAEENAETKFVGVDVTAPGFPENVRNIIYDTAQGAFLAGYLAA
+GMTETGTVATYGGMEIPTVSIFMDGFARGVEHYNEVKGEDVRVLGWDTENRTGSFIGDFS
+NQNAGKTNTANFINEGADIIMPVAGPVGLGTIDAVKEANGGGKDVKVIWVDSDGYETTQD
+GEVILTSVMKRMGDAVKQVIAEDINDEFTSEAYVGTLENDGVALAPFHDFEDAVPQELKD
+ELEALEAGIVSGEIEVGSEDSPEA
+>GCF_020097155.1_02389
+MGIVSPLAGRRRLAVPAALLSSGLLLAGCGAPPAENSGSASGSGAAVSADAAAGSDNKDY
+KSCIVSDAGGFDDRSFNQSSYEGLKAAEEAYGIETNKAESKDASEFTPNVNAQVNAQCDS
+IIGVGYMLGDTIKPIAQKNPDIHFLGVDVTADGFSDNVKKLTYDTAQAAFLAGYVSAGMT
+KTGTVATYGGMEIPTVTVFMDGFAAGVEHYNEVKGKDVKVLGWDREAKTGSFTGDFDNQA
+NGKTNTANFINQGADIVMPVAGPVGLGTLDAVKEANAGGKSVAVVWPDSDGYESTKDGAL
+ILTSVVKNMGQSVSDVIGQDLKGEFSADPYVGTLENKGVELAPFHDFDSKVPQELKDEVQ
+TLQEDIISGKVKVDSEYSPKS
+>GCF_023573625.1_00442
+MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASDSGAAESEAIATVDGVGSD
+NNDYKACIVSDEGGFDDRSFNQSSYEGLKAAEEAYGITTSEAESNEPSEYTPNVTAMVNG
+DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTDGDFTDNFQKLTYDTAQAAFLAGYLA
+AGTTETGTVATYGGAEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF
+ENVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK
+DGNLILTSVKKNMGQSVTDVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK
+DELKDLEAKIISGELKVGSEYSPEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000469.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000469.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce9b1d056b9db03afd9b4fc2613c93cbedd7b44f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000469.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00440
+MRLELRGISKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLREDGTAIVFISHKLREVKAVSDDITVLRRGRVVGTADPSAEAAELAALMVGRSVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGADVAAGTPGTAGEAPAAHPTTEGERP
+>GCF_003691675.1_00161
+MRLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLRADGTAIVFISHKLREVKAVSDDITVLRRGRVVGTAEPSAEAAELAALMVGRNVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGTDVAADTPGTAGAAPAAHPTTEGERP
+>GCF_005280335.1_02517
+MKLELRGITKRFGTFTANDSVDFVVRSGEVHTLLGENGAGKSTLMNVLFGLYDPTEGEIL
+VDDRPVRFAGPGEAMRAGIGMVHQHFMLVPVFTVAENIALGDEHTRAAGVLDLEATRRKI
+RAISDEYGFAVDPDAVVEDLPVGVQQRVEIIKALVRDAKVLILDEPTAVLTPQETDELLA
+IIDRLRQDGTAIVFISHKLREVKAISEHITVLRRGKVVGTAEPSASAAELAALMVGRQVS
+LNRAKTAPTLGEETFKVQDLTVVSPTGQVLVDHVSFAIRQGEILGVAGVQGNGQTELTEA
+IMGLHKATGSVTLDGRELVGRSTRQIIRAGVGYVPEDRSTDGLVGSFTVAENMVLNRFDR
+EPAGSALQLRPRAVRELAEARVQEFDVRTQGVVSPVSSLSGGNQQKVVMARELVDELRLF
+IASQPTRGVDVGSIEFLHERIVRERDNGTPVMIVSTELDEILELSDRIAVMYHGRIVGIV
+DGDASRETLGLMMAGQTPESLATETATTEEGPRA
+>GCF_020097155.1_02388
+MKLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGQIL
+LDGEPVAFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRGAGVLDLEATRRKI
+REISDAYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLA
+IIRQLRADGTAIVFISHKLREVKAISDDITVLRRGRVVGTADPSASAAELASLMVGRDVV
+LNRRKTAPQLGEETFRVEHLTVVSPTGQVLVDDVSFGIRQGEVLAVAGVQGNGQTELTEA
+IMGLQAKAAGSIRLDGRELLGRSTRQIIHAGVGYVPEDRSTDGLVGSFSVAENMVLNRFD
+VAPAGSAVQLRPRAVRELAERRVEEFDVRTQGVDVPVSSLSGGNQQKVVMARELVDGLRL
+FIASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVRELADRIAVMYHGRIVDI
+VPGDASREHLGLLMAGQTAEDTHQEGARA
+>GCF_023573625.1_00443
+MRLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLRADGTAIVFISHKLREVKAVSDDITVLRRGRVVGTAEPSAEAAELAALMVGRNVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGADVAADTPGTTGAAPAAHPTTEGERP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000471.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000471.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8aaad9e9539e253c4e1806da20f097df9cd79f6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000471.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00442
+MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPEATATFRLSH
+ASDAVVLPDLTADPVLGGWLLVGLMAVLTAVAWLATLRSGRTPGWAAALFAVAFVAAFLI
+WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV
+VGTATGSPWAGLVAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL
+TDGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG
+RSRGPAASGVPYVKE
+>GCF_003691675.1_00163
+MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPETTATFRLSH
+ASDAVVLPDLTADPVLGGWLLVGLMAVLTVVAWLATLRSGRTPGWAAALFAVAFVAAFLI
+WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV
+VGTATGSPWAGLAAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL
+TGGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG
+RSRGPAASGVPYVKE
+>GCF_005280335.1_02515
+MSTAAQTNPVQPTPAGTGRAPSAEAPREGGTVVVRSWTTPIVFTVFTVLALVVFGLNAPD
+AAATFRVSTEADAFRIPDLVADGAGGGWIVTAILVVLTVLAWMRAARGRAVGAVLGISFA
+LVFVAGFLIWVVGSAANTSVFLTGLIAGSFALAVPLIFGSMAGILSERAGVVNIAIEGQL
+LAGAFTAALVGSMTGSPWAGLAAAVVAGVLVSVILAVFSIKYLVNQVIVGVVLNVLVAGL
+TGFLFSTVLSENSSGLNSPPRFETLRIPGLADIPVIGPILFEQTLLGYGMYLIVAVIYIG
+LFHTRWGLRVRAVGEHPKAADTLGINVLRTRYVNVLLGGAVAGMGGAFFTLVQSSSFSRE
+MTAGMGFIALAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVT
+IFAVAGLVGRSRAPAASGVPYVKE
+>GCF_020097155.1_02386
+MSTAAPARESATPSERAGAASSGVVVRHWSTPVLLSVFTLVSLVVFALGASDSTAVFRIS
+EASDAVRLPDLLADPAVTGWALTAVMAAITAAAWVLTLRGRRLPGWAAGLFALAFTAAFL
+VWVVGAATNNEVFLTGLIAGSFTLAVPLIFGSMAGILSERSGVVNIAIEGQLLAGAFMAA
+VVGSLTGSPWAGLGAAIVAGVLVSWLLAVFSIRYLVNQVIVGVVLNVLVAGLTNFLFSTV
+LTADSDLNAPPRFPDLRIPLLADIPVIGPILFDQTILGYLMYAIVALLWFGLFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYVNVLLGGAVAGMGGAFFTLVSASSFSKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQFVFAILGTPVPSPFMAMLPYLVTVFAVAGLVG
+RSRGPAAAGEPYVKE
+>GCF_023573625.1_00445
+MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPEATATFRLSN
+ASDAVVLPDLTADPVLGGWLLVGLMAVLTAVAWLATLRSGRTPGWAAALFAVAFVAAFLI
+WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV
+VGTATGSPWAGLAAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL
+TGGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG
+RSRGPAASGVPYVKE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000472.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000472.fa
new file mode 100644
index 0000000000000000000000000000000000000000..932872635f3addf8768eb7cfe894c96dcddf748b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000472.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00443
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVSGCNIENASY
+GLTLCAECALLAELRMGGGGRLAAFVCVDGAGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP
+>GCF_003691675.1_00164
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVAGCNIENASY
+GLTLCAECALLADLRMGGGGRLAAFVCVDGAGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP
+>GCF_005280335.1_02514
+MAAEGTTTAPGVDWDRLRRAALAATEHAYVPYSGFRVGAAALTEDGRLVTGCNIENASYG
+LTLCAECALLADLRMGGGGRLAAFVCVDGQGVLTMPCGRCRQLLHEFRAPDMVLLTPAGE
+RTMGQVLPDAFGPEDLERAAAR
+>GCF_020097155.1_02385
+MTGTTTPPACAAPVAEADWDRLRAAAADAMERAYAPYSGFRVGAAALTEDGRLVSGCNVE
+NAAYGVALCAECALVGQLHMTGGGRLRAFLCVGGDGRLITPCGRCRQLLWEFRAPGLAVL
+TAAGVTTVEALLPEAFGPDALEA
+>GCF_023573625.1_00446
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVSGCNIENASY
+GLTLCAECALLADLRMGGGGRLAAFVCVDGDGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000475.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000475.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58057f4d6a1cc1eae22841d263d4f7994db9eb93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000475.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00446
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQAGLDEAVEADAAAGHAIRVGQLVTAMRHADRAQEIAELAVRHRAA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD
+>GCF_003691675.1_00167
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQAGLDEAVEAADAAGHVIRVGQLVTAMRHADRAQEIAELAVRHREA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGIVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD
+>GCF_005280335.1_02511
+MTATQLPDTASPSPLEVDLAALPKVSLHDHLDGGLRVGTVLELATEAGVDVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQEGLDEAVDAAEAQGRLIRVGQLVTAMRHADRAQEIAELAVRHRER
+GVVGFDIAGAEAGFPPSRFAETFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEFGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+EAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLAELLDLQLNAAE
+AAFLAVDEREDLAEILVAGWGEVISGDDAGPVLEELDEDDEDEDA
+>GCF_020097155.1_02382
+MTISSQTPADAAPSPLTIDLGALPKVSLHDHLDGGLRVATVLELAREAGVEVPADTVDGL
+ADWFAEHANGESLEKYLETFALTTSVMQTHEQLRRVAREFVEDLVADGVVYGEIRWAPEQ
+HLASGLTLDEAVEAVQEGLDEAVDAADEAGHVIRVGQLVTAMRHADRAQEIAELAVRHRD
+RGVVGFDIAGAEIGFPPSRFADTFTWLAQQHLPVTVHAGEAEGLSSIQDALVSGRALRLG
+HGVRIADDIQVEFGGLDEDGVPVDADTGIVDLGETAAWVRDRQIALEICPSSNLQTGAVD
+AAAGIAGHPIDLLVQLGFRVTVNTDNRLVSNVSLTDELYLLAETFGYSLSELLDLQLNAA
+EAAFLAVDEREDLAEILVSGWGEVISGAGGTVALEELEADTDDEADA
+>GCF_023573625.1_00449
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLTLDEAVEAVQAGLDEAVEAADAAGHVIRVGQLVTAMRHADRAQEIAELAVRHREA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000477.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000477.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40201f2096b5ef876e45960c016f63cda2bfcb40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000477.fa
@@ -0,0 +1,27 @@
+>GCF_002008305.4_00449
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTASPKADAPTPTPEATTPTPAATGAEVIDL
+HSVQERRQAGHHGHLDGHPDADRADTAPAAPASPSAPPRRTAPARPAGRRTRPAPRRAAS
+AAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAAREEI
+ATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETETETDTEAED
+TPAARADEVVNTRLPWAEGLWDSAVRAGLE
+>GCF_003691675.1_00170
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL
+QSIQERRQAGHPDVDRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPRGAASAAA
+TAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAAREEIATM
+QAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATETEDTPAAG
+ADEVVNTRLPWAEGLWDSAVRAGLE
+>GCF_005280335.1_02507
+MAARRRAPLPDPVPARQITGRSLLVVAVLLVAAVLVAPTLRAFLNQQLEIAAAEEEIAAM
+QAQREDYEERIRLWDDPGYVTQQARERLQLVMPGETLYSVTGVPEEAPRDPRPEAPAGEP
+VNTRLPWAEGLWDSAVRAGPRVSPGPRPDPGSGPARP
+>GCF_020097155.1_02379
+MSARRPRVPRVAVPDTAPERATPAVVEPVVVEPAPVAPAAPEAPAPPAPPGPQVIDLQEA
+AQRRRHEATRPSPRPDAERAAAQRVARLREERRRATVREHAAARRRVPLPEPVPARQLTG
+RSLVVLAVLIIAAVLVAPTARLMLNQQLEISAAQQDIAEQQRRKAEYEEQIRRWDDPGYV
+AQQARQRLELVMPGETLYTVTGLPDESGAVPADSVPQEKVNDRLPWVEGLWDSAVRAATE
+>GCF_023573625.1_00452
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL
+QSVQERRQAGHPGHLDGHPDADRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPR
+RAASAAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAA
+REEIATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATET
+EDTPAAGADEVVNTRLPWAEGLWDSAVRAGLE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000479.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000479.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb403d4fcffb90078414559f7fc5f7c1477fa736
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000479.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00451
+MSLTPELSPKPRLLIVGGGYAGFQLAKELQTKVKDRGGVVTVVDPLPYMTYQPFLPEVVG
+GHIVGRNVVVDLATHLKDAEVLRGTVVKVEHARRVATVRGEDGHEFELPYQDIAMTAGAT
+TRVFPIKGLGEHGIGLKTVEEAVTLRNQILERLDAASLMVDAEARRRALTFVVVGGGFAG
+IETVGEMEHLIRTAVARNPRLSQSEVRIVLVEAMGRIMPEVGEDQAVGVVEHLKDRGIEV
+LLNTSLGDATDGIMTLVDMKDKSEKEKFGADTLVWTAGVAANAVAKQTDFPVEERGRIEV
+TPTLQVKDGENGVFEGAWGCGDVCAVPDLTGAGPGGFCVPNAQHAGRQAKQLAANYMAVR
+HGEGEVQEYVHKSLGAVAGLGFFKGVGNPLGVKISGPAAFLAHRGYHAYAMPTLDRRFRI
+LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG
+>GCF_003691675.1_00172
+MSLTPELSPKPRLLIVGGGYAGFHVARELQKKVAERGGVVTVVDPRPYMTYYPFLPEVVG
+GHIEGRHVNVDLQTHLKDAEVVRGAVVSVDHAGRTAVVRGEGGDEFEIPYQDIVMTAGAV
+TRVFPIPGLGEQGIGLRSVEEAVQLRNQILERLDAGSLMTDAEERKRALTFVVVGGGFAG
+IEAIAEMENLIRNAVERNERLSQSEIRIVLVEAMGRIMPEVSEEQAQGVVEHLKDRGIEV
+LLNTSLGDATDGVMKLVAMPSKEEAETFAADTLVWCAGVVANSVVKSTDFPVDDRGRVEA
+TPTLQIKDGEAGALEGAWACGDVSAVPDLTGAGPGGFCVPNAQHAIRQAKRLAANYMAVR
+HGEGEVQEYVHKSLGTVAGLGFGRGVGNPLGTKIAGIPAFLAHRGYHGYAMPTLERKFRI
+LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG
+>GCF_005280335.1_02505
+MSLTPELSPKPRLLIVGGGYAGFHIAKELQKKVKDAGGVVTVVDPLPYMTYQPFLPEVVG
+GHIDGRNVVVDHATHLKDAEVLRGTVVKVEHARRVATVRGEDGHEFEVPYQDVVMTAGAT
+TRVFPIAGLGEHGIGLKTVEEAEALRNQILERLDAASLMVDAEARRRALTFVVVGGGFAG
+VETVGEMEHLIRTAVSRDPRVSQSEVRIALVEAMGRIMPEVSEDQAAGVVEHLKDRGIEV
+LLNTSLGDATDGIMTLVDMKDKSEKEKFGADTLVWTAGVAANSVAKQTDFPVEERGRIEV
+TATLQVKDGQGGVLEGAWGCGDVCAVPDLTGAGPGGFCVPNAQHAGRQAKQLAANYLAVR
+HGEGEVQEYVHKSLGTVAGLGFFKGVGNPLGVKISGPAAFLAHRGYHAYAMPTLDRRFRI
+FAGWVAETLFGRDSTSVEGQDRPFNAFRRAAGVELEPGRFERKRALESSKG
+>GCF_020097155.1_02377
+MSITPDLSPKPRLLVVGGGYAGFHIAQTLQSKVKDRGGVVTVVDPRPYMTYQPFLPEVVG
+GHIEGRHVIVDLQTHLKDTEVVRGAVTKVEHARKVAVVRGEDGAEFEVPYQDIVMTAGAN
+TRVFPIPGLAEQGIGLKTVEEAVALRNQILERLDAAALMTDAEQRRAALTFVVVGGGFAG
+IEAIAEMENLIRTAVSRNENLSQTEVRIVLVEAMGRIMPEVSEDQAQAVVAHLKGRGIEV
+LLNTSLGDATGGVMKLVNMADKSEADSFRADTLVWTAGVAANGVAKQTDFPVEDRGRIEV
+TPTLQIKDGEGVLEGAWACGDVAAVPDLTGAGPGGFCVPNAQHAGRQAAQLAKNYMAVRH
+GEGEVQEYVHKSLGAVAGLGFLKGVGNPMGVKLFGVPAFLAHRGYHAYAMPTLERRFRIV
+SGWIAETLFGRDSTSVDGQETPFNAFRVAAGAEPVPSTLEKKRAGELAAK
+>GCF_023573625.1_00454
+MSLTPELSPKPRLLIVGGGYAGFHVARELQKKVAERGGVVTVVDPRPYMTYYPFLPEVVG
+GHIEGRHVNVDLQTHLKDAEVVRGAVVSVDHAGRTAVVRGEGGDEFEIPYQDIVMTAGAV
+TRVFPIPGLGEQGIGLRSVEEAVQLRNQILERLDAGSLMTDAEERKRALTFVVVGGGFAG
+IEAIAEMENLIRNAVERNERLSQSEIRIVLVEAMGRIMPEVSEEQAQGVVGHLKDRGIEV
+LLNTSLGDATDGVMKLVAMPSKEEAETFAADTLVWCAGVVANSVVKSTDFPVDDRGRVEA
+TPTLQIKDGEAGALEGAWACGDVSAVPDLTGAGPGGFCVPNAQHAIRQAKRLAANYMAVR
+HGEGEVQEYVHKSLGTVAGLGFGRGVGNPLGTKIAGIPAFLAHRGYHGYAMPTLERKFRI
+LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000482.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000482.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ddc336261d4018264a9fe4e048014b2bedc2820b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000482.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00458
+MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAELGDQLGQAVDD
+AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVSLGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE
+RTGHALEPGGAEDETAGSHRYRPSAHDDAALASEADAGTRHGDDA
+>GCF_003691675.1_00176
+MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAQLGDQLGQAVDD
+TIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVTFGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE
+RTGHALEPGGAEDEAAGSHRYRPSAHDDAALASEADAGTRHGDDA
+>GCF_005280335.1_02489
+MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVLVGLGILWWLLSFVSLVLIPVLVAALLA
+TLLAPLFEGMRRIGIPGIAASLLCVVLLIVVVVGLVVVAGQQIAQGFSDLGDKLTQAVDG
+AIAWLASIGVELPTAGGGLEGLWQTLRDNSGTLLDSAMTFGSTAVNIGAGFFIALFSLIF
+FLYDGDRIWRFILVFVPKAHRATVGRAGQTGWRALGNYVRVQIFVAFVDAVGIGLGALIL
+GVPLAIPLAVLVFLASFIPMIGATVTGAIAVLFALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSAVLGLAGAVFAVPVLAFVNSFIRALTADPPEQLTD
+RSDQALAPGSAADEAVGSHVFEPTKHDDAALASEDDAGTSGDLR
+>GCF_020097155.1_02373
+MSSTLSTDAKLEKDIPYGLTVAAGWSWRVIAVAAMLWVVWHFAGFASLVIIPVLVAALLA
+VLLAPIYRALRRARIPGVLAAVLSIVLLLAAVVLLAWVAGLELVQGFSDLSDQLGASVEH
+LVTWVQGMGVPVSFDAAALDNVWSTVKDNSGVLVDGALAFGSTAANVLTGLFIALFTLIF
+FLFDGERIWRFLLAFVPHTSRSRVDVAGRTGWNALGSFVRVQIVVAFIDAVGIGLGAWLL
+GVPLALPVAVIVFLFSFVPTIGAIASGALACVLALTANGLVNALLMLGVVILVQQIESNL
+LQPLIMGRAVSLHPLAVFLGVAAGGVALGLVGAVFAVPLLAFANAFVQALRAKGPGEEIL
+PGEKVFRPSDEVIAAARRDAKLDPKLDPTSFDDDSGPDGDVEDGRTGSTRTELKP
+>GCF_023573625.1_00458
+MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGIAAALLCVLLLVVVVVGLMGLAGQQIVQGVAQLGDQLGQAVDD
+AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATLMNSAVSFGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE
+RTDHALEPGGAEDEAAGSHRYRPSTHEDAALASEADAGTRHGDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000484.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000484.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c05d9227d0c0372355967a34438bf22ebb2b058
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000484.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00460
+MLTVEKAHLLLTREDGRSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLGQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGRLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPCDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+TLTREDLLVQAVRRAVGGTCGTVTAAAAGSVA
+>GCF_003691675.1_00178
+MLTVEKAHLLLTREDGLSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLAQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGCLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPSDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+ALTREDLLVQAVRRAVGGTCGTVTAAAAGSAA
+>GCF_005280335.1_02487
+MLTAEKTHLLLTREDGRSESPSHHGVALAAAALADYRAAGIVTVEDAPVDRARVLVTAAG
+VTGHPVLDARLGKVDALAGTPVTAAVAAGRPNLRKAVIARLTETGDLAEHKAFMATRHLP
+RGGTRAELLDRLTAVVLDEREATDEDVLLLGVLQHLNLAWRLLPGTHERYGRRELVRRVE
+SLTRSDLLVQAVRRAVGGTAAAVTAAAAGSLA
+>GCF_020097155.1_02371
+MLTSEKLHLLLTREDGRSLSPSHHGVALAAAVLADLRDAGIVSLEDAPVSRARVLVTGAG
+STDHPVLDALLPELDGLRGKKVAAVVGKGRPKARKPVVAHLVETGELVEHKALLNTRHTP
+VGPGRPALVAGLTSALDGDSPSDEDRLLLGVLHQLNVLRRVLPEAGAEGESRREQSRRLE
+RLTHDDLLVQAVGRTVSTAAAAAAAAG
+>GCF_023573625.1_00460
+MLTVEKAHLLLTREDGLSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLGQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGRLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPSDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+ALTREDLLVQAVRRAVGGTSGTVTAAAAGSAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000485.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000485.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41a1afc8dd99c97a24bf7c0fb3ed9181d7ffabb9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000485.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00461
+MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
+>GCF_003691675.1_00179
+MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
+>GCF_005280335.1_02486
+MTTSQSDAPWLTQEAFDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAEDDEHL
+EVYSERSPLGEAINGAAKGDKVTYTAPNGKEIKVEIKDVKPYSG
+>GCF_020097155.1_02370
+MATTPSDAPWLTQEAFDRLSKELAHISGPGRQEIIERIEAAREEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGETQAADGVVTPGTVVTAVVAGDEMTFLFGNREIAADGEDL
+EVYSERSPMGEAINGAKQGDKVTYTAPNGKDIAVEITDVKPYQA
+>GCF_023573625.1_00461
+MTTSQSDAPWLTQEAYDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000487.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000487.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9aafeb1223274f2f5eaecc84072618defbaae1e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000487.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00464
+MTPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL
+RVMVRSVRRVQQRSPQAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ
+EPAPEPQAPDTGRD
+>GCF_003691675.1_00182
+MTPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL
+RVMVRSVRRVQQRSPEAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ
+APAPEPQAPDTGRD
+>GCF_005280335.1_02483
+MSPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL
+RVMVRSVRRVQQRSPEAEAMLVDRHQQHLPEDVRELAPEDEERDAQDRLRHLQEKYPGYL
+QEPAPRPQSPDDGRS
+>GCF_020097155.1_02367
+MSLAPLALSAVSLAASVSPSAPMPAVPEPTLKPGLDKQDISPGIEGFLFTALMVVMAIIV
+FRLMVRSVRRVQQRSPEAEAMLVDRHQQHLPEEVREGGERLDGDAHDRIERLRRRYPGYL
+QDPTPEPESPDTGREPR
+>GCF_023573625.1_00464
+MTPLSGLPLVLNALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVF
+RVMVRSVRRVQQRSPQAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ
+EPAPEPQAPDTGRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000488.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000488.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ce11687739a08c1b6ff8c9edb336ab731c527f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000488.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_00465
+MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL
+RWASAVYAVTGLLLFAVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP
+DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL
+IVAGGVAYITGAVCYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVA
+>GCF_003691675.1_00183
+MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL
+RWASAVYAVTGLLLFAVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP
+DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL
+IVAGGVAYITGAVCYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVT
+>GCF_005280335.1_02482
+MDPLTPAREPEAARRLRWRIERIRDPEHPLFKPRLRGWIHAAMAPLTLAAGIVLIVLAPT
+ATLRWASAVYAVTGLLLFGVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLAL
+LPPGKAHLLLTLVWAGAVAGVAFRLLWTDAPRWLYTPVYVVLGLAALLYIGDFFAADVAA
+GWLIVAGGAAYIVGAVFYALRAPTIHREWFGFHELFHVFTVGGFVCHAVAIYRAVLVVA
+>GCF_020097155.1_02366
+MWEHGGMVTRAPSVENRTGRPLKWRIERIRDPEHPLYKPRLRGWVHAVMAPLVLVAGIVL
+IVLAPGATLTWACVVYVVTGLLLFGVSATYHLVQWNETVSRVLKRLDHTNIMLVIAGTYT
+PLSLAMLPADKAWTLVTAVWVGAALGVAFRLLWTDAPRWLYTPVYVALGLAAVVYLGDFF
+AASVPAAVLICAGGAAYIVGAVFYALKAPTIHREWFGFHELFHVFTVGGFVCHYIAVMMA
+VLAA
+>GCF_023573625.1_00465
+MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL
+RWASAVYAVTGLLLFGVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP
+DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL
+IVAGGVAYITGAVFYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000492.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000492.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f416547037b4e734446ea2b2a1bc025c78c03af3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000492.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00469
+MSGVGWAWTHGAPATAVLWSLGLVWFAVCAGVLVRTDLREHRLPNRWTLRLALGGLTMMT
+GGALLAGRGDLTLCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA
+>GCF_003691675.1_00187
+MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT
+GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA
+>GCF_005280335.1_02478
+MDGVGWAWAQGLPATAVLWSAGLAWFAVCAAVLVRVDLREHRLPNRWTLRLALGGLAAMA
+GGAALAGRADLVLSSVLGGLGYAAAMLVLHVLSRGSLGMGDVKLAAGLGAYTGVLGGSAV
+VAAGLGAILLGGAVAAVLVAARRASRSTALPFGPPMILAAAAVLAFAPAGG
+>GCF_020097155.1_02362
+MTWWTGAWEAGERLTAMLWAAGLVWFLLCSVVLARTDLREHRLPNRWTGRLALGGVVAMG
+GGAVLGGLWSVVASCLLGGLGYALAMLALHVLTRGGLGLGDVKLAAGLGLYCGVAGLAAV
+LAAAVLAVLLGGVVAVVLVLARRADRHTALPFGPAMVAGALGVLLLA
+>GCF_023573625.1_00469
+MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT
+GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000493.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000493.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b09e1b241a5a0541c19f344234700bfc7c5ad43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000493.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00470
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
+>GCF_003691675.1_00188
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
+>GCF_005280335.1_02477
+MTAQNPEQQFRIEHDTMGEVKVPIDALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGVISQERADAIVAAADQVIAGEHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKDAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTGALINELIPALDHLAVSLEKKE
+KAFANIVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERVESSLPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNVAYSIMKINNDL
+RWMGSGPNTGLGEIFIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVSLSSTNGA
+FELNVGIPVMAANLLESIRLLANTSRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDTALDTMSMTHPE
+>GCF_020097155.1_02361
+MTAQNTEQQFRIEHDTMGEVKVPVDALYRAQTQRAVENFPISGKTLEPAHIHALAQIKKA
+AAKANAELGVISQERADAIVAAADEVISGKHDGEYPIDVFQTGSGTSSNMNTNEVLATLA
+TRRLKDAGSSEEVHPNDHVNASQSSNDVFPTSVHVAVTGALVNDLKPALEHLAESLERKA
+EEFQGIVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIEASLPRVAEVPLGGTAVGTG
+INTPQGFSARVIELLAEETGLPITEARNHFEAQANRDGLVEASGQLRNIAYSFIKINNDL
+RWMGSGPNTGLGEIALPDLQPGSSIMPGKVNPVICEAAIMVAAQVIGNDTTISLSSTNGA
+FELNVGIPVMAANLLESIRLLANTSRVMADKMIDGIEANEERCTFLAGASPSIVTPLNKV
+IGYEAAAAIAKHAVKNKMTVREAVVDLGYVERGEVTEEQLDKALDTMSMTHPGE
+>GCF_023573625.1_00470
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000494.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f813ccd33c9025c728682d15863dee40d2e5a47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000494.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00471
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLAEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
+>GCF_003691675.1_00189
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLAEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
+>GCF_005280335.1_02476
+MSTENTATAAAAAHDDGAAGSRPTPQEAWETLAEGNRRFVAGDPGHPNQNAERRSTLTSG
+QEPIAVIFGCSDSRLAAEIIFDVGLGDVFVIRTAGQVIDDAVLGSLEYSVDVLKIPLIVV
+LGHDSCGAVTATVESYISGDMPPGFIRSLVERITPSVLAGRRRGLEEIDDFVAEHVDQTC
+DRLVETSQAVRDAVEAGRTAVVGLTYSLAGGTAQPGRVLGALQV
+>GCF_020097155.1_02360
+MTTAAETTPARPTPAEAWRTLQEGNRRFVAGTPGHPNQDSERRHGLTEGQAPIAVIFGCA
+DSRLAAEIIFDVGLGDVFVVRTAGHVVDDAVLGSLEYAVDSLDVPLIIVLGHDSCGAVTA
+TVESYISGTMPAGFVRSLVERITPSVLAGRRRGLEEVDDFVAEHVDQTCDRLLETSQSVR
+AAVEAGRTAVVGLTYSLAEGTASPGRVHGRIEA
+>GCF_023573625.1_00471
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLVEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000495.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000495.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81505e180324066e5f9786dc0743200e25bbb91a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000495.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00472
+MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE
+DRVDVAAEAATIPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL
+QQAEDVDPTWVSLRVDQVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD
+QAVLEDLAHGVAKETR
+>GCF_003691675.1_00190
+MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE
+DRVDVAAEAATIPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL
+QQAEDVDPTWVSLRVDQVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD
+QAVLEDLAHGVAKETR
+>GCF_005280335.1_02475
+MLTVSSTHPTDPTDPNAPAPRPVLTAKQAQRARQPWIGMVLSVVALLALVAVVLILNPEP
+PQRPREDRVDVAAAAATVPHDDGVLPALAPEVPESWYANFARLQTMDGVSTWDVGWVVTD
+TVFAGMQQAHDVDPTWVTLRVDSVPATETLEIDGLAWDLHADPRAPEKRLVTEVEDTTVV
+LTTTGDRAVLEDLARGVAKETR
+>GCF_020097155.1_02359
+MPGMSSPDPAAPPAPRPVLTPKQAQRARAPWIAMVLSTLAVLGIVLVALMVNQPPPAPAQ
+ADRVDVAAAASTVPHDDGALPALAPDVPEPWDSTYARVERLQGVDTWDVGWAVNDAVFAG
+LKQTSRADPTWLALRVGSAPAVGTVDVDGITWDHYAPQDSKDQHLVAEVRGSTLVLTTSG
+DQAVLEDLARAVAKEIR
+>GCF_023573625.1_00472
+MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE
+DRVDVAAEAATVPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL
+QQAEDVDPTWVSLRVDHVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD
+RAVLEDLAHGVAKETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000496.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000496.fa
new file mode 100644
index 0000000000000000000000000000000000000000..890aaf14929433c562e9814948dcdc82250b349c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000496.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00473
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR
+>GCF_003691675.1_00191
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR
+>GCF_005280335.1_02474
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVSMAGTVVIGEGEKDEAPMLFNGEEVGDGSGAPVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDLRLPVKQNVALVAKALDKPASQVTVCVLDR
+PRHEGLVKEIREAGARVKFILDGDVAAAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGVIQGRLAPTDETEKQKALDAGLDLDAVLSTNDLVTSDHCYFAATGITDGDLLRGVRFV
+DGRVVTQSIVMRSWSGTVRTVDAEHDVRKWSKWLEDRGTRTGR
+>GCF_020097155.1_02358
+MTSASSENTGYENHVPDRNLAMELVRVTEAAAIAASPWVGGGDKNRADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGERVGDGKGASVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRAAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGVIQGRLAPTDDAEKQKALDAGLDLDAVLTTDELVTSDHCYFAATGITDGDLLRGVRFA
+GGRVHTQSIVMRSKSGTVRTVDAEHHVDKWSQWLKNRG
+>GCF_023573625.1_00473
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDADHDVKKWSKWLEDRDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000497.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000497.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8202cc5c4f0838c3f6c518fd9d1898ecce57d77c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000497.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00474
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGARVGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPQ
+RNYKDANHKPEMLLALTPFAAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHMDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTASLALAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
+>GCF_003691675.1_00192
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGAHIGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPE
+RNYKDANHKPEMLLALTPFSAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTARLVLAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
+>GCF_005280335.1_02473
+MHVLKPVIRDYAWGSPTLLARLQGREPTGRPEAEIWLGDHPGAPCGVVVGDGSVTGLDEL
+TAADRERCLGPNVDTDRLPYLAKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPH
+RNYKDANHKPEMLVALTHFSAMCGFRSPEVSSDSFEALAHALTEHADGDTSAVAVAAARI
+SQTLAAGDLEDAFTAILDPESVWAAPGSVAQVVEVLRAAEDLAERDPSLATALEVAEHYP
+DDPGVIVAILLNRVDLAPGQALHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTAKHVDVE
+ELRRVVTFEAVPVPSTEPERVADSVVAFRPPFDEFELLQATLEDDAVRELDVHGPGIAVV
+TRGSAHLGLAGQEVTLGPGESVFLPAAETATGPLAVRAADGAPATVHVTDLPRR
+>GCF_020097155.1_02357
+MHLLEAVVRDYAWGSPTLLAELEGREPSGAPEAEKWLGAHPGAPCTVSGPEGRCGLDELI
+AADPAPMLGEAARFGRLPYLMKLLAAGRPLSIQAHPTRERARAGFAAEEAAGVPVDAPHR
+NYKDDNHKPEMIVALTPFSALCGFRRPEDAAATFERMADALAEWADGDATDVGIAARRIA
+AHLAAEDVEAAFADILDPDAVWSAGGVDRLIEAVRAQPDLVAHDPALATALEVAEQCPGD
+PGVLVTLLLNRVDLVPGQAVHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVPEL
+RRVVAFAPLPVPYTDPVEDGAGVVRYRPPFEEFELTRLAADAGGPSAEARVAGPAIAVAV
+DGPAVLACGADAVRLEAGAAVFLPAEETAAAPLTLSPATDDAPARVFVAALPTA
+>GCF_023573625.1_00474
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGARVGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPQ
+RNYKDANHKPEMLLALTPFAAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTASLALAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000498.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000498.fa
new file mode 100644
index 0000000000000000000000000000000000000000..057e21fbeb09d67db8b041462d5a0648ef0506bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000498.fa
@@ -0,0 +1,52 @@
+>GCF_002008305.4_00475
+MSSATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLI
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGQQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESVTAGSEPTGVSATPLLTVLAVVAQE
+TQTPDVDEDDPATWPAPPTRTDGEPFTAEDLMTAEDLGQEDVLNHASSTNGLCVPAP
+>GCF_003691675.1_00193
+MSPATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLM
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGEQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESATAGSEPTGVSATPLLTVLAVVAQE
+TEAPDVDEDDPATWPAPPTRSDGEPFTAEDLMTAEDLGQEGVLNHASSTNGLCVPAP
+>GCF_005280335.1_02471
+MSPATGSVPAGHAQPDPLRDPRVASPTERTRRALILTLLTLFVPGGAQVVAGSRPLGRAA
+LRVTVAVWGVLLAGLLWWLVHRASLISLLARDGVLLVLAIALGLLAVGWAVLWIDTLRLI
+RLHLLAPGARKATAVATVLALVLTSGALLYGGWATNAGRGALGSVFGDGPAVARTEGRYN
+ILVMGGDAGEGREGLRPDSIHVASVDARSGAVVMFSLPRNLQNAPFTEGSPLWGVYPDGF
+SCGDECILNALYTDVETNHPDLYPDAENPGAEAMMDAAGGILGLEISGYALMDMGGFAQL
+IDAMGGVDLVTGGYVVHRGVRPDGEWGNIWWEPGEHHFDGKDALAFARSRHWSTDYARIR
+RQQCMQAAMLAQFSPGTVLTRFEQILDAGQQIVTTSLPQSQLGTFVDLAERSRGQKMRRL
+TIGPPDFGDTRDQFTTFPDYDLVHERVDEMLAEEPGQAGGATGGEAGHAAGVGSGASALP
+LLTVLAVAAQEAVPDEVDEDDPATWPAPPTRPDGGAYTAEDLMLAEDLGQEDLLNHASST
+NGLCAPGR
+>GCF_020097155.1_02356
+MPASAASSPVLTRDPVRDPRQATGPERRRRAGILLLLTLLVPGGAQAVAGSRRWGRIALR
+VTLAVWAAVLLALVLALTARAALVSVLANPVVLVLLGVVLVTLAIGWGLLWVDTFRLIRV
+HLLGPRARAATAAATVVALVVTSGGLGYTAWMTQSGRGALGSIFGSGPAIEAADGRYNIL
+VMGGDAGEDRVGLRPDSMHVASVDAETGAVTLFSLPRNLQNAPFTPDSPLWQAYPNGFDC
+GDDCILNALYMDVEEKHKDLYPDAEHPGAEAMMDAAGGVLGLEITGYAMMDMAGFAQLVD
+AMGGVDVVSGGYVTHRGARPDGTWGDIWWEPGTHHFGGDDALAFARSRKFATDYARIRRQ
+QCMQAAMLQQFTPATVLTRFEGIVSAGTQIVTTNVPQSQLGTFVDLADRSRGYRMARLTI
+GAPDFGTANDRFTTRPDYDLVHRRVAELLDEEPTKAGSASTAAPAASPGATPLLALTAAI
+PAPLLVAEASPAATGTGGTTRPGVDPDDPSTWPSAPTGPNGEPYSAMELMRIQDAGDEAQ
+LVRIASTNDLCAPGG
+>GCF_023573625.1_00475
+MSSATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLI
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGQQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESVTAGSEPTGVSATPLLTVLAVVAQE
+TQTPDVDEDDPATWPAPPTRTDGEPFTAEDLMTAEDLGQEDVLNHASSTNGLCVPAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000499.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000499.fa
new file mode 100644
index 0000000000000000000000000000000000000000..819c3a5f6d4aa16f5a021cce694cabe89f08c6bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000499.fa
@@ -0,0 +1,43 @@
+>GCF_002008305.4_00477
+MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG
+WPMILKTARGGYDGKGVLKLDDADDARASAADGTLAAWLGAGITPLLAEALVPFSRELSA
+QVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG
+VVMKNVLGGAREDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV
+RTAESAAALLRDDAPTTGTETEARP
+>GCF_003691675.1_00195
+MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG
+WPMILKTARGGYDGKGVLTLDDADDARASAADGTLAAWLGAGIAPLLAEALVPFSRELSA
+QVARTPSGEVAVYPIVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG
+VVMKNVLGGAREDLHAGSVVALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV
+RTAESAAALLRDDAPTTGTETEARP
+>GCF_005280335.1_02470
+MMAGPAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRVLQEVGVAVRPGPEALQHAQDKLVMRAAVERLGLPNPAWAAVRDLDEVLAFGDEHG
+WPMILKTPRGGYDGKGVLKLDDADDARASASDGTLGTWLGAGIAPLLAEALVPFTRELSA
+QVARTPSGRVAAYPVVDSVQVAGVCDLVVAPARDLDPAVAEAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQINELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGDTAPRGAG
+VVMKNLLGGAREDLHAGLADALAAHPQAKVHLYGKAVRPGRKVGHVNVVADHGLTLEQAV
+RAAESAAAVLRDGAAPDAVDASPSSPATPHPAGGPPMTATPQNPAQPLQDDAPVVSVVMG
+SDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEMVEFGARAHERGIRVIVAGAGGAAH
+LPGMLASVTPLPVIGVPVKLKSLDGLDSLLSIVQMPAGVPVATVSVDGARNAGLLAARIL
+ASADTEEGERLRAALTEHAAELNAQAQAKGARLRERMAADR
+>GCF_020097155.1_02354
+MIGGGQLARMMAGPAAELGVPFRVLAEAPDASAAQVAPHMVGDHASLEDLRAFAATVDVV
+TFDHEHVPTEHLRTLEAAGVAVRPGPDALQYAQDKLLMRGLVERLGLPNPAWAPVSSLEE
+VIAFGDEHGWPMILKTARGGYDGKGVLKVDSADDARSGAADGTLGTWLGAGIAPLLAEAM
+VPFARELSAQVARRPSGEVAAYPVVASLQTQGVCDVVTAPAPDLAPAVAEAASGAAVRIA
+EELDVTGMLAVELFETPGTDAGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDMPL
+GGTAPRGDGTVMKNVLGGAHEDLHSGFSEALAAHPEAKVHVYGKGVRPGRKVGHVNVVAE
+HGLSLADAERIAESTAAVLRDATAPSAPTPKA
+>GCF_023573625.1_00477
+MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG
+WPMILKTARGGYDGKGVLKLDDADDARASAADGTLAAWLGAGITPLLAEALVPFSRELSA
+QVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG
+VVMKNVLGGAREDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV
+RTAESAAALLRDDAPTTGTETEARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000504.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000504.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66833233160b516c7898fe4b3869a4a100373b64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000504.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_00482
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD
+>GCF_003691675.1_00200
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD
+>GCF_005280335.1_02465
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRLAEPHTYDLCAEHARRTTAPRGWEVLR
+LELPGHYEAVAPDGTVHTVPTAPRAVPAAPPADVASRPSLAAPRPAPAVPPVDADEPEAP
+APPTRPGLRLVRDDDPLPPA
+>GCF_020097155.1_02349
+MRRCSKTGCQEPAEATLTYNYAGSQVVIGPLAQRAEPHAYDLCAAHAARTTAPRGWEVLR
+LAPAAPAAPGVAAPTHPALRLVTDPVEGTAG
+>GCF_023573625.1_00482
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000505.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000505.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f0f33c8fb79e1d8cf6f70ab5c8db4c3cf5521f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000505.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00483
+MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE
+EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG
+TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH
+MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLGGGTEAERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY
+>GCF_003691675.1_00201
+MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE
+EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG
+TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH
+MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDGGTEAERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPFKADHYRY
+>GCF_005280335.1_02464
+MTETPAESRTPDVDPAYANRATVPGAAFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE
+EYGESQPLAGARIAGSLHMTVQTAVLIETLTALGAEVRWASCNIFSTQDEAAAAVVVGSG
+TPEDPQGVPVFAWKNETLEDYWWTASQILTWPGAAEDPERGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLAEDPQRWTRTASTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGQGDLFVTTTGGKDIIMAEH
+MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDAGTDSERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKSQAEYLGVDVAGPYKADHYRY
+>GCF_020097155.1_02348
+MTETSSARPTPDVDPAFANRSTVPGATFDFAVRDLSLAEAGRHQIRLAEHEMPGLMALRE
+EYGESQPLKGARIAGSLHMTVQTAVLIETLTALGAEVRWASCNIFSTQDEAAAAIVVGSG
+TPDAPAGVPVFAWKGESLEEYWWTASQILTWPGAAEDPDRGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLAEDPQRWTRTASTLRGVSEETTTGVLRLYQ
+LAQEGTLLFPAINVNDSVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVEQGDLFVTTTGGKDIIMAED
+MLRMKDKAIVGNVGHFDNEIDMAGLGRVDGVVKTEIKPQVHEWTFDTGTEDERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELYDGSTGQGALTGEHYEKQVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY
+>GCF_023573625.1_00483
+MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE
+EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG
+TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH
+MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDGGTEAERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000506.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000506.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e172bf5d027e3978dd629dff0297f46d23c0be2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000506.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00484
+MASHQAGRGRDERAGAEDFDSGLDYGAFVEDDAADDPNRTQALPAMGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDAGRPAADADRDIVASRAVPEGGRRPLPGADELGPLSAAVG
+ARAAGSSAAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAILAPLA
+LVLATVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIAAAALVVLLVVCALLIASLLRTSPGGVRRALFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVRDALIRLYPQQFWVDAAVVVGL
+VTLLASLVTLVLTWPTRRRRELSADRREQLLRTRLRWAREDDAVVR
+>GCF_003691675.1_00202
+MASHQAGRGRDERAGAEDFESGLDYGAFVQDDAADDPNRTQALPATGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDADRPAPDADRDIVASRAVPESDRRPLPGADELGPLSAAVG
+ARAAGSSAAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAILAPLA
+LLLAAVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIATAALVVLVVVCALLIASLLRTSPGGVRRALFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVQDALIRLYPSQFWIDAAAAVGL
+ISLLTALLTLVFTWPTRRRRERTADQRSAFESTRLRWAREEDAQLR
+>GCF_005280335.1_02463
+MASHQAGRGREERAGAEDFESGLDYGAFAEDDAAEDPNRTQALPASGRDDAGVQHTSALS
+PEDLAALRGGDAAAADGRAERSAERGMPDARERDIVASRAVPSSDRRPLPGADELGPLSA
+AVGARSASGSSAADPADRYPQDASAAYAASSSAALQGPTPEERARLPKAGPRVAQVLLAI
+LAPLALLLAAVRFVASPAFLWLEYHRPGFPADRFGFDTGDRMHYGSAGLDYVTNLAGSRY
+LSSLTHQGEPLFTEAEVSHMTDVKVVLWIALAVLVALVVVCALLIAHLLRTSPGGVRRAL
+FAGALWLPLALIALAVLAVLGWEIFFAGFHSLFFADGTWTFSVRDALIRLYPEQFWVDAA
+LVVAAIAVIASLVTLVFTWPTRRRREMSADRRGQLLDTRLRWAREEDSPVR
+>GCF_020097155.1_02347
+MASHTPGRSDGAGSGSSDFESGLDYGAFVEDDDAQPTQALPRTTEEHGAQRTLAFDRDEL
+AAAAAGAGTGAGRSGAGSRAAGAAHGVAGEDITASRPAPAPAPSPASPWGADRYPSDATV
+PASAPAAADTRTPEERARLPKAGPRLAQVLLAVLAPLVLLLGAVRLVATPLFLWLEYHRP
+GFPADPYGFSTADRMTYGSAGLDYLHNLAGPRYLSELTFQGKPLLSEAAVSHMTDVKTVM
+WIATAVLVLLGLACLLLALYLRRTSPGGVRRALFAGALGLLVVIVVLAAMAATGWQGFFA
+GFHSLFFAEGTWTFSVSDPLIRLYPAQFWVDAAVAVAVLALIGIIAALVAGAPTRRRREM
+SQDRRAQLEATRLRWAREDAHGVR
+>GCF_023573625.1_00484
+MASHQAGRGRDERAGAEDFESGLDYGAFVQDDAADDPNRTQALPAMGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDAGRPAADADRDIVASRAVPEGDRRPLPGADELGPLSAAVG
+ARTAGSSTAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAVLAPLA
+LLLAAVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIATAALVVLVVVCALLIASLLRTSPGGVRRGLFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVRDALIRLYPQQFWVDAAVVVGL
+VTLLASLVTLVLTWPTRRRRELSADHREQLLRTRLRWAREDDAVVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000509.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000509.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4167d7e8933cd02d2701166e67598c74846d8c34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000509.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00487
+MPEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHH
+EHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVT
+TALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLADALAVVAEVL
+GAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEAS
+EADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG
+>GCF_003691675.1_00207
+MTGRIVLAATPIGNLGDASARLRELMAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHHE
+HNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVTT
+ALALSGLPTDRFAFDGFVPRKDGDRRRWLTSLLTEARTVVAFESPQRLADALAVVVEVLG
+AERPVCVARELTKLHEEVVRGTAADVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEASE
+ADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARS
+>GCF_005280335.1_02459
+MTPRPTDLPSPSGRIVLAATPIGNLGDASARLRELLAEADVIAAEDTRTARRLCQGLGVT
+PAGRVVAHHEHNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVT
+CAPGPSAVTTALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLAD
+ALAVVVEVLGAERPVCVARELTKLHEEVVRGTAAEVHAWAAERHAGEGIRGEIVLVIGPA
+SPDAASAGGATEADAVAEVGVLVDSGTRLKEAVATVAAAHGLRSRTLYQAVLAARG
+>GCF_020097155.1_02343
+MSLPAASGRIVLAATPLGNLGDATGRLRELLATADVIAAEDTRNTRRLCQGLGITPAGRL
+MAHHEHNEAASAAGLLERVRAGETVVMVSDAGMPTVSDPGFRLVEAAVAAGLPVTCAPGA
+SAVTTALALSGLPSDRFAFDGFLPRKDGERRRRLEEIRTDPRTVVYFESPQRTASALAVI
+AEVLGGARPVCVARELTKLHEEVVRGTADELVAWAVEREAGEGIRGEVAIVVGPAAPDAG
+AGADEADVLAEVAALTDSGTRLKEAVAAVAAAHGLRSRELYQAVLDARRG
+>GCF_023573625.1_00487
+MPEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHH
+EHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVT
+TALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLADALAVVVEVL
+GAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEAS
+EADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000512.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000512.fa
new file mode 100644
index 0000000000000000000000000000000000000000..858c36075cd975d98376fb9f01b4caba93375174
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000512.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00492
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPTGGASRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEVSA
+>GCF_003691675.1_00213
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPAGSTSRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEEVVA
+>GCF_005280335.1_02455
+MIDPNTIRRIVQAAGVGPDEHVLEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAERLPHTV
+QEFRPASADALAVLHADALRMTAADLDAVRPAAAPGGPTALVANLPYNVAVPVLLHALAE
+LPGLRHGLVMVQEEVADRLAAGPGSRVYGVPSAKAAWYAQVDKAGTIGTQVFWPAPRIHS
+GLVAFTRREPPTSAVSRAETFAVVDGAFAQRRKTLRAALAGWAGSPQAAEDALVAAGVDP
+RTRGEALGIEAFARIAEHGPRRAAGEGSA
+>GCF_020097155.1_02339
+MVPPPDAPATAPLLSAADVRRLAAELDLRPTKQWGQNFVIDPNTIRRIVAAADLAPDEHV
+LEIGPGLGSLSLGLLDAASAVTAVEIDPVTAARLPATAAEFRPERAADLAVLHADAMTLT
+AEGLDSVRPAGAASGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSRVYGVPSAKAAWYADVRKAGVIGTQVFWPAPRIHSGLVAFTRREPPTQAVDRREVFA
+VVDAAFAQRRKTLRAALATWAGSPALAEEALVAAGVDPKARGEALDIAAFARIAEHRPEA
+AS
+>GCF_023573625.1_00491
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPAGGASRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEEVVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000515.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000515.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20f3d0f34d12ed05b3f0d3f53944bf7860f2eb07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000515.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00497
+MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLSPEHLVAVVRH
+ERARVAEHIETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL
+LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEAT
+GDDSFVAIREVNSGIYAFDAALLRRTLPEISTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL
+GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVNKHRTVIG
+AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTLEGWVPAKRPGTS
+SAEAARAAGAEGSGAQG
+>GCF_003691675.1_00218
+MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLAPEHLVAVVRH
+ERARVADHLETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL
+LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEST
+GDDSFVAIREVNSGIYAFDAALLRRTLPEISTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL
+GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVAKHRTVIG
+AHVRTGSNTVFTAPVSVGDGAYTGAGAVVRDDVPAGALALNAVAQRTIEGWVPAKRPGST
+SAQAARAAGAEGSGAQG
+>GCF_005280335.1_02450
+MPQSSVRPSAVIVLAAGQGTRMKSTTPKIMHPIGGRSLVGHALAAAHSLAPEHLVAVVRY
+ERDRVAEHIESVAEGLGIASLAIADQDEVPGTGRAVELGLAALPKDLEGTVVVTYGDVPL
+LTPETLERLVAAHEADGNAVTVLTAALEDATGYGRIVRDGEGLVERIMEHKDALAHAEST
+GDSSFVEIREVNSGIYAFDAALLRRTLPAISTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRRLNDRVLRHWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATQVATGAVVGPDTTLTDTRVGERAVVKRTDATEAVIGADATVGPFTYLRPGTVL
+GEEGKIGAFYETKKVTIGRGAKLSHLGYAGDAEIGDYTNIGCGNITANYDGEKKHRTVIG
+AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTIEGWVPAKRPGTS
+SAQAAQAADAQGDAPQG
+>GCF_020097155.1_02334
+MPQTAVRPSAVIVLAAGQGTRMKSATPKIMHAIGGRSLVGHALAAAQSLAPEHLVTVVRH
+ERDRVAAHIEEAAADLGVTGLAIADQDEVPGTGRAVELGLAALPEDLEGTVVVTYGDVPL
+LTPETLQRLVAAHEADGNAVTVLTATLADATGYGRIVRDADGLVERIMEHKDALAHAEAT
+GDSSYVEIAEVNSGIYAFDAALLRRTLPQLSTENVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNERVLRRWMKDGVTVVDPSSTWVDVTVELAADVTLKPG
+TQLHGSTTVATGAVVGPDSTLVDTRVGERGTVKRTDATEAVIGDDATVGPFTYLRPGTVL
+GEEGKIGAFYETKKVTIGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVDKHRTVIG
+SHVRTGSNTVFIAPVTVGDGAYTGAAATVRQDVPAGALALNAVDQRNVDGWVVSRRAGTA
+SAEAAQAAGAVGRDQATEAAQD
+>GCF_023573625.1_00496
+MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLAPEHLVAVVRH
+ERARVAEHLETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL
+LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEST
+GDDSFVAIREVNSGIYAFDAALLRRTLPEVSTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL
+GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVNKHRTVIG
+AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTLEGWVPAKRPGTS
+SAEAARAAGAEGSGAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000516.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000516.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4c20c50c14e44ccd647b5296f4515d7db8215ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000516.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00500
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
+>GCF_003691675.1_00221
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHAVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
+>GCF_005280335.1_02449
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRTRVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKEAGAKDVIIAATHAVFSEPAAQRLGECGAREVVVTNTLPILEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGDA
+>GCF_020097155.1_02333
+MTELSRSEDKRLVLAAGRAHPGLAQEIAEALGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFVIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRGQVEGEKVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVRILKEAGAKDVIIAATHAVFSDPAAQRLGESGAREVVVTNTLPIPEEKRFDNLTVLS
+IAPLIARAIREVFEDGSVTSLFDGDA
+>GCF_023573625.1_00499
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000519.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000519.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8560abf9c9e00fbc82fe5b8bdd029028d1c92f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000519.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00504
+MAAQSTTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVVAAAPYQPAVVSPQV
+VNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEHAL
+VWKGQRR
+>GCF_003691675.1_00224
+MAAQSPTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVAAAAPYQPAVVSPQV
+VNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNVLRQARGVDVDARAVLRDEHAL
+VWKGKRR
+>GCF_005280335.1_02446
+MAAQSTAAAVTVVIPHYGDPAPTLALVDRLLADPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLSEVDTDLALVLNSDALITGEQIDALVAAAAPFQPAVVSPQV
+VNEDGSPQWSGRHFPTVLHQGVEWLTPLARFRHLPLLHEAVGHDVAAARSAAPVAVDWVM
+GAVMLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRDRGVASIVVPSVRVEHGMHGSSDPL
+RRRGWLVDSRFRYARKFGRPRALKAVLTAATGVNYAVNRVRQARGTDVDAAAVLRDEHAL
+IWKGTRR
+>GCF_020097155.1_02330
+MPASRIAPSVTVVIPHYGDPEPTRALVDALLAAPGRSVAGVVVSDDASPEPYPQPAPGRE
+GLTVVRREANGGFGANVNTGLAEVRTELALVLNSDAEITGEQIDALVEAARPYQPAVVSP
+QVVNEDGSPQWSGRHFPTVTHQTVEWLTPLARFRHLPALHEAVGHDVRAAEADSPVAVDW
+VMGAVMLLPMAEVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSVVVPSVRVVHGLHGSSD
+PLRRRAWLVDSRFRYARKFGRPRLLRGALTAATGVNWAVNRVRQTRGTDVDANAVFRAER
+DLIWKGTRR
+>GCF_023573625.1_00503
+MTAQSPTAAVTVVIPHYGDPAPTLALVDRLLSDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDADITGAQIDALVAAAAPYQPAVVSPQV
+VNEDGSPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAAARSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEHAL
+VWKGRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000520.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000520.fa
new file mode 100644
index 0000000000000000000000000000000000000000..668eed496e7b3eb2a21497d0a15cfb5afb0d6ac2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000520.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00505
+MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL
+EAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPQVPRRDELVFVGSRYPNRVELLARLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA
+>GCF_003691675.1_00225
+MSATGYTVAAPPEARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL
+DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPEVPRRDELVFVGSRYPNRVELLTRLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRIVADPAWGARIREAGRRRSHVEHTFAHRAAMAQGWWA
+>GCF_005280335.1_02445
+MSGTGYTVPARGARGTGRAERLFLVSPAFHGYHRSIARAWAAQGFDVTVHCYDAYATVPM
+KLRNKALLELPQKAGVDRTAARVAWDTERAVAALRAARPDRVLVIKGDSLGEAFWSEVVE
+AGLPRLLWLYDDLSRHDYSPEFLRAIGPVLSYARSEAEQLAGEGVDAHYLPNGFDPDMAL
+PSLPRREELVFVGSRYPNRVELLTTLAEAGVPVRAYGRQWSHHPVDRLRTWEVTRPALPA
+ERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYEPGEEV
+LVFENPEHLVELGRRVVAEPSWGERIREAGRSRSHAEHTFAHRAALAQEWWT
+>GCF_020097155.1_02329
+MSAGTYTIAARGERPVSGRPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYADLG
+MKLRNKLALELPQKAGLDRTAARVAWDTDRAVAALRAAAPDRVLVIKGDSLGDAFWDEVT
+GRALPRMLWLYDDLSRHDYSMDFLRGIGPVLSYARSEAESLAAQGVDAHYMPNGFDPEMV
+LPAVPRTEELVFVGSRYPNRVELLRALASAGVPVRAYGRQWSHHPVDRLRTWELSRPDLP
+AERDIPLAEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRPDVAEFYVPGEE
+VLVFEDTEHLVELGRRIVAEPAWGDRIRAAGRRRSHAEHTFSHRARMAQEWWA
+>GCF_023573625.1_00504
+MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIASAWAAQGFDVAVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSAIL
+DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPQVPRRDELVFVGSRYPNRVELLSRLTAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000523.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000523.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ad6835355864e0b02ed352f33d3ae84ab7bd402
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000523.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_00508
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLLAQPE
+ASLDVAAADVAHRDPATAPLGATPAEMREALPAGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAEDMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIREAAALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLRVGATITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFEFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFSEPMPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPHEEEPIMVITMGGFTLDRHIRPEERLPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>GCF_003691675.1_00228
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLLAHPE
+ASLDVAAADVAHRDPATASLGASPDEMREALPAGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAADMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIRESVALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLQAGVTITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFQFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFREPLPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIVEVQRTIDITRDLKRWFPNEEEPIMVITMGGFTLDRHIRPEERRPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>GCF_005280335.1_02442
+MITERHLTPYLVFPEDSLLVALQKMTDNRERIVFVVDSHGFLAGSLTDGDFRRWLLANPG
+ASLEVAAVEAANRTPATGPVGASPAEVLAALPAGALHLPLLDERGRLAALAINRESELRI
+GEHRIGPGRPAFLIAEIGNNHQGSVDLARELVDLAVEAGADAVKFQLRDMDALYRQSGAG
+TAGEDLGAQRTLDELAKFSLPAEDMVRVFDHVRDAGVALMCTPWDAPSMRVLAQYPVDGV
+KIASADLTNHGLLRDAAAARLPMVLSTGMSREDEIKEAVELVRSSGVPFAVLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVPLAAVARGASIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTREIEESIGVAAERVVSTGEAMNRINLAKSLVAARPLAAGETVTED
+AVTVKSPGRGLQPNELPRLVGRTLHRDMAEGDFFFAGDLTDTVPTGRQFEFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFTEPLPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPKEEAPIMVITMGGFTLDRHIAPAERQAKYDRIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>GCF_020097155.1_02326
+MIIERHLTPYLVFPEDSLTVALQKMTDNRERIVFVVDTHGFLQGSLTDGDVRRWLLAHPG
+AALDSPAVAAANPSPATGLVGDAPSSVLAALPEGALHLPLLDERGHLTALAINRESELRI
+GSHRVGEGRPAFLIAEIGNNHQGSVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSVDDMVKVFDHTRAAGVALMCTPWDAPSMQVLADYPVDGV
+KIASADLTNHGLLRDAASRGIPMVLSTGMSREEEIQESAALVRSYGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQAPVGYSGHERGFHVALAAVVRGASIIEKHFTIDRSLEGNDHK
+VSLLPDEFAQMVRQTREIEESIGVAGERVVSTGEAMNRINLAKSLVAARSLTAGDVVAEA
+DVTVKSPGRGLQPNQLPQLVGRTLHRDLEEGDFFFAGDLTDSVPTGRQFEFRRPWGLPVR
+YHDYAALTKDCTPDFLEFHFSYKDLEIDIDTVFREPMPGGFTTHLPDIFAGDFLVDLASM
+DEQVWERSIAEVQRTIDITRDLKRWFPSEEAPIMVITMGGFTLDRHIRPEERQPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>GCF_023573625.1_00507
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLVAHPE
+ASLDVAAADVAHRDPVTAPLGASPAEMREALPTGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAEDMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIRESVALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLQAGATITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFQFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFTEPMPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPNEEEPIMVITMGGFTLDRHIRPEERLPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000524.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000524.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9bed158febab94443b60555fff15784cc79d75aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000524.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00511
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRL
+GGPGRLGYLRALRAWDRGRGKDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA
+LARPGALAVLAPSRFAADRIRGARVLHNWVPAPTTPQAGRARDADEPLTVGFLGRLSEDK
+GIVTLLEAAALLRKTDPGAFVFRVAGESRFVADDEAERLATALKAAGEDVQVLGWQDTAE
+FLASVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGSEHPFVFPQRDAAAL
+ADRLQAVRAVDLGAVAHSQQRRWESLFSPEAGRAAVAELLDDLSL
+>GCF_003691675.1_00231
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRV
+GGPGRLGYMRALRVWDRGRGGDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA
+LARPGALAVLVPSRFAADRIHGARVLHNWVPGPTTPQAGRARGTDEPVTVGFLGRLSEGK
+GIVTLLEAAALLRRTDPGAFVFRIAGESRFVAEDEAERLATALKAAGEDVQVLGWQDTGE
+FLTSVDVLAVPSQWAESFGLVAAEAMAAGVPVVASDAGAVPEVVGSDHPFVVPQRDAAAL
+ANCLRAVRAVDLGEVAHSQRHRWASLFSPEAGRAAVAELLDDLSL
+>GCF_005280335.1_02440
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAANGFDVVRV
+GGPGRLGYLRALRAWDRDRGNDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA
+LARPGALAVLAPSRFAADRIRGARVLHNWVPGPTTPPARRARDADEPVTVGFLGRLSEDK
+GIVTLLEAAALLRKTDPGAFVFRVAGESRFVAEDEAERLATALKAAGEDVQVLGWQDTAE
+FLASVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGNDHPFVFPQRDAAAL
+ADRLQAVRAGDLGAVAHSQRRRWASLFSPEAGRAAVAELLDDLSL
+>GCF_020097155.1_02323
+MTRRIWIAANQGEVGGGEVMLHHLATALHELGRDIAVVAPAAPSATAARLEADGFTVDRV
+GGPGRAGYMRALRRWHNGHREDVVWCNGLLPATALAGRPRRIVHLHQWLIRPRDRVLGTL
+AMRGALAVIAPSESVAREIPGCRVLHNWVPRPLPLSGAAPARRRPGEGGALRVGYLGRLS
+FDKGFHLLMDVAEELHREQPDEWRFFVAGEPRFTTGDDAREIRERLAASRAVTALGWQAP
+GDFLPTVDVLVVPSLAPESFGLVAAEAMAAGVPVAVSDSGALPEVAGDDHPLLFECDDHE
+ELAAALRRARQIDLAPLVAAQHRRWEALFSPEAGRAGVAALLEELHV
+>GCF_023573625.1_00510
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRV
+GGPGRLGYLRALRAWDRGRDGDDVAWCNGLLPATALAGRPRRIVHLHQVPEKPVLRVFSA
+LARPGALAVLVPSRFAANRIRGARVLHNWVPAPTAPQTRPARGADDPVTVGFLGRLSEDK
+GIVTLLEAAALLRKTDPGAFVFRVAGESRFVAEDEADRLATALKAAGEDVQVLGWQDSGE
+FLATVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGSDHPFVVPQRDAAAL
+ANCLRAVRAIDLGAVAHSQRHRWESLFSPEAGRAAVAELLDDLSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000526.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000526.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69fddc58822ac024d49e4a818aa25aee11a34fb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000526.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00513
+MTDMTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS
+PLNRVGVLRKDPRRALPLLPLASSLLHVKEPVAVVSTSGWAHGFRYDGATLVYCHTPARW
+VYLLDDYLGEGGRNSIKGRIARALRPGLRRWDRAAVRRRSRYVANSTVVKERIEDVYGLD
+GVDLVFPPHSVSTDGPQEPIPGAERLAEDGFLLSVARLMPYKHVDVAIEAAARAGRPLVV
+IGKGPEEARLRAMAGEDVVFGQDLTDAQLRWAYAHAIALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTIVDGVNGTFVLDASIDAVGEGIKKLQAARWDTAAMRRHVEKFSEREFA
+LRIRALVEGLPGA
+>GCF_003691675.1_00233
+MSEQTPATIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFEDAHIVTS
+PLNRVGVLRKDPRRALPLLPLASSLMHVKEPIAVVSTSGWAHGFRYDGATLVYCHTPARW
+VYLLDDYLGEDGRNSIKGRIARVLRPGLRRWDRAAVRRRSRYVANSTVVKKRIDDVYGLD
+GVDLVFPPHSVSTDGPQGPIPGAEQLAEDGFLLSVARLMPYKHVDVAIEAAARAGRPLVV
+IGKGPEEARLRAMAGEDVVFGQDLTDAQLRWAYAHATALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTIVDGVNGVFVEEPTVDAVAGGVERLLAHDWDRAAMQAHAERFSEAQFG
+RRIRALVAESPAGPAHRGRQ
+>GCF_005280335.1_02438
+MTDTTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS
+PLNRVGVLRRDPRRALPLLPVASSLMHVKEPVAVVSTSGWAHGFRYHGDTLVYCHTPARW
+VYLLEDYLGEEGQKSMKGRVARVLRPGLRAWDRAAQRRRTRYVANSTVVKERIEEAYGLT
+DVPIVFPPHSVSTDGSQEPIPGAEHLAEGGYLLSVARLMPYKHVDVAIRAAERTGLRLLV
+IGKGPDEARLKAMAGDGVVFAQDLTDAQLRWAYAHATALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTITEGVNGVFVEAPTVEAVTDGVEQALARDWDPPAMRAHAERFSEDQIA
+RQVRTQLGQLQNHARNKGAM
+>GCF_020097155.1_02321
+MKIHASRPLSARRASQPGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYNPEGTF
+PEFKKARIITSPLNRVGVLRSDPRRALPLLPLASSLMHVKEPLAVVSTSGWAHGFRYEGD
+TLVYCHTPARWVYLLEDYLGEGGQRSLKGRVARALRPALRAWDSAAQLRRTRYVANSTVV
+KRRIEEVYGVANVDLVFPPHSVSTDGPQAPIPGAEDLAEGGYLLSVARLMPYKHVDVAIR
+AAERTGRRLLVIGKGPEEARLRALAGQGVVFAQDLTDAQLRWAYAHAVALIAASHEDFGI
+TPLEASAWGVPTVALRAGGYLDTIVEGVNGVFVPEPTVEAVTDVVEQVLAQDWDRGAMQA
+HAEHFSEVAFRERLARLLDDPHGAV
+>GCF_023573625.1_00512
+MTDTTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS
+PLNRVGLLRKDPRRALPLLPLASSLMHVKEPIAVVSTSGWAHGFRYDGATLVYCHTPARW
+VYLLDDYLGEGGRDSIKGRIARVLRPGLRRWDRAAVRRRSRYVANSTVVKERIEEVYGLI
+DVPVVFPPHSVSTDGPQEPIPGAEHLAEGGYLLSVARLMPYKHVDVAIRAAERTGLRLLV
+IGKGPEEARLKAMAGDGVVFAQDLTEAQLRWAYAHATALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTIVEGVNGVFVNGTSVAAVAGGIEWVRAHNWDRAAMRSHARRFSEFEFG
+QQVQAQLGWIGISR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000527.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000527.fa
new file mode 100644
index 0000000000000000000000000000000000000000..980be4ba26c3144a72c36079c84f1bd28d3dc543
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000527.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00516
+MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGIRDILVITTPQDAEQ
+FQRLLGDGSQFGVSLTYVQQPSPDGLAQAFVLGEEHIGVDHVALVLGDNIFYGPGMGQQL
+RRHTDVEGATVFGYWVKDPTAYGVVEFDTNGKAVSLEEKPAQPKSNFAVPGLYFYDNDVV
+EIAKDLKPSPRGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFTDLNDASNFIHAVE
+SRQGLKVGSPEEAAWRQGLLTDDQLRERAERLVKSGYGRYLLDLLDSGR
+>GCF_003691675.1_00236
+MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAQQ
+FQRLLGDGSQFGISLSYVQQPSPDGLAQAFILGEDHIGDEHVALVLGDNIFYGPGMGQQL
+RRHAQVDGATVFGYWVVDPSAYGVVEFDDAGKAISLEEKPEEPKSNYAVPGLYFYDNDVV
+EIAKSLKPSARGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE
+SRQGLKVGAPEEVAWRQGLLTDDELRERAEPLVKSGYGRYLLELLESGR
+>GCF_005280335.1_02435
+MKGIILAGGTGSRLHPITHAISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAGQ
+FQRLLGDGSRFGISLTYVQQPSPDGLAQAFLLGEEHIGDDHVALVLGDNIFYGPGMGQQL
+RRHTEVHGATVFGYRVADPTAYGVVEFDGTGRAVSLEEKPTAPKSHYAVPGLYFYDNDVV
+EIARALKPSARGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE
+SRQGLKVGAPEEVAWRQGLLTDDELRERAEPLVKSGYGRYLLDLLENAR
+>GCF_020097155.1_02317
+MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAEQ
+FQRLLGDGSQFGVSLSYVQQPSPDGLAQAFILGEEHIGDDRVALVLGDNIFYGPGMGQQL
+RRHTEVEGATVFGYWVADPTAYGVVEFDGAGKAVSLEEKPKEPKSNYAVPGLYFYDNDVV
+QIAKDLKPSPRGELEITDANRVYLERGMLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE
+SRQGLKVGSPEEVAWRQGLLTDDELRQRAEPLVKSGYGRYLLGLLDRADPIGRSSR
+>GCF_023573625.1_00515
+MNPDRTALNLHHRIGPMKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILA
+GISDILVITTPHDAEQFQRLLGDGSQFGISLSYVQQPSPDGLAQAFILGEDHIGDDHVAL
+VLGDNIFYGPGMGQQLRRHSEVDGATVFGYWVADPTAYGVVEFDGDGKAVSLEEKPAQPK
+SNYAVPGLYFYDNDVVEIAKELKPSARGELEITDVNRTYLERGALNVEVLPRGTAWLDTG
+TFKDLNDASNFIRTIESRQGLKVGSPEEVAWRQGLLTDNELRERAEPLVKSGYGRYLLDL
+LETGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000531.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000531.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3682267c2d28eb0aa07c66d5de62f3c3c0f69a69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000531.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00529
+MAFSAQQSIPHPPAAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA
+DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRAGTTTITVPSAKATADGALRLTAA
+GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVNRQARALSSWLERDGGAARG
+>GCF_003691675.1_00250
+MAFSAQQSIPHPPAAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA
+DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRAGTTTITVPSAKATADGSLRLTAA
+GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVDRQARALSSWLERDGGAARS
+>GCF_005280335.1_02423
+MAFSAQQSIPHPPAAVAAALASEEFHRSVVEQLGGSLVSFRVEGSPEGPMTVTTVRSAPA
+DRLPEMARKFIGSSLQVEQVERWEAPAADGSRVGTTTITVPAAKATAEGAQRLTAAGEGS
+QYSVDGTVTCKIPLVGSKLAAKAEPMVGKVVNRQARALTSWIGRDGGAAGA
+>GCF_020097155.1_02305
+MAFSAQQTIPHPPAAVAEALFSEDFHRSVAESLGGGLVSFARQDQADGGVELTIVRSGPT
+DRLPDMVRKVVGENLNIEQVERWSAPAADGSRTGTTTIRVPKAKATAEGTLRLAAAPAGT
+EYGVNGDLQVKIPLVGSKMAQMAEPMVGKVVARAGREVSAWIDRGGRG
+>GCF_023573625.1_00529
+MAFSAQQPIPHPPSAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA
+DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRTGTTTITVPSAKATADGSLRLTAA
+GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVNRQARALSSWLERDGGAARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000534.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000534.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0989b3dab514d474e6d5e6093556465e21c399b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000534.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_00532
+MTVETTEGWTLAPNIAWARTAGGQAAVMTLEAGQPLLLGASGDVIWDVLVGGRTPEDDLV
+ADPPASLSTTDVTVQVAEAFGLAPADVAADVHAFLEMLEAHGVLVRVRTA
+>GCF_003691675.1_00253
+MTVETTEGWALAPDIAWARTAGGQTAVMTLEAGQPLLLSASGDVIWDVLVGGRTPADDLV
+ADPPAPLSTTDVTVQVAKAFGLYPADVAADVHAFLEMLEAHGVLVRVRTA
+>GCF_005280335.1_02420
+MAADRLPAPFGMTSERGSAWAVAPGVAWALTDGGDAAVMHLEHGVPLLLSPTGHAVWDVL
+VGGRTPEDDLTAAPPIPLPEEAVAAETAAAFGLAPEDVAADVGAFLAMLEQHGVVVRVGG
+VLPRP
+>GCF_020097155.1_02302
+MSDAEHPPFAQAPAARAWRVAPTTAWVRSGEHQVTVMDLDEGNPQVLSPTGSAVWELLLD
+GRTPEDDLAADPPKPVEEEALCGAVAEAFGVDVEVVAADTRAFLGMLAGHRLVVPAVLP
+>GCF_023573625.1_00532
+MTVETTEGWALAPDIAWARTAGGQAAVMTLEAGQPLLLSASGDVIWDVLVGGRTPEDDLI
+ADPPVPLSTTDVTVQVAEAFGLDPADVAADVHAFLEMLEAHGILVRVRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000535.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000535.fa
new file mode 100644
index 0000000000000000000000000000000000000000..868dc844a1e09414ef18be93a74fd1051cfbdbfe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000535.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00533
+MGERATRQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDHRRSS
+DVDLLVHPADATAVIELLRSHGWEPVATFSEGSIFQHAATLWHDQLGYVDVHRLFPGLGA
+SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE
+SWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRSAATA
+RERAVLVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR
+>GCF_003691675.1_00254
+MGEHATGQRPAAPPSLDLEVRVRLAHARITHLLERAGIRGLHLKGYATEPGVYPDHRRSS
+DVDLLVPPADAAAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFPGLGA
+SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE
+SWAALREEARRLDAGAAWHVATGEAADGVDTRQLTLFAALHESQSGLELFRTRWRSAATV
+RERAALVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR
+>GCF_005280335.1_02419
+MTETGTTDQRAAAQPALDLAVRVRLGHARIAYVMEEAELRGLHVKGYAAEPGVYRGRRSS
+SDVDLLVHPSDAAAAVELLASHGWAPVADFSEGSIFEHAATLWHDHLGYVDVHRLFPGLG
+TDAARTFDALWAERTTRVIAGRPVPVPGPVHQRLVVIVHAARDSHRGALDVRHIRDTSSP
+AEWDALRQEARRLHATAAWHVATGEDADGMDAHDLALFEALQDDESGLDLFRTRWRTAHS
+ARERARLVLHTLPVNRPHLQMRLGHAPTRADLWREQRSRATALARWAWTRGVRRGR
+>GCF_020097155.1_02301
+MTAAPAPLETRVRLAHARITHLMAAAGVRSLHIKGYAMGPGVYAGGRTSSDVDLLVHPAD
+LSHALDALTSHGWRRIADFAEGSVFEHAATLWHDQLGYVDVHRRLPGLGRSPVDAFEALW
+GERTTTVVAGHAVPVPSLRHQRLVVLVHGARDAGRGRFDVDHLRHTLDAGQWAELRVQAQ
+ILGAGAAWSIATGETDVAGVDEREALLLSAVRGDESGIRLLATRWHAARGWRERLHLLVR
+TVPVNRAHLQMRLGRPPTTADVLREQASRGAALTRWAAGKAVPRVGR
+>GCF_023573625.1_00533
+MLAAMGERATGQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDH
+RRSSDVDLLVPPADADAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFP
+GLGASPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRES
+LPAESWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRS
+AATVRERAALVARTIPVNRPHLQMRLGRPVTRADLWREQGARLGALAGWAWTKAVRRDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000537.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000537.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f82369f00b57d4f3671c1c7d1c47a3edb37fee1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000537.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00535
+MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRS
+LMVPYLVWAALMSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVL
+RRFLERFPSAVAWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRRVQP
+HVRRHRTLIGVGLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTV
+ERLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALAL
+SWLAGLALLATPLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP
+>GCF_003691675.1_00259
+MVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRSLMVPYLVWAAL
+MSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVLRRFLERFPSAV
+AWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRRVQPHVRRHRTLIGV
+GLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTVERLLRSFARRT
+GTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALALSWLAGLALLAT
+PLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP
+>GCF_005280335.1_02414
+MDALRLVSIAAVVLGHAYLADLTFSRYLEIWRMPLFFFLTGYFWTRGRPVARDARGRFKA
+LMVPYLVWAVVMSAAALAWFGDDPERLQRLMAAGWYGGADQEPPWWAFWFISVLFFATVL
+RRFLERFPTAVAWGVGLAGLAWAYLVPESAIARTPLGVGLALPCLLFILSGEAFRRRVQP
+RIRRHRTLLGLALVGLGLAAVALGLEPHNIKFGGFGTPLLTPLVGVLMSAGMVLVFGAAV
+ERILREFARRTGSGQALRRVITALVRTGTVVVLLHGWVLMWVMRQGVEDNLLKFVLALGI
+SWLVGLALLATPLSKPLTGARRRWFPLHRLRGEEPPHPPTSALPRVTTASERTHP
+>GCF_020097155.1_02296
+MDALRLVSISAVVLGHAYLADLTFSPYLEIWRMPLFFFLTGYFWTRGRPWAADALSRFRS
+LMVPYLLWSVLMTLVVLSWSRRSQIDGVTLADLVSAGWYGGADQPPPWWAFWFISVLFFV
+ALLRRALERAPSWAGWAVALAGLAAAELVPESAIARTPLGIGLAAPCLFYVLAGEAFRRR
+VQPRIRRHRTLIGVALVAAGVGAVALGLPPHNIKWGGFGLFPWTPLTGIAMAAGMVLVFG
+AFVERRLRAFARDTGTGRAIRAGITALTRTGTVVVLLHGLVLMEAMRVGIEDNLMKFVVA
+LTVSWAVGLALLATPLARPLTGVPQQWFPFGREAGA
+>GCF_023573625.1_00538
+MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVRGRFRS
+LMVPYLVWAALMSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVL
+RRFLERFPSAVAWAVGLAGLAWAHFVPDSAIARTPLGVGLALPCLLFVLSGETFRRRVQP
+HVRRHRTLIGVGLVLLGLVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTV
+EGLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALAL
+SWLAGLALLATPLSKPFTGARRRWHPVHRLRRVEPPHPVTSALPRVPTASERTHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000538.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000538.fa
new file mode 100644
index 0000000000000000000000000000000000000000..581fd79e647806875b21bf4bd0a01d7ed9c0bc32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000538.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00537
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELAGS
+DVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD
+>GCF_003691675.1_00261
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELADS
+DVLTCTVIGFPLGANTSEVKAFEARQAIDAGADEVDMVLDIAAARAGDRARLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGEDIGVKASGGVRTREDALAMIEAGATRIGASSALAILGSD
+>GCF_005280335.1_02412
+MTRTLSTAELAQYIDATALKTETSEADVRRLVAEARQAGVKSVCVNPRWVPLVSAELAGS
+DVLTCTVIGFPLGANASEVKTFEARQAIEAGAHEVDMVIDVAAARAGDRARLVEDVRAVA
+EAAHAAGPAGQGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGEHVGVKASGGVRTREDALAMIEAGATRIGASSALAILGTD
+>GCF_020097155.1_02294
+MSETPQLTTAELAKHIDHTLLKPEASREDILRVVAEAREAGVKSVCVNPRWVREVRAGLE
+GSDVLTCTVIGFPLGASSSAVKAFETTQAIADGADEVDMVIDIAAARAGDRARLEEDVRA
+VVAAAHASGPAGRAGTLVKVIIETALLDDAAKVLACEAAVAAGADFVKTSTGFSTGGATV
+EDVALMRRTVGPEIGVKASGGVRSREDALAMITAGATRIGASSALAILGDD
+>GCF_023573625.1_00540
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELAGS
+DVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000540.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000540.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76e8479a3ee0157b0630cee955792d58b92ac249
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000540.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00539
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGDE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL
+>GCF_003691675.1_00263
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGEE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLAGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL
+>GCF_005280335.1_02410
+MSEQTFSPSPASPLAGDHPGFDQARAAAAVIADATGVAEHRIAVVLGSGWGEAAGLIGEE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGAKTVVLTNGCGGLDPEIAPGTPVLISDHLNLTGATPLVGATFVDLTDLYSPRIRQI
+AREVDPSLREGVYVQFSGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGMS
+LVTNLGAGISETALSHGEVVEAGQAAGPRISRLLADIVWRL
+>GCF_020097155.1_02292
+MSEQSTPTPTPASLARLAGDHPGFAEARAAAEAIAEATGCAEHRIAVVLGSGWGEAAELI
+GVERARIDLADVPGFHAPKVPGHNAVIRSVELADGSRALVFGSRTHFYESRDAQAVAHTV
+RTAAAAGAATVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDVYSPRI
+RAIAQEVDPTLTEGVYVQFSGPQYETPAEVRMATALGGDLVGMSTALDAIAARHAGLEVF
+GISLVTNHGAGIQETPLSHQEVVEAGQAAGPRISRLLAEIVGRL
+>GCF_023573625.1_00542
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGDE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000541.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000541.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32612f85f172cca9e642d7a435a64373d6bf812b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000541.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00540
+MEPVSEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGLGGAAVLTDVVPSKT
+LIAAADSMRRVGASVDLGVDLGGADVHADMGRVGHRILNLAHEQSSDIRAGLERVGVRVI
+DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ
+VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE
+GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV
+GVKLTGSGHVLVDGVSRTSVPSIYAAGDCTGKLALASVAAMQGRIAVAHLLGDALKPLRP
+HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG
+SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI
+>GCF_003691675.1_00264
+MEPVTEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGVGGAAVLTDVVPSKT
+LIAAADSMRRVGASVDLGVDLGGAEAHADMGRVGHRILNLAHEQSSDIRAGLERVGVRVI
+DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ
+VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE
+GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV
+GVKLSGSGHVLVDGVSRTSVPSIYAAGDCTGTLALASVAAMQGRIAVAHLLGDALKPLRP
+HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG
+SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI
+>GCF_005280335.1_02409
+MVAAKLGARVTLVERQGVGGAAVLTDVVPSKTLIATADSMRRVGLAEDLGVDLGDAEPRA
+DMRQVDRRILDLAGEQSRDIRAALERRGVRVIDGVARVVGPNEVSVRTLQDADAEPEVIT
+SDAILVAVGASPRELPTAVPDGERIFNWKQLYAMTELPEHLIVVGSGVTGAEFASAYNRL
+GAKVTLVSSRDRVLPGEDADAAELLEKVFQDNGLTVVARSRAEAVERTETGVRVELSGEG
+AADTPYVEGSHALVAVGGIPNTAGLGLEDVGVELTESGHVKVDGVSRTTVPSIYAAGDCT
+GNLALASVAAMQGRIAVAHLLGDALKPLRPHLLASNIFTSPEIATVGVTQAQVDSGQYQA
+DVLRLDFATNPRAKMSGVQEGFVKIFARQGSGTVIGGVVVSPRASELIYALALAVTHKLH
+VDDLADTFTVYPSMSGSIAEAARRLHVRI
+>GCF_020097155.1_02291
+MNVTEENTTFLPSLTIIGGGPGGYEAALVAAKLGARVTVVERAGMGGSAVLTDVVPSKTL
+IATADSMRRVMAASGLGVDLGEAQPHADMHAVDRRILELAGQQSSDIHRALEKRGVRVVI
+GDAVVTGPHEVTVRRRGIEEGEEPEVITSDAILVAVGASPRELPTARPDSERIFNWKQVY
+ALQDLPEHLIVVGSGVTGAEFASAYNQLGAAVTLVSSRDRVLPGEDPDAAELLEDVFAQN
+GLDVAGRCRAESVERTETGVRVHLSGEGADGRPYIDGSHCLLAVGGVPNTAGLGLEEVGV
+ELTESGHVKVDGVSRTTVPSIYAAGDCTGQLALASVAAMQGRIAVAHLLGDALKPLRPHL
+LASNIFTSPEIATVGVTQAQVDSGQYQADVIRLDFATNPRAKMQGVSTGFVKIFARQGSG
+TVIGGVVVAPRASDLIYSLALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRV
+>GCF_023573625.1_00543
+MEPVSEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGLGGAAVLTDVVPSKT
+LIAAADSMRRVGASVDLGVDLGGGDVHADMGRVGHRILNLAHEQSSDIRAGLERVGVRAI
+DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ
+VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE
+GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV
+GVKLTGSGHVLVDGVSRTSVPSIYAAGDCTGKLALASVAAMQGRIAVAHLLGDALKPLRP
+HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG
+SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000542.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a006559d6b9cf94e1ca4b8b69a9a27bca18a4c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000542.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00541
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLSEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNGPLMVAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQKFDVSYVGYYLAAASAITVIALVLSPETRHTDLDTVTSARERRAAR
+>GCF_003691675.1_00265
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQKFDVAYVGYYLAAASAITVIALALSPETRHTDLDTVTSARERRAAR
+>GCF_005280335.1_02408
+MSRTTTPADGTAAGLEAAAEVPRGRVITASLVGTSIEFYDFYVYATAAVSVFPLIFFPGD
+DQTTALLASFAVFGTAFVARPIGSVLFGHFGDIMGRKVTLIGSLLTMGIATFLIGLLPTA
+FQIGLWAPAMLVVLRFCQGLGLGGEWSGAALLATEYAAEGKRARAAMWPQLGAPIGFFLA
+NGLFLALVIGFGHDSTNPDHDGAFLNWVWRLPFLLSIVMVAVGLYVRVKLEETPVFQRAI
+ANDTRVKAPLGEVFKRNWWELILGTFIMYATYVLFYLMTTWILSYAIGKTENGMLGVPYA
+EFLVLQLIGILFFAAFVPASGWLADRFGRKPTLLTVSALMVLFGLSFGLWLSAERMGTGA
+GVNVPLMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGISYNVSSILGAALTPFL
+AAWLVKEYGVAYVGYYLAAASVITMIALALAPETRHTDLDGVTSARERRAASV
+>GCF_020097155.1_02290
+MSHTTARSAEAPSVEDVPKSRVILASLVGTSIEFYDFYVYATAAVSVFPLIFFPGDDPTT
+ALLASFAVFGTAFVARPIGSILFGHFGDRMGRKVTLIGSLLTMGIATFLIGLLPTAFQIG
+LWAPAMLVVLRFCQGLGLGGEWSGAALLATEYADHGKRARAAMWPQLGAPIGFLLANGLF
+LILVRAFGHDSTNPQLEGSFLTWVWRVPFLLSIVMVAVGLYVRVKLEETPVFQRALEDDT
+RVKAPLGEVFKRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKTQNGMLGVKYADFLV
+LQLVGILFFAAFVPVSGWLADRFGRKPTLLVVSGLMVVFGLSFGAWLSPAAMGQGDALNV
+PSMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGAALTPFLAGWL
+VKEFGVATVGWYLAIASVITMAALALSPETRHADLHEVTSARERRAAAR
+>GCF_023573625.1_00544
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTSPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQRFDVSYVGYYLAAASAITVIALALSPETRHADLDTVTSARERRAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000544.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000544.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73df7424598026f1c17b21d42fed4b85ff1e6100
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000544.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00544
+MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALELQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA
+AGGFFPGLVERAEAADVVDDALAARIRSGADAAAQAYRDFADTLEAELRPHAPEADGVGI
+EYYRLASRDFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLSKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
+>GCF_003691675.1_00269
+MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQSIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA
+AGGFFPGLAERAEAADVVDDALAARIRSGADTAAQAYRDFADMLEAELRPHAPEADGVGI
+DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLTKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
+>GCF_005280335.1_02403
+MTQNTPVAADRGARTPSAIDALAERYVADVLALHPDEATTLGFPGHETEYADFSPAGTRA
+DDELNARLLADLEALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVIEQARAHGA
+AGGFFPGLVERAEATDVVDAALAERIRAGADAAAQAYRDFADTLQAELRPHAPEADGVGI
+ELYRLGSRAFLGAEIDLEETYRWGQEELARIIAAQEADAERIKPGATIEEARALLDADPE
+RTLNGTAALQAWMQRLSDEAVQAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRTEHEEREGEGFDLK
+AFHTRALRLGGMGLDTLRAALA
+>GCF_020097155.1_02286
+MTQTTSAPEGARTPSAVDALAERHVAAYLALRPDEATSLGMPGHETEYPDLSPAGAAALD
+ELNRTTLEELAGLEPADDVDRVTVAAMRERLGLEREIHATGRTELNNIASEAQGIRAIFD
+LMPTDTAEQWGHIAGRLENLPAALRGYAESLLASRDAGHVAAVRQVEIVVEQARAHGAEG
+GFFPGLVERAEAADVVDAALAERIRTGAAGAAAAYAEFADTLEAELRPHAPEADAVGIEH
+YRLASRVFLGAEIDLEETYRWGQEELDRIIAAQEADAERIKPGATIEEARAILDADPART
+LTGTKALQEWMQRLSDEAVEAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSRPG
+RMWWSVPAGEEEFTTWAETTTVYHEGVPGHHLQIATAMMNRGTLNLWRRNFAWTSGHGEG
+WALYAEKLMEEFGFLDDAGDHLGMLDMQRMRAARVVFDIGYHCGFEMPASEGGGEWTPEK
+GYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEAREGADFDLKAF
+HTRALRVGGMGLDTLREALA
+>GCF_023573625.1_00547
+MTQHTSEAAADGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGG
+AGGFFPGLVERAEAADVVDDALAARIRSGADTAAQAYRDFAATLEAELRPHAPEADGVGI
+DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLAKHLMISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000545.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000545.fa
new file mode 100644
index 0000000000000000000000000000000000000000..912cefec9baa0c7d5d85dc0a36af298150ee4008
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000545.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00545
+MSALLGPGAPDENDESTQATPASADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AAAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ
+>GCF_003691675.1_00270
+MSALLGPGAPDENDASTQATPAPADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AEAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ
+>GCF_005280335.1_02402
+MSAAHEPRTPNAAGTPDDAAAEPTTADPLQLRGVELDPEEMAALTAVLAHARAAEAEAAR
+AAAEAADPRPLDRTLRRRGDLGLWARPGRGQWRRGAGLQ
+>GCF_020097155.1_02285
+MSAALPDDAADREVQDPEPMRLTGSSLEPEEMAALTAVLAQMRAQGGAAVPQAGRSGRLR
+RPDRSLVRRGDLGLWARPGEDQWRRAAGRR
+>GCF_023573625.1_00548
+MSALLGPGAPDENDESTQATPASADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AAAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000546.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000546.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05f84c8af14ecfaaee678b3ffe99021ad7bfd44b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000546.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00546
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
+>GCF_003691675.1_00271
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLAVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
+>GCF_005280335.1_02401
+MSDPDLTTTAGRLADLHRRLEATAAPGGEGAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPETTDEDLALDEIVPDSANQPYDMLEVIGAIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPQQLAGTLDIAASEKAARFVRFCDAF
+NIPILTLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATQDAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGALIRALRATLHKREARPAKKHGNMPL
+>GCF_020097155.1_02284
+MSAPELSTTAGRLADLHRRLEATAAPGGEAAVERQHSRGKHTARERIDLLLDEGSFVELD
+ALATHRTTAFGMDAKHPAGDGVVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVMASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTTGTAHYMATSEE
+DAIAYVQDLLEYLPSNNLAEAPVFEAESLEETEQDLALDTIVPDSANQPYDMLEVIAALV
+DDGHLLQLQEMYAPNVITGLARLDGMSVGVVANQPQQLAGTLDIAASEKASRFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGPQGAVNILYRRELAAAEAAGEDVEARRAQIVADYEAELLN
+PYQAADLGYVDAVVPPRQTRAHLVRALRATFHKREARPAKKHGNMPL
+>GCF_023573625.1_00549
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000549.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000549.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f64b69f6e3266168d8d99b2d4e2ee625e5bd3143
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000549.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00550
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
+>GCF_003691675.1_00275
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
+>GCF_005280335.1_02396
+MEPSAETPAAAPRPEAAGATHVGAVRELNEDAWTLVGDPLVLAAVADGMGGHEAGEVASA
+AAIEVLRRRGPEVLAPGVAHTPEELGHLVHEADAAVVAAGGGRSGTTLTVLACIDTAANR
+WAVANVGDSRIYLRPAGAPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGS
+SEPLTVDVAEIPVASGDRLLLCSDGLTGELLDEEIRALIDDADELEDALVKLVEAALWRG
+GRDNVTAVLVRIP
+>GCF_020097155.1_02280
+MSEPHAADAAPAEPGAWASVPRPEAVAVTHVGAVRELNEDSWAVVGDPLLLAAVADGMGG
+HEAGEVASAAAVAELHRRAPSVLAPGVAHTPQELGALVHEANAAVLAAGGGRAGTTLTVL
+ACLDTEVGRWAVANVGDSRIYLRPVGAGVLQQVTVDHSAVQLMVDAGELTPAEARVHPRR
+NVITRALGSTQALTVDVMELDVAPGDRFLLCSDGLTGELLDDEILAIMDDAATLDEAAER
+LVEAALWRGGRDNITAVLVRIP
+>GCF_023573625.1_00553
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000550.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000550.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f245c2fe42184d0912f16c9f65afa1a2fc965bf2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000550.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00552
+MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR
+RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA
+VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR
+DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV
+ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAM
+TGERA
+>GCF_003691675.1_00277
+MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR
+RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA
+VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR
+DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV
+ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAM
+TGERA
+>GCF_005280335.1_02393
+MSSPTRVAHVPSQPPGISGLLVVAKAAARAGADVLARRWTGHHPAVPLGREEIGAETKTS
+GSDWVTDYDRRAEQAVREVLVAYRPQDEITGEEYGATVPAEPSGLRWSIDPLDGTTNFVR
+GLPQFCTSVAVTGPVDEETAALLGVPAGTRRWLAGVVAAPALGRTWFASAGRGAFSTADA
+TTAGVDVPDRDAAPVRITGPAPGRSGRLLATGFGYDPARRAMQVRALAALLPAFGDVRRI
+GSAALDLCMVADGTLDAYAEFGTQEYDWAAGALIAEEAGVRVRRPASGDGTAHPDWMVAG
+DVDEAALAAAQEETA
+>GCF_020097155.1_02278
+MSAAPARPASPAGLLVIAKAAARAGADVLAERWAGHHPAVPLTSDELGADTKSSGSDWVT
+DYDRRAEDAVRAVLTGYRPHDEITGEEHGSTAPVEPSGYRWSIDPLDGTTNFIRGLPQFG
+TSVAVEGPVDEETAALLGVLPGSRRWLAGVVAAPALGRTWFASAGRGAFSTADATTAGVA
+VPDRDAAPVRLTGPVPGRSGRLLATGFGYHPGRRAMQLRALAALLPAFGDVRRIGSAALD
+LCMVADGTLDAYAEFGTQEWDWAAGALIADEAGVPVDRPASGDGTGHPDWMTAGDVDAAA
+LAAAKEATA
+>GCF_023573625.1_00555
+MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR
+RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA
+VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR
+DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV
+ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAV
+TGERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000551.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000551.fa
new file mode 100644
index 0000000000000000000000000000000000000000..155e90eca090b917c43b81b5dbf4acb42001dac6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000551.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00553
+MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA
+GAQAHVERGGVVVFWRPGCPFTRRLVKELTAQERDRAYWVNIWQEPAAATFLEGLHESRD
+GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQHAGGDA
+>GCF_003691675.1_00278
+MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA
+GAQAHVERGGVVVFWRPGCPFTRRLVKELTAQERDRAYWVNIWQEPAAATFLEGLHESRD
+GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQHAGGDA
+>GCF_005280335.1_02392
+MRRLVGDPWFWPVLFGSAGLVFLVWGTLRRDVVVLVAALAMLWMLRRHLPQLRVRSRPLA
+GAQAHVQDGGVVVFWRPGCQYCQALLRDLDPAQRDAVYWVNIWTDKDAVPVLRRLHAGRD
+GHAHEAVPTVWARRKDFVAADEASRSRLKDMLRDARPAGGPRTREEGPR
+>GCF_020097155.1_02277
+MRRLVGDPWFWPVLFGAAGVVFLVWGTVRRDVIAIVAGVAMLWMVWQYLPALRVRSCPMA
+GAQAHVDAGGVVVFWRPACRYCLALIKDLDPAQRAAVYWVNIWTDPDAVPVLHRLHATRD
+GHAHEAVPTVWSRRRDFVVKDEATRRRLTDMLGAVRHIPESGR
+>GCF_023573625.1_00556
+MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA
+GAQAHVERGGVVVFWRPGCSFTRRLVTELTAQERERAYWVNIWQEPAAATFLAGLHEARD
+GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQHAGGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000552.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000552.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51a123a66149f82a135a05570c98e238f0b84949
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000552.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00555
+MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILEHVSAVQAAAGDDVTPTSHPIALE
+NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE
+>GCF_003691675.1_00280
+MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILKHVSAVQAAAGDDVTPTSHPIALE
+NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE
+>GCF_005280335.1_02390
+MPEITRDQVAHLARLAHIQMSDEELATVSGELEQILGHVSAVQAAAGADVAPTSHPIAMS
+NVFREDVPAGMLTQEQAVDQAPDAQDGQFKVPAILDGE
+>GCF_020097155.1_02273
+MAEITRDQVEHLARLAHIRMTDEELDVMSGELESILESVSQVQAVAGEDVVPTSHPIPLE
+NVFREDVPTGMLTQEQALDQAPDAEDGQFKVPAILDGE
+>GCF_023573625.1_00558
+MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILEHVSAVQAAAGDDVTPTSHPIALE
+NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000554.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000554.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55595f36ccbc68d158893fb1fb679229fbeba58d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000554.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00557
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVAAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>GCF_003691675.1_00282
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEIEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVTAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>GCF_005280335.1_02388
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNREVVEYAVRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASNSLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVKAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAALLAAGGTVTQETRHWHEDTRTTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAEMPELPAVRNKRLKAEWGYTDEEFRDVVNAGVLDEIVATVEAG
+ASPAAARKWWMGEIARLANVRETAVAELGVTPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGTPKEIVEAKGLAVVSDDGALTEAVDAAIAANPDVAEKIRGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>GCF_020097155.1_02271
+MSTAELMDFQEAMDRFDPVLGFEVHVELNTKSKIFSTGANAFGDEPNTNVTPLDLGLPGT
+LPVLNREAVESAIALGLALDAQIAPSCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLDV
+ELEDGTVFRVEIERAHLEDDAGKLTHQGGSGRIQGASASLVDYNRAGVPLIEIVTRPIVG
+AGDRAPEIARAYVTALRDIVKAIGISDARMEHGNVRCDANVSLMEKGASAFGTRTETKNV
+GSTRAVQHAVTHEIQRQAAILAAGGTITQETRHWHEDTRTTTSGRPKSDADDYRYFPEPD
+LLPVVVDEAWIERVRAGMPELPAVRNKRLKGEWGFSDEEFRDVVNAGVADQIAQTVEAGA
+SPAAARKWWMGEIARLANLREVEAAELGVTPAHVVEIEELIAAKTINDKIAKQVLGLVAD
+GEGAPKQIVAAQGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMQAVGALIGPVMKAT
+RGQADAGRVREIVLERLGVA
+>GCF_023573625.1_00560
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVAAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000555.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000555.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e86a871da3de2d83c1c6f07a1f233153ac2c191
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000555.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_00558
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLASALAERDVSWAVPVALSDPVSAG
+PGAAVLQRFLPGGPYPPHEGDPDVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPAR
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAALTDAVTTWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDLACAWGPALNVAYLALWHGEQKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG
+>GCF_003691675.1_00283
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG
+PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAALADAVTTWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDLACAWDPALNVAYLALWHGEEKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG
+>GCF_005280335.1_02385
+MASDPVDSELELVHRALGRLRPHVSPADARALHEADWSAGTVEEGGQFNRVLVCAGAGVL
+RMTRAHEVGAAPAARWSPERDPARQLGRRMALLDGLDAALAEQGVAWTVPVALSDPVPAG
+TGAAVLQRYLPGGPHPPHEGDPAVLRRLLDEIAAVDVADPRIAPHLGRPFSFRGPWTAQR
+AEHVAGIPGRLAPRLGAWPGDDVDARTGADAWADAVARVTRAVTAWTEEPPVPPSLVHGD
+LAGHNMRWRAMPAADDAPGEVRWELAGVLDWDLACAWDPALNVAYLSLWHGEDQVERLAV
+DAGEAARARVWLGAMALETLDDAAARDELVGGLPNGSWRRLLRKALPRVARALTALG
+>GCF_020097155.1_02269
+MASDPARSELDLVAAALQRLRPGLDDGVAARLRGADWSAGRVEEGGQFHRVLVLEDVGVL
+RMTRVHEAGAAPAARWTPERDPAVHLPRRLALLDGLAAVLAEAGVRWSLPTALSAVVEDG
+PGAAVLQRYVPGFPHPPHEGDPAVLRGVLADLAAVDVADPRVAPHLGRPFTFRGPWTPER
+AAHVAGLPARLAPRLGAWPGDALGHAGDETAAGEAAVRLRADAWGESVTALTGVVSAWTR
+EPPVPPALVHGDLAGHNMRWRVVPAAATPDAEVPDAPVRWELAGVLDWDLACAWDPALNV
+AYLGLWHGEDLVEAIAADPAEARRARVWLGAMALETLDDAGARDVLVGGLAESSWRRLLR
+KTLPRVGRALAAAAA
+>GCF_023573625.1_00561
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG
+PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAAVTDAVTAWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDFACAWDPALNVAYLALWHGEEKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000561.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000561.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2849b4c55425901ffc662525c210d3ad170ecf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000561.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00564
+MPLARLAGVNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHVT
+VAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLL
+GFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELDEPRLRELFTRDDDVARVRPKVFWG
+RGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG
+>GCF_003691675.1_00289
+MNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHFTVAAVRAPL
+PLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLLGFSQGMAM
+ATSLLRLDPEAYACTVALSGFVVDPELTEPRLRELFTRDDDVARVRPKVFWGRGQEDPII
+SEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG
+>GCF_005280335.1_02379
+MNNDTANTAPSSETAPFTVRWSRPEGERTEDLLILLHGYGANEDDLFGLVPHLPERFTVA
+AVRAPMTLQPGGYAWFPLSQDPVTGEIGSDAASVRTAIEDLHAWVGAVREGFRTVSLLGF
+SQGMALATSLLRLDPTAYAATVALSGFVVDPTREESGLAGLFDGDDEVARVRPKVFWGRG
+QDDPIISEARVEASHAWLNAHVDLMKIVYAGLPHAINQQELGHVKEYLEHMVR
+>GCF_020097155.1_02263
+MNDTTPRDPAPFAVRWSRPEGERTEHLLVLLHGYGADEDDLFGLVPQLPEAFTALAVRAP
+MDLPQGGAAWFPLTQDPATGEIGSDAGAVRAAVEDLHAWLPGVSGGFRTVSLLGFSQGMA
+MATSLLRLDPAAYAATVALSGFVVDPLHVEPELEGLFPADETVDAVTPKVFWGRGQEDPI
+ISAQRVEESHGWLTAHTDLTKVVYAGLPHAISPQELGHVREYLTHVVL
+>GCF_023573625.1_00567
+MPLARLAGVNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHVT
+VAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLL
+GFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELAEPQLRELFTRDDDVARVRPKVFWG
+RGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000562.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000562.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a6502181ae51f80de6c537b674bb3595136a5d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000562.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00565
+MTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRRGAQL
+HDGDVVEFAGEAFVVQAEQA
+>GCF_003691675.1_00290
+MMDTMTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRR
+GAQLHDGDVVEFNGEAFVVQAGQA
+>GCF_005280335.1_02378
+MMDTMTETNPADARPLPIRDASIRLGQALKLAALVEDGAMARDVVQDGLVTVNGAVETRR
+GAQLKDGDVVEFHGEAVVIEAGSAD
+>GCF_020097155.1_02262
+MTSSSDVQPLPIRDESIRLGQALKLASLVEDGAMARDVVQDGMVSVNGEVETRRGRQLHD
+GDVVEFNGEEIVVEAGQS
+>GCF_023573625.1_00568
+MTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRRGAQL
+HDGDVVEFAGEAFVVQAEQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000563.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90fa8838221cdc444a689c16a31d780aebf38a40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000563.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00566
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA
+EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAGQHFDRWVEDCWDWFID
+LGIDPAHLRKFDVPADERAHYSDATIDLEYDFGFTGGDGWGELMGIANRTDYDLGRHTEH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPTTQSLAAELRTLWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK
+>GCF_003691675.1_00291
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA
+EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDRWVEDCWDWFID
+LGIDPAHLRKFDVPAEDRAHYSDGTIDLEYDFGFTGGDGWGELMGIANRTDYDLGQHTTH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPATQSLAAELRGLWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK
+>GCF_005280335.1_02377
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHKRHRQDHLLEAFEAKKGRPSASMD
+EIVCPDCGTKGAWTEPQMFSGLVKTFLGPVDNEEGLHYMRPETAQGIFVNFLNVLGASRK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDTWVEACWDWFID
+LGIDPENLRRLDVPEEERAHYSDGTIDLEYRFGFGGGDGWGELMGVANRTDYDLGRHTEH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGTDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPATQALAAELRALWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQAVTIRERDTMSQERVALSQVKSYLLERLVK
+>GCF_020097155.1_02261
+MAAKSPLDNVINLAKRRGFVFQAGDIYGGSRSAWDYGPLGVELKENIKAEWWRTFVRSRE
+DMVGLDSSIILPRQVWEASGHVATFTDPLVECQQCHRRHRQDHLLEAFEAKKGRAAAGME
+EITCPDCGTTGKWTEPQMFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGASRK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKEHFDTWVEACWDWFID
+LGIDPANLRKFDVPEEERAHYSDGTIDLEYRFGFAGGDGWGELMGVANRTDYDLTSHANA
+SGAKLQYFDQANDVHYTPYVIEPSFGLTRSMMAFLVDAYTEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKLELQEPSQRLAAELRAHWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQSVTIRERDTMSQERVALAQVRAYLAERLTK
+>GCF_023573625.1_00569
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA
+EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDRWVEDCWDWFID
+LGIDPAHLRKFDVPADERAHYSDATIDLEYDFGFTGGDGWGELMGIANRTDYDLGRHTEH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPATQSLAAELRTLWNIETDDSGAIGRRYRRQDEIGTPYCI
+TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000566.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000566.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2090f9fd0c171aef03948357bc6b781b435bdcaa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000566.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00573
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHAGDSFLTLAAYHEHPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDGGGAAPPSEA
+>GCF_003691675.1_00305
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHTGDSFLTLAAYHEHPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDGGDAAPASEA
+>GCF_005280335.1_02360
+MTEQPQDPRQDQTAAEPAPEPAEALAAETTDAVAPEAAPGEAGQPSPEMLELAGRMFDAA
+RSGDAETLEAYIVAGLNPDLQNGKGDTFLTLAAYHDQPGVVEMLIRVGADVEKANDRGQR
+PLTCATFKGDVASMRLLLAAGADPDAGTPSARQTAQMFGGEEITAVLDEPR
+>GCF_020097155.1_02251
+MTEHQDTQGQHAPATPPAEPAVESAGPSPEMLELAGRMFDAARTGDVDTLEAYIVAGLNP
+DLQNGKGDTFLTLAAYHDQPAVVEMLIRVGADVEKANDRGQRPLTCATFKGDVASMCLLL
+AAGADPDAGTPSARQTAQMFGGERVAAVLDEAR
+>GCF_023573625.1_00574
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHAGDSFLTLAAYHERPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDREDAAPSSEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000567.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000567.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec0397bd8acd3780c557c88253c0940d27afec32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000567.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00574
+MTSSHTLPAAAVTDADDVAHYAKSAGAGRRITDDDQLHEARHPAPTTDRLTLPPLRLGPL
+TIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHDPDEVP
+RSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKAELFASIV
+KAAVTEAAKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAV
+WDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGDLQAAF
+EGRQDRFQPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYLKGYPVGSEIRTA
+LSTVPDLATMREILARVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNAEQQAM
+IQAAELDVSGG
+>GCF_003691675.1_00306
+MTSSHTLPAAAMTDADDVADPHAAHYAKSAGAGRRITDDDQLHEGRHPAPTTDRLTLPPL
+RLGPLTIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHD
+PDEVPRSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSEL
+FASIVKAAVTEAAKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFY
+SGTAVWDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGD
+LQAAFEGRQDRFQPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYFKGYPVGS
+EIRTALSTVPDLATMREILTRVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNA
+EQQAMIQAAELDVSGG
+>GCF_005280335.1_02359
+MTVSSSTTTPERGAATDGLSAADPAAGAPAAVDPHASHYAKSAGAGRRIADDEQLHEGRH
+AAPTTDRLSLPALTLGPITVDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALV
+ERKPESMRIIKHDPDEVPRSVQLYSVDPVTTGAAVRMLVEEDRADHIDLNFGCPVPKVTR
+RGGGSALPWKSELFASIVKAAVTEAGRKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVA
+AVALHGRTTRQFYSGTAVWEDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVI
+GRGCQGRPWLFGDLQAAFEGRHDRFRPTLGMVADTLYRHAELLVDTFEGDELKALRDIRK
+HVAWYFKGYPVGSEIRTALSTVPDLATMAEILSRVDRDQPYPGLDAEGPRGRSGAPKRPH
+LPDGWLDSRELNAEQKAMIAAAELDVSGG
+>GCF_020097155.1_02250
+MTASHTLPDAAVDPHYAKSAGAGRRIADDDQLHEGGHAAPRSDRLNLPPLKLGPITVDVP
+VVLAPMAGITNTAFRRLCREYGGGLYVNEMVTSRALVERKPESMRIIQHDPDEVPRSVQL
+YSVDPVTTAAAVRMLVEEDRADHIDMNFGCPVPKVTRRGGGSALPWKSELFASIVKAAVT
+EASKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAVWEDIA
+RLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWMFGDIQNAFEGRPE
+RFHPTLGMVADTLYRHAELLVDTFGGDEVKALRDIRKHVAWYFKGYPVGSEVRTGLSTVP
+NLATLRELLDRLDRDMPYPGAPAEGPRGRAGAPKRPHLPDGWLDSRELNEEQRAMIHAAE
+LDVSGG
+>GCF_023573625.1_00575
+MTSSHTLPAAAVTDADDVADPHAAHYAKSAGAGRRIADDDQLHEARHPAPTTDRLTLPPL
+RLGPLTIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHD
+PDEVPRSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSEL
+FASIVKAAVTEASKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFY
+SGTAVWDDIARLREALPDIPVLGNGDIWSAEDAIAMVERTGVDGVVIGRGCQGRPWLFGD
+LQAAFEGRQDRFRPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYFKGYPVGS
+EIRTALSTVPDLATLREILARVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNA
+EQKAMIQAAELDVSGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000568.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000568.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ad074b8ed5f42db0244c1cad5751a4d1e26611a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000568.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00575
+MAEPTTPEPAAGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYPPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATGDRYLEPM
+FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
+>GCF_003691675.1_00307
+MAEPTTPVPAAGTPAAPSSHWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLEATGDRYLEPM
+FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
+>GCF_005280335.1_02358
+MAEGWAGPAHQPVLFGPQGRPPYAGRAVQTPGYTPWDRERWLPEPPKSSYRSDFERDRAR
+VLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGRSLGCDPDLVDTACLSH
+DLGHPPFGHNGEKALDALSADVGGFEGNAQTLRLLARLEQKKLFEDGSSAGLNLTRAALD
+AACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFREGVSGSRKSMEAQVMDLADDIS
+YSVHDVEDGVVNAAFQLKWLAIPEHRERVVETTRQWYLPLTDPAEVDEALARLEATDVWV
+SEMDGSRRALAAMKDMTSQLIGRFCTAAFDATRQVFGNEPLTRHGADVVVPAETETEIAV
+MKGIAAAYVMASEQRQPLYARQRELLAELVELLDASGDRYLEPMFAFDWREAADEAARRR
+VVLDQVASLTDSTALEWHHTLVQGAEFTRVWI
+>GCF_020097155.1_02249
+MAEPQPTLFGPADRPPYAGRPVPTPGYTDWDRRRWLAEPPKSSYRSDFERDRARVLHSAA
+LRRLGAKTQVVAPDLDDFSRTRLTHSLEVAQIGRELGRSLGCDPDLVDTACLSHDLGHPP
+FGHNGEKALDAVAEAAGGFEGNAQTLRLLARLEQKKSFPDGSSAGLNLTRAALDAACKYP
+WVREDAPLRPDGKRSRKFGVYADDLPVFEWFRQGVHGARKSMEAQVMDLADDISYSVHDV
+EDGVVNSAFQLRWITEPGERRARVLETTRDWYLPGGDLEEIDAALTRLESQDVWMGEMDG
+SRRALAGMKDMTSQLIGRFCTAAFDATREVFGNEPLTRHAADVVVPAHTEHEIAVMKGIA
+AAFVMTSEQRQPLYARQRDLLTELVDLLMTTGDRYLDPMFAADFQDAADDAARARVVIDQ
+VASLTDSTAIEWHRTLVRGETFQRVWL
+>GCF_023573625.1_00576
+MAERTTPAPADGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGDKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATEDRYLEPM
+FAFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000569.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000569.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eff1bf40d0a83f9bd9c22cb84af0568f2b106cab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000569.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00579
+MADPHPVLAASAPVLADPHPVLAASAPDLDPDALDAVRALVAAAERPVVLSGAGMSAESG
+IPTFRDARTGLWERFSAEELATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ
+RRTPGLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECWAPADVDPGAPADEATAGSE
+ADLEAMLREAPPACTVCGDGLIRPGIVWFGEMLPAEPWDRAFAALEDCDLCVVVGTSGIV
+QPAASLPFVALGAGAAVVEVNPVETELSGAVTHVLRGPAGAVLPALVAGVWPGPSGALST
+ARHVTW
+>GCF_003691675.1_00311
+MADPHPVLAASAPVLAASAPVLAASAPDLDPGALDAVRALVAAAERPVVLSGAGMSAESG
+IPTFRDAQTGLWERFSAEQLATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ
+RRTPDLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECGAPADVDPGAPSDVDAAGSE
+ADLEAMLREAPPACPACGTGRIRPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLI
+QPAASLPFVALGAGVAVVEVNPVKTELSGAVTHALRGSAGAVLPALVAGVWPGPSGALST
+ARHVTW
+>GCF_005280335.1_02354
+MPVEPGRDDVGPAGEAGRAVVGAGQRRRVVNPVAATPPSYLGRHYPVPMSHPSPGDLSET
+VPTADLDAVRALVAQARRPVVLTGAGMSAESGIPTFRDAQTGLWERYSPEQLATEDAFLA
+DPDLVWSWYRWRARMVRARRPNPGHDAVAHWQRAVPGLEVVTQNVDDLHERAGARVLAHL
+HGSLFEHRCAECGAPADVDPGAPADAEAAGSEADLEAMLREAPPTCPACGTGRIRPGVVW
+FGEMLPQEPWERAYEALERCDLALVVGTSGLVQPAASLPFVALGAGAAVVEVNPVETELS
+GAVTHALRGSAGAVLPALVAGV
+>GCF_020097155.1_02248
+MSPTQPSDPAALGAVRRLILEAERPVVLTGAGVSAESGVPTFRDAQTGLWERYSPEQLAT
+AEAFAADPSLVWSWYLWRARMVRAVEPNAGHRALAAWQARTPALRIVTQNVDDLHERAGA
+DVLSHLHGSLFAFRCAECDTPADVDPSAVVALAESAAPGSEAGLEALMHLEPPLCAACRR
+GRVRPDIVWFGELLPERAWGDAQAALEECDLCVVVGTSGVVQPAASLPFLALGAGAPVVE
+VNPDRTALSDAMTHVLRGPAGTVLPALLG
+>GCF_023573625.1_00580
+MADPHPVLAASAPVLADPHPVLAASAPDLDPGALDAVRALVAAAERPVVLSGAGMSAESG
+IPTFRDAQTGLWERFSAEQLATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ
+RRTPDLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECGAPADVDPGAPSDVDAAGSE
+ADLEAMLREAPPACPACGTGRIRPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLI
+QPAASLPFVALGAGVAVVEVNPVETELSGAVTHALRGSAGAVLPALVAGVWPGPSGALST
+ARHVTW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000571.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000571.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f2771ac6f6a762a8fde018a25f8a47d1b3a67b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000571.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_00583
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHATQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGALRHAVPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRAPRRGPEPEARPAPADDGQAIGPQGRHGEAAAPAPRIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD
+>GCF_003691675.1_00316
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRAPRRGPEPEARPAPADDGQAIGPTGRHGEAAAPAPKIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD
+>GCF_005280335.1_02351
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGEHGDVISFLMELEHTTFTETVERLAARVGVELHYEDGGTGPDKAETGRRRRLLE
+ANKVADEFYRRALGSAEAQTGRDFLTQRGFTQEHAEQFGLGYAPQGWSHLLDHLRQKGFR
+DEELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKMA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTYVAVEPSGMDPCDLRMQQG
+DEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRGQRRGGGSEPRREPERGPEPDQAPGQGRGPAPEGPSVGP
+QGRHGEAAAPAPQVLVPVDPRDPVARCERESLEVVLQHPTLLSAEQWTALYAARFTIPQY
+AAVHHGVKVAGSSGATPQRWVDAVRYAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIM
+NRLFALQIVHRKEELLGRLQRLGPDGDPAEFTALNSELMELEARRRALRADD
+>GCF_020097155.1_02246
+MVRMAGLIVRKDIDLVRERADLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGV
+GTYHCFGCGEHGDVISFLMEMEHTTFTETVERLAARAGVELHYEDGQGPDRAETSRRRRL
+LEANKLADEFYRARLAAPDAQPGRDFLTGRGFTQEHAEQFGLGYAPQGWSALLDHLRQQG
+FRDDELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGNTIGFGARKLFEDDPGPKYLNTPE
+TPLYKKSQVLYGIDLAKRAIAKERQLVLVEGYTDVMAAHLSGVETAVATCGTAFGADHIK
+IARRLISDDGTGGEVIFTFDGDAAGQKAALKAFDEDHRFLAKTFVAVEPNGLDPCDLRMQ
+QGEEAVRALIASRRPLFEFAISAGLKDYDLNTVEGRAGALRHAAPIVAGIKDSVLRPGYE
+RELAGWLGMDPNVVSRAVAQELRGRRRGGPSGGSAERTPAPERAPEGANAGQAPGEEPAA
+PRPALIVPVDPRDPAARRERESLEVVLQHPTLLSAEQWTAFYQARFTIPQYAAVHHAVKV
+AGTAGATPSRWVDAVRDAAPGEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFSLQIV
+HRKEELLGQLQRLGPEGDHDEFMRLNAELMELETRRRALRADD
+>GCF_023573625.1_00584
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFMETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLGPNAVHRAVAAAGRAPRRGPEPEARPTPASDGQAVGPTGRHGEAAAPAPRIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKVAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000572.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000572.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2763c4f574a882d6a6cdd72889b52eee57dc136b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000572.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00584
+MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPEVDASSSLASTPATDDASGS
+ATSSSASSASASSTAAAAGSDSATGQADDPAYAVIDAVLEKYGDGIIVAVDADDDDTTWE
+VDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDGVTLDE
+MDLDDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDEH
+>GCF_003691675.1_00317
+MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSVSPEVDASSAVASTPATDDASTT
+SASASSSASSTSASSTAAAASSGSGTGQADDPAYAVIDAVLEKHGDGIIVEVDANDDDTT
+WEVDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDGVTL
+DEMDLEDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDER
+>GCF_005280335.1_02350
+MNATSLARKTALTGTGLLAALALAACGTADDDTAANPQETAVQQSPTQAATTAPASASGS
+ASASASGSASASASGSASPAAASGSVERQGDDPAYAAIDAILGLHDDGVIVEMDLDDDDA
+KWEVDVVVGDDVKEYDVTTGGQVSEGVRPQIDDDVRRAGEAQVTAETAISTALQGRTDQT
+VDEVDLDEEGGTLVWKVELDRENGEDGAEVKIDAKTGDVIEVEEG
+>GCF_020097155.1_02245
+MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSASLEVDASSAVASTPATEDASTT
+SASASSASSAPASSTAAAAGRDSATGQADDPASAVIDAVLEKYGDGIIVGVDANDDDTTW
+EVDVVVDKEVKELDVTADGDITETDRESDPEDVQKAKDAEVTAQQALDTARKGRDGVTLD
+EMDLDDDNGTLQWEVEFDREDGSDGPEVEIDATSGEVLTVDEH
+>GCF_023573625.1_00585
+MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPGVDASSAVASTPTTDDASGS
+ASSSASSASASSTAAAAGSGSATGQADEPAYAVIDAVLEKYADGIIVAVDANDDDTTWEV
+DVVVGEGAKELDVTADGDITETDRESDPEDVQKAKEAEVTAQQALDTAREGRDGVTLDEM
+DLEDDNGTLQWEVRFDREDGSDGPEVEIDATSGEVLTVDER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000578.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000578.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eef2ffcb68b3083329e288e0487bf1a9ee279fe6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000578.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_00641
+MDTTRFDDDLRAMLGEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGLAAWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR
+>GCF_003691675.1_00378
+MDTTRFDDDLRAMLDEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQAMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGLATWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR
+>GCF_005280335.1_02321
+MDTTRLDDDLRAMLAEVESDRRGEPSDYLEDVAGQHVDGLAAAVCTVDGHQAAAGETDHA
+FALQSVSKALTYAVVLQEVGLDAVLERVGVEPSGEAFNHLSLHDDGRPYNPLINAGAIMA
+HALLPAGDHEERVALLVRRYSALAGAELEVSQDVLDAELTRADRNLGLAHLLADAGQLPV
+SAREAVAGYLAQCSVTVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLTCGM
+YDATGQWVAEVGVPAKSGVSGALLGAVPGALGIATWSPRLDERGNSRRGIGIFEGLSARW
+DLHVLQHRGALRGLRASR
+>GCF_020097155.1_02184
+MGIGSLIATMLPSSIAFLPACTGMVIGWRWLGLPLGPNARSSAHRDRPGARPRPGRPSTT
+VTGMDTTRFDDDLRAMLGEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGET
+EHAFALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGA
+ILVHSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGR
+LPISAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLT
+CGMYDASGQWVAEVGVPAKSGVSGALLGAVPGALGLAAWSPRLDEQGNSRRGIGLFEGLS
+SRWDLHVLQHRGALRGLSGPR
+>GCF_023573625.1_00611
+MDTTRFDDDLRAMLDEVESDRRGEPSDYREDVAGQHVDGLAAAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HALLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQAMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGIATWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000580.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000580.fa
new file mode 100644
index 0000000000000000000000000000000000000000..158fad88ebe85d46a2e9adf7a09c52e00387f3cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000580.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00643
+MTARLLADVDTGIDDACALLHLVGAHRLGAGPELAAVTTTGGNATARDCALNTAAVLDLA
+GRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRRPERLSPRPAVDVWLDELRAHP
+GETAILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPDAAK
+EVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGAHPVGWSADRPRVAGPDAA
+TGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVVDVEADSE
+LLRGTTVHDTRDIWGRRPNAQLVTANDPAEVFAAFARAVGAVVAGERTLDGGSPAR
+>GCF_003691675.1_00380
+MTARLLADVDTGIDDACALLHLVGAHRLGVGPELAAVTTTGGNATARDCALNTAAVLDLA
+GRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRRPERLSSRPAVDVWLDELRAHP
+GETTILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPDAAK
+EVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPVGWSADRPRVAGPDAA
+TGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVVDVEADSE
+LLRGTTVHDTRDIWGMRPNAQLVTANDPAEVFAAFARAVGAVVAGERTLDGGSPAR
+>GCF_005280335.1_00385
+MGARILADMDTGIDDACALLQLVGAGAELAAVTTTGGNATARECALNTAALLDLMGRTDV
+EVAVGAEAPLQRPPETTPETHGDGGLGYARLAHRPERLSARSAVDVWVEELRARPGRTTI
+LCTAPLTNLALALRAEPALPELAAGVVIMGGAFYYPGNTTPTAEWNTWCDPDAAKEVFAA
+FEGLPEDRLPLLCPLETTERIEYTPALLDALLTGVGHAPTGWSVDRARHAGPQADTGSPV
+LDVLADALRFYFEFHHDYDQGYVAHLHDLFAAQVALGTAQIRTQATVVDVEADSDLLRGT
+TVHDDRHIWGRRPNARRVVDADPAGVFAAFAQAASAAARAGDDAGR
+>GCF_020097155.1_02182
+MAAVTARLLADVDTGIDDACALLHLVGAHRLGAGPELAAVTTTGGNATARDCALNTAAVL
+DLAGRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIDRRPERLSPRPAVDVWLDELR
+AHPGETTILCTAPLTNLALALRAEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPD
+SAKEVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPARWDVARPRVSGP
+AADTGHPVTDVLADALRFYFEFHHDYDQGYIAHLHDLVAAQVAAGQADVTLQATVVDVEA
+DSELLRGTTVHDDRRIWGRRPNARRVTGCDPRRVFEDFAQAVGALTGAGVG
+>GCF_023573625.1_00613
+MAAVTARLLADVDTGIDDACALLHLVGAHRLGAGPELVAVTTTGGNASARDCALNTAAVL
+DLAGRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRHPERLSPRPAVDVWLDELR
+AHPGETTILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPD
+AAKEVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPVGWSADRPRVAGP
+DAATGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVIDVEA
+DSELLRGTTVHDTRDIWGRRPNAQLVTANDPAEVFAAFARAVGAVVAGERTPDGGAPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000581.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000581.fa
new file mode 100644
index 0000000000000000000000000000000000000000..617acf651f6824dfcac723d7c7cbb99ffec8765f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000581.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00645
+MSHQAPPADASKVRAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELELAKRHVAAK
+GKKAGIGAGIAVVGLFFLALMVVALVVTLIGAFADPTFWFPALMVALAFLVLGLIFAGVG
+LMMVKGAMPLVPQEIVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKEENKKARKNGEAAPHPDRADASEAEIRRRADLRRRHLGDIRSGLDEKTSVKGQLAAF
+AAQRKGRGVTPETAHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR
+>GCF_003691675.1_00382
+MSHQAPPADASKVRAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELELAKRHVAAK
+GKKAGIGAGIAVVGLFFLALMVVALVVTLIGAFADPTFWFPALMVALAFLVLGLIFAGVG
+LMMVKGAMPLVPQEIVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKKENKKARKNGEAAPHPDRADASEAEIRRRADLRRRHLGDIRSGLDEKTSVKGQLAAF
+AAQRKGRGVTPETAHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR
+>GCF_005280335.1_02318
+MSHQAPPADALKAGAPRPAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELALAKGHVVAK
+GKKAGIGAGVTVVGLFFLALVVVALVVALIGAFADPTFWFPALMVAAAFLVLGAIFAGIG
+LFMVKGAMPLVPQETVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAKRAEERRK
+VEKEENKKARKNGEAAPHPDRDEASEAEIRRRADLRRRHLGDIRSGLEEKTSVKGQLAAF
+AAQRKGRGVTPQTAHATDQTAPFTGAARAGEKAAEAEDYVKDNWQPLALLGASSAAFLAL
+AGRLRRR
+>GCF_020097155.1_02177
+MSHAAPTAAPRAPRPTTPVTPQTRASSLTDLLAAVVRLLPLQLKDELALAKGQAAAKGKK
+AGIGAALAVVGLFFLALMTIALVVALIGAFANPPFWFPALMVALVFLVLGLVLAGVGAMQ
+IKGAMPLVPQETVRNLEYDLGYLKEGNDFDPAEYDRLKAERAEAKRLEKQREAERKKVEK
+EENKQARKDGLAAPHPAKDDASEDEVRRRAELRRRHLGDIRSGLDEKTSVKGQVAAFTAQ
+RKLRGTTPDTAHATEQTAPFTTAARAGEQTAAAEDYVKERWQPLALLGASGTAFAVLASR
+LRGRKG
+>GCF_023573625.1_00615
+MSHQAPPADASKARAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELALAKGHVAAK
+GKKAGIGAGVAVVGLFFLALMVVALVVTLIGAFADPSFWFPALMVALAFLVLGLIFAGVG
+LVMVKGAMPLVPQETVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKEENKKARKNGEAAPHPDRDDATEAEIRRRADLRRRHLGDIRSGLDEKTNVKGQLAAF
+AAQRKGRGVTPETTHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000582.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000582.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83565138c329c0ed2f31890f947720f9f91a62fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000582.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00647
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKTSFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPVSNGIDASAYELQPGERVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGAADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERIARIL
+DLSDAERAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRALL
+>GCF_003691675.1_00384
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKTSFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPISNGIDASAYELQPGEKVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGAADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERIARIL
+DLSDAERAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRALL
+>GCF_005280335.1_02316
+MSDRPGTAADRPLKVLIAADTYPPHVNGAATFCHRLATALHARGHEVHVVMPRGEAGPDT
+VEERPEATVHLLRAIPAPTHEYYRLVMPWHAKAAFRRIYREVQPDVVHVQCHYMVGEAAI
+NEAERRRIRMVSTNHFMPENLEPFLPFPQWFLDIVSRVSWRDMGRLMGKGAAVTTPTALA
+ARAMAEHAGLDNVLPVSNGIDAAAYELQPGETVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARVRPDLDVHAEIVGDGEQRDRIRAAVESEGVADRVLLRGHVSDEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERVARIL
+DLPEAERAAMGEASHAKAMHHSAQKTVDVFERLYRGATPAEVRELL
+>GCF_020097155.1_02175
+MTSSARPAQERPLTVVIAADTYPPDVNGAAVFCFRLASALHERGHRVHVIAARNEPGPDT
+VEERPEATVHRLESHRAFTHEYYRLVFPWHASRSIDRILAEVRPDVVHAQCHYMIGEAAI
+NVADRRRIRTVSTNHFMPENLEPFLPFPQWFLNIVSKNSWRDMGRLMGKGAAVTTPTALA
+AAAMAEHAGLDRVLPISNGIDASAYELAPGEVVERAAHPTVLFVGRLAVEKHVDVLVRAV
+AHLARTRPDLDVHAEIVGDGEQRTALDAVIAEEGVADRVRRLGHVSDAELHTAYLRADVF
+CQPGTAELQSLVSLEAMSASTPVVLADALALPHLVDDGVNGWLFPPGDHVALAERIARVL
+DLPEAGRAAMGEASHAKAVRHSQAKTVDLFERLYRGATPAEIRAAL
+>GCF_023573625.1_00617
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKISFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPVSNGIDASAYELQPGERVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGVADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALADRIARIL
+DLSDADRAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRAML
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000583.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000583.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbfa31f856677b0e28b534d8651c8ee90442d71c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000583.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00649
+MSVTSSHAAVRRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETAYTVRSGDGWWII
+AQRTGVSMSRLQSLNGMTAATVLHPGMVLKTSGTATPTPAPAPSTSGSTYTVLAGDGWWI
+ISYRTGVSASILQSINGMSSSTMLHPGMVLKTTSVSTSSAPAVAPAPAPASKQAAVDYVR
+SAVRNPSSYYVWGGNGPSGFDCSGLTQQAMARAGISIPRRAGDQYLAAKSYVPISQAQPG
+DLVFYANQSTGRIYHTAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY
+>GCF_003691675.1_00386
+MSVTSSHAASRRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETTYTVRSGDGWWII
+AQRTGVSMSTLQSLNGMTAATVLHPGMVLETSGTATPAPAPAPSTSGSTYTVLAGDGWWI
+ISYRTGVSASILQSINGMTSSTMLHPGMVLKTTSVSTSSAPALAPASAPASKQAAVDYVR
+AAVRNPSSYYAWGGNGPSGFDCSGLTQQAMAQAGISIPRRAGDQYLAAKSYVPISQAQPG
+DLVFYANQSTGRIYHVAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY
+>GCF_005280335.1_02314
+MSVTSSRAASRRAPRTAAASLALALGAGALAGVGSVTAAETAQAVETTYTVRAGDGWWVI
+SQRTGVSMSTLQSLNGMTSATMLHPGMVLKTSGTAAPAPAPAPSASTYTVLAGDGWWIIS
+YRTGVSASVLQSINGMTSSTVLHPGMVLKTSVVASSAPAPAPAPVTNGKQAAVDFVRSTV
+QNPSSYYLWGGNGPYGFDCSGLTQQAMAKAGISIPRRAGDQYNAAKSYVPISQAQPGDLV
+FYANQSTGRIYHVAMYMGGGQLAHALNEDAGLLFTSTTIMKSDMLAVAARY
+>GCF_020097155.1_02171
+MPEALLTPARRPRAAAASLALALGAGAGVTAGAAVIAPQAVAAETYTVQAGDGWWIISQR
+TGVSMATLMQLNGMTSADMLHPGMVLKTSGTVTAAAGTYTVKAGDGWYAISRATGVPVST
+LTSLNGMTITSMLYPGMVLKTTGTPASTAPAPAPAPAPVVRQSSKQAAIDFAVAKVNDPN
+TYYAWGGNGPYGYDCSGLTKAAFAAAGITIPRVSHDQYVNAPAYAPLSQAQPGDLVFWAN
+QSTGRVYHVAVYIGNGKVAHALNTTDDLVITSTDVMTSNRLAVVGRY
+>GCF_023573625.1_00619
+MSVTSPHAAARRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETTYTVRSGDGWWII
+AQRTGVSMSTLQSLNGMTAATVLHPGMVLKTSGTATPAPAPAPSTSGSTYTVLAGDGWWI
+ISYRTGVSASVLQSINGMTSSTMLHPGMVLKTTSVSTSSAPAPAPAPASKQAAVDYVRSA
+VRNPSSYYVWGGNGPSGFDCSGLTQQAMARAGISIPRRAGDQYLAAKSYVPISQAQPGDL
+VFYANQSTGRIYHTAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000584.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000584.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07b5f64e749c7e5e493fa619b9bdf646c37356e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000584.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00651
+MTPRTHLPRPLPRPHIAGCVAAALLAWLVLASGVGGLDAVPRATSAPSGRDALLLVAASP
+AGPGSTAAPVAWHAPVAGAAPDDVLRAFVAPERPWGRGHRGVDLAVPSGAAIRAPAAGRV
+VFAGVVVDRPVLTLEHEDGTRSSLEPVEADVAVGAVVAAGDPVGRLAGAPPHCTRACVHW
+GVREPDGWRVGDAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP
+>GCF_003691675.1_00388
+MTPRTLLPRPLPRPRIAGCVAAALLAWLVLALEMGDLGPASRATPAPSTRDALLLVAASP
+AGPGATAAPVAWHPPVAGAAPDDVLRAFVAPERPWSRGHRGVDLAVQTGAPIQAPAAGRV
+VFAGVVVDRPVLTLEHADGTRSSLEPVEADVAVGAVVDAGDPVGRLAGAPPHCPRACVHW
+GVREPDGWRVGDAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP
+>GCF_005280335.1_02312
+MTARSPAPRRARPAASPHRLLAVLLLCVLGLALAFALGPGIGAATPSSIRAEDGPTADAR
+LAVAATPARAWTAPAAGVRPGDVLRPFAAPERPWGRGHRGVDLAVSPGAAVLAPAAGTVV
+FAGTVVDRPVVTLEHADGTRSSLEPVEAAAPVGARLERGAPLGTVADAPAHCAVPCVHWG
+VRVPDGWRFGDATFDRYLDPLVLIGWSGPSVLWPHAAPPPAGPAPARE
+>GCF_020097155.1_02169
+MNEASTPPPRLRAAAVLAVALLATASAARAEDAPAAPPVTGALLAPTPGAGPSDVLRGFA
+GPERPWSRGHRGVDLATSSGLVTAPAAGTVRFVGSVAGRGVLTLAHPDGTLSSFEPVTSD
+LTAGQAVAAGQEVARVQEGAAHCPVRCVHWGVRREDAWAVGAARFDRYLDPLLLLGWSGP
+SVLWPVGDAG
+>GCF_023573625.1_00621
+MTPRTLLPRPLPRPRIAGCVAAALLAWLVLALGMGDLGPVSRATPAPSTRDALLLVAASP
+AGPGATAAPVAWHPPVAGAAPDDVLRAFVAPERPWSRGHRGVDLAVQTGAPIQAPAAGRV
+VFAGVVVDRPVLTLEHEDGTRSSLEPVEADVAVGAVVAAGDPVGRLAGAPPHCTRACVHW
+GVREPDGWRVGEAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000586.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000586.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a71022cbd11daeb2d63f34c1c4fd1a0788fd3d74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000586.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00653
+MANYTAADIKALRERTGAGMMDVKKALDEADGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASEHEGRT
+LGDYVTEEGALLGEKVAVRRLARVEGAYVDAYLHKTSKDLPAQVGVLLAVDADSAEAKTA
+AHDIAVHVAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN
+>GCF_003691675.1_00390
+MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASDYEGRT
+LGDYVTEEGALLGEKVAVRRLARVEGAFVDAYLHKTSKDLPAQVGVLLAVDADSADAKTA
+AHDIAVHTAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN
+>GCF_005280335.1_02310
+MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKAEKFITLGDVVLRAAVASGAADVESLLASEHEGRT
+LGDHVIEEGALLGEKVAVRRLARVEGALVDAYLHKTSKDLPAQVGVLLAVDADSAEAKTA
+AHDIAVHTAAYSPTYLSREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLEDQPFAKDPKQTVGKVASDAGTKVTGFARFRVGN
+>GCF_020097155.1_02167
+MANYTAADIKALRERTGAGMMDVKKALDEANGDADKAVEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFISLGDVVLKAAVASGAADVDSLLASDHEGRT
+LGDYVTEEGALLGEKVAVRRVARVEGAHVDAYLHKTSKDLPAQVGVLLAVDADSDAAKTA
+AHDIAVHTAAYSPTYLTREDVPAETVENERRIAEESARAEGKPEQALAKIVEGRLTGFFK
+EGVLVDQPFAKDPKTTVGKVASEAGTAVTGYARFRVGN
+>GCF_023573625.1_00623
+MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASDYEGRT
+LGDYVTEEGALLGEKVAVRRLARVEGAFVDAYLHKTSKDLPAQVGVLLAVDADSADAKTA
+AHDIAVHTAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000587.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000587.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68804dbed79e75bd4339416a2e58d5a7bbcd1dd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000587.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00654
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>GCF_003691675.1_00391
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>GCF_005280335.1_02309
+METNRAPEDPKTAHVPQTSDDTGRRRVLLKLSGEVFGGGKVGVDPETVRGIAEQIAVAAD
+RVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVSTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVVFGAGTGLPYFSTDTVAAQRALEIGADEVLMAKSG
+VDGVYTADPKKDPSAELLTHLTYDEALLRNIRVMDLTAMTMCKDNNLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>GCF_020097155.1_02166
+MSPAQQPENHAVDAEDTGRRRVLLKLSGEVFGGGSVGIDPVTVRGIAEQIAEAAEQVEIS
+IVVGGGNFFRGAELSESGMDRRRADYMGMLGTVMNCLALQDFLLQAGVSTRVQSAIHMEQ
+VAESYIPLRAVRHMQKGRVVVFGAGTGLPYFSTDTVAAQRALEIGADEVLMAKSGVDGVY
+TADPKKDPTAQRLEHLTYDEALRKDIRVMDLTAMTMCKDNGLSMRVFGMEGPGNVTRALL
+GEEIGTSVTP
+>GCF_023573625.1_00624
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000590.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000590.fa
new file mode 100644
index 0000000000000000000000000000000000000000..504e8197145f982e1af764b7f4f7206112362b5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000590.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00658
+MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFGDEEAGA
+>GCF_003691675.1_00395
+MTLVDHTRPTGGQSAGSPLPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
+>GCF_005280335.1_02305
+MTLVDHTRPAGGEAATSPPPGEPAEAPMLQVLDAEGRRHAQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALREDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSGWDPQATGVATQQIIIGAQALHAVGYAMGVQRDQADAATIVY
+FGDGATSQGDVNEAMVFSASYRSPVVFFCQNNHWAISEPVKLQTRRSIADRPWGFGIPSL
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALESLVEDGAELLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
+>GCF_020097155.1_02161
+MTDVHLPEQDAPPRSDRPAEQLQVLTPDGRRSPSPELDPWLTDVDEEMLARLHRELTLVR
+RLDTEATHLQRQGRLALWPPLRGQEASQVGAAAALRPADHVFPSYRENGLCLLRGVEAGE
+LLRVWSGSSFSGWDPAATGVATQQLVIGAQTLHAVGYAMGVQRDAADVSTLVCFGDGATS
+EGDVHEAMVFAASYQAPVVFFCQNNHWAISEPVGLQARRSIADRAWGYGIPALRVDGNDV
+LAVLAAVRRGVDRAAAGAGPMFVEAVTYRMGAHTTADDPTRYQDPAELEAWARRDPLERL
+TAHLRDVGADADAVVDASEAAADDLAARMRADLDALPEEGPEALFAHVYAEPHQELARQQ
+RDLQLHLDGLDAGEEQA
+>GCF_023573625.1_00628
+MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDAEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000591.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08376560ef2719938a9f30b26d88aa0819ba28c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000591.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00659
+MSERMTFGRAINRGLQRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD
+KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR
+>GCF_003691675.1_00396
+MSERMTFSRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD
+KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR
+>GCF_005280335.1_02304
+MSERMTFGRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQDEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTPGLRVVSPSSPQEGHDLIRAAIASDDPVVYLEPKRRYHD
+KGEVDLDADIPPMSTAKILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGVDRALGRPNSLDSVDAFAAPETAEQFLAAQTAGEETR
+>GCF_020097155.1_02160
+MSEQMTFGRALNRGLHRALADDPKVLLMGEDIGRLGGVFRITDGLQEEFGVDRVVDTPLA
+EAGIVGTAIGLALRGYRPVVEIQFDGFLYPAFDQIVANLAKLRARTRGRVAVPVTIRIPY
+GGGIGSPEHHCESPEAYFLHTPGLRVVSPSSPQAGYEMIRAAIASDDPVVFFEPKRRYHD
+KGPVDLDAAPGPLSVGRVLRPGADVTLVAYGPLVKTALQAAEVAEQEGVSVELIDLRSLS
+PLDTGLVEASVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLESPPVRVTGLDIPYP
+PATLEHLHLPDLDRILEGVDRALGRPNPQDAVDAFAPPQTAEDFLSARADSSEVPA
+>GCF_023573625.1_00629
+MSERMTFGRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD
+KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000593.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000593.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9e6a5773c66de0a01fa51e1c6626596dd42e5dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000593.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00661
+MAGTRDGDAVEPRPERSTAVLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFD
+YHWAHLLGDEDTVVRTIEHEGRAVGALVCTQQDGVGELSFWTAQDYWGLGLTTAAVDRFL
+EEHTARPLRAHVPEDNVGSVKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD
+>GCF_003691675.1_00398
+MLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFDYHWAHLLGDEDTVVRTIEH
+EGRAVGALVCIQQDGVGELSFWTAQDYWGLGLTTAAVDRFLEEHTARPLRAHVPEDNVGS
+VKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD
+>GCF_005280335.1_02302
+MLLRDVRPEDLDEFFLHQQDEQASLMSAFAPRNPRDRGVFDYHWSSLLAAETAVVRTIEH
+EGRAVGAIVCTEHDGVGELSFWTAQDYWGLGLTTAAVDAFLREHTRRPLRAHVPEDNAGS
+VKVLSRRGFETVGQEKVFSNARAEVITELVMELPAGAE
+>GCF_020097155.1_02158
+MPLRDVRPDDLDAFFLHQQDERANLMSAFAPRNPSDRGVFDYHWAHLLGDDATEVRTIEH
+EGRPVGALVCTRVDGVDELSFWVAREFWGQGLTTSAVDEFLSTHRERPVRAHVPEDNLGS
+VKVLTRRGFREVGREKVFSNARAEVVEELVLELPGA
+>GCF_023573625.1_00631
+MLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFDYHWAHLLGDEDTVVRTIEH
+EGRAVGALVCTQQDGVGELSFWTAQDYWGLGLTTAAVDRFLEEHTARPLRAHVPEDNVGS
+VKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000594.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000594.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38771cd9e5c1f74c7eda8afa7c500adc3b09060b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000594.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00662
+MPAADPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP
+AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI
+RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPREDQATAVFRAQAVLGLLNSTP
+RSVRRTAADRAARRATLVAMAWAAATAPGPLSGED
+>GCF_003691675.1_00399
+MPAVDPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP
+AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI
+RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPHEDQATAVFRAQAVLGLLNSTP
+RSVRRTAADRAARRATLVAMAWAAATAPGPLSGED
+>GCF_005280335.1_02301
+MPAAVDPSAPAASAAAPTSRVAAKARRREDLLAAAARLFAARGFDAVRLEDIGAEVGISG
+PAIYRHFAGKAAVLVAILATASQDLLEGALATEREHDAGEDALRALIAFQTDFALAQRDV
+IRVQDRDMSALPEDERAAVTGTQRAYIDVWARQLRVVHPSEDQATAVFRAQAVLGLINST
+PRSVRRTAADRAARRATLVAMAWAAATAPGPAADRP
+>GCF_020097155.1_02157
+MPHAPDTAAPGPTGTPRERAKARRRAELLAAAARLFAAHGYEATRLEDIGAAAGISGPGI
+YRHFAGKAAVLVEILSSASLFLLDGAEAVAARGLSGAEAVHDLIAFHTDFALANRDVIRV
+QGRDMSSLPPADGAEITRVQRRYIDLWGAQLRRLHPGEDHATARFRTQALLGLINSTPFS
+VRRSRADRGARRDALIGMAWAAARTPGGTARPEPPVVP
+>GCF_023573625.1_00632
+MPAVDPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP
+AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI
+RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPHEDQATAVFRAQAVLGLLNSTP
+RSVRRTAADRAARRATLVAMAWAAATAPGPLPGGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000598.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000598.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea21e267e3c69838ed55d56996f3555c52b3c185
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000598.fa
@@ -0,0 +1,44 @@
+>GCF_002008305.4_00670
+MTHGSLTDYTLPAPAPAHDGGAPRAVALIGSTGSIGTQGLDVIAQDPARLRAVALAGGAN
+TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPAPRPVLFTGPRAAEQIAAWP
+GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAARPGQLVPVDSEHS
+ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS
+LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL
+CWPRRLPGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD
+AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR
+W
+>GCF_003691675.1_00407
+MTHGSLTDYTLPAPAPADDDGAPRAVALIGSTGSIGTQGLDVIAQDPTRLRAVALAGGAN
+TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPSPRPVLFTGPCAAEQIAAWP
+GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAAAPGQLVPVDSEHS
+ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS
+LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL
+CWPRRLSGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD
+AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR
+W
+>GCF_005280335.1_02292
+MTHGSLTDYTLPAAGAPSASNAHDDGAPRAVALIGSTGSIGTQGLDVIAQDPARFRAVAL
+SGGANTGLLAEQAVRFEVQAVGSATATEDELRAAIADAAARLGLKPAPRPALFTGPTAAE
+RIAAWKGADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAAAPGQLVP
+VDSEHSALAQALRGGTADEVRRLVLTASGGPFRGLDRAALAEVTPAQALAHPTWDMGRVV
+TTNSASLVNKALEVIEAHLLFDVPLERIDVVVHPQSVVHSMVEFTDGSTLAQASPPDMRL
+PIALGLAWPARVPGAAAGCDWTRAATWAFEPLDEDAFPAVRAAKEAAAASPTHMAVFNAV
+NEEAVDAFHDGRIRFDAIVDTVRAVVGEYEPARVLGAAGHGHVAQDLTVEAVLAAEDWAR
+TAARARW
+>GCF_020097155.1_02154
+MTHGSLTDYTFPADHGPGASDGACRAVALVGSTGSIGTQGLDVIAQAPERFRAVALSGGA
+NTALLAEQAVAHGVEAVGSAAASEEELRAALADAAARLRRPDPRPALFTGPEAAARIAAW
+EGADTVLNGITGSIGLAPTLAALRAGHRLALANKESLIVGGALVKAAAAPGQLVPVDSEH
+SALAQALRGGTAGEVRRLVLTASGGPFRGFSAAQLAEVTPAQALAHPTWDMGRVVTTNSA
+SLVNKALEVIEAHLLFDVPLERIDVVVHSQSVVHSMVEFTDGSTLAQASPPDMRLPIALG
+IGWPHRVLGAAAGCDWTQAAQWTFEPLDEAAFPAVSLAKEAAASSDTHMAVFNAANEEAV
+DAFHGGRIRFDQIVETVRAVLGEYRPDGVLAAAGADPDELTVEAVLAAEDWARAAARGRW
+>GCF_023573625.1_00640
+MTHGSLTDYTLPAPAPADDDGAPRAVALIGSTGSIGTQGLDVIAQDPARLRAVALAGGAN
+TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPAPRPVLFTGPRAAEQIAAWP
+GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAARPGQLVPVDSEHS
+ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS
+LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL
+CWPRRLPGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD
+AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR
+W
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000601.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000601.fa
new file mode 100644
index 0000000000000000000000000000000000000000..142e486f508ce68c8e5eded7e3b6add704badd7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000601.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00673
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDDDAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA
+AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPHVVQAQP
+HDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHTGRVFIDPGPRDAGGPLRFKA
+DIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY
+ERVGFERRGTFATVLY
+>GCF_003691675.1_00410
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDDDAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA
+AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPHVVQAQP
+HDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHAGRVFIDPGPRDAGGPLRFKA
+DIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY
+ERVGFERRGTFATVLY
+>GCF_005280335.1_02289
+MTRLPPVPRWSPSTDRQVRAATGGRVRLLTDADTPALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDAGEGRDDDGAPVAGLRAALWVGSNVVPVAAAETPDAGWAPGDAE
+ALGAAAVALRRRYGSLYGPAEPVLAVGSALAAAGHRARSVREDQPLLVLGADGAAETSPH
+VVQAHPRDFERVLPASAAMFEEELGFSPFLGGAAQYRDRVERLIRAGRVFIDPGPADAGG
+PLRFKADIGLLSSRCAQIQGVWMAPAARGRGLAAAAMAAVVEYVRLQAPVVSLYVNAYNT
+PALRTYERVGFERRGTFATVLY
+>GCF_020097155.1_02151
+MDLAAASDGRVRVLTDADTPALTALAAADPVANVHAASLLEAGRLAGPRGGRADGTLFLG
+VEDPDRPGALRSACWVGSTVVPLAGHDDDVPALAASVAALRRRFASVYGPAVTVLAVGRT
+LRDAGHRPRAVREEQPLMVHARTPGDLVPDPAVRAAAPGEWESVVPASAAMFEEELGFSP
+FLTGAAQYRDRVRRLVADGRVFTAPGEPVVDDPTSGVRFKADIGLLSASCVQVQGVWLHP
+SRRGRGEAAPAMAAAVALMARRAPAVSLYVNGFNTPALRTYERVGFERVGTFATVLY
+>GCF_023573625.1_00643
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDDDAPGAGGLRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA
+AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPSVVQAQP
+RDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIQAGRVFIDPGPRDAGGPLRFKA
+DIGLLSSRCAQIQGVWMAPAARGRGLAVSAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY
+ERVGFERRGTFATVLY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000604.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000604.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d7cc948d1f1caf3906e5c97f69ad3eb237350df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000604.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00676
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
+>GCF_003691675.1_00413
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
+>GCF_005280335.1_02286
+MDSTDRHDDAASLRARVEEALASADVVVEEVRVAGAAAHPTVEVVVDRASGTEGLSLDEL
+AGLSGRVSAALDALGDHVPGVGAGEYLLELTTAGVDRPLTQPRHFARNVGRLVEVAVDGG
+EPFTARLLAADEDAVELAEVRPGAKKGMKAKELPAQRVELARLGPAVVQVEWTPAQQAAD
+AAAAGEQTAEHTEA
+>GCF_020097155.1_02148
+METVPAALTELVEGAVSHRGVVVESVRVAGAADAPTVEVVLDRLEGTEGLSLDEVAELSG
+LVSDALDACGDEVPGVGAGEYLLEVSTAGVDRPLTGPRHWLRNVGRLVEVSIDAALPVTA
+RVLGVEASGVELEVVRPGAKKGMPAKVLPAEHVDFSRLGPGQVQVEWSTAAEQSGAEQTA
+EQTEA
+>GCF_023573625.1_00646
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGAAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSIDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000606.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000606.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3b7dc3515b5262769d3591e0167b99cbb2a2506
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000606.fa
@@ -0,0 +1,81 @@
+>GCF_002008305.4_00679
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP
+GSTPAAPGRSAAPKPAAAPSPRAAAPTSNVGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP
+AAPAEPKAPQPPATPGSAAPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR
+PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP
+GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP
+RKGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK
+VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE
+ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL
+TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI
+DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA
+NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA
+ADPSRPVQVLGLSTVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD
+QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA
+TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG
+SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSDHLKIESLRRFKDDATEV
+REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV
+>GCF_003691675.1_00416
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP
+GSTPAAPGRSAAPKPAAAPSPRAAAPTSNAGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP
+AAPAEPKAPQPPATPGSAVPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR
+PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP
+GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP
+RRGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK
+VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE
+ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL
+TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI
+DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA
+NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA
+ADPSRPVQVLGLSAVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD
+QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA
+TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG
+SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSEHLKIESLRRFKDDATEV
+REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV
+>GCF_005280335.1_02284
+MMPKQITPAPAPARGGGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGARKGRKS
+KRAKRQEFEQAHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVKVLFTLG
+EMASANQSLDEDTFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEEANEDEADLEPR
+PAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVQHEGEDRRLTFIDTP
+GHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKIDKDTAQ
+PDKIRGQLTEYGLVPEEYGGDTMFVDVSARNGINIDQLLEAVLLTADAALELTANPSKDA
+RGVAVEANLDKGRGAVVTVLVQTGTLRVGDNMVVGSAHGRVRAMFDENGAPVEEADPSRP
+VQVLGLSSVPRAGDSFLVTEDDRTARQIAEKREAADRNAQLAKRRKRITLEDFDQAVAEG
+KLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLATVDDAI
+IIGFNVRPAERVADLADKEGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVALGSAEVRE
+VFRSSKWGSIAGSLVRSGLIRRNAQARLVRDGAVVADNLKIESLRRFKDDATEVREGYEC
+GIGLGSFNDIKEGDVIETFEMREKPRA
+>GCF_020097155.1_02145
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRGAYPGAGAKGSAK
+PAAAAPAAPKPAGGSAPSPAAAKPAAASAPGASAPKPGSAAPQPGSAAPKPGGSAPKPGA
+SAPAPAAQKSAPAAPKAPAAPAPQAPAPKPGASAPKPGASAPKPGGAKPAPRPGNNPFTS
+KAGSAGPRPGGGRSGGPRPGNNPFAPSQGMRSGREDRAPRPGGPRPAAGAGGPRPGGPRP
+AAAGAGGPRPGGPRPNPGMMPKHITPAATPARGGGRGRPGAGGPGGGPGRPGGGPAGRGG
+GRGNAQGAFGRGGGARKGRKSKRAKRQEFEQQHTREIGGVKVLKGDGTTVVRLRRGASLA
+DFAEKIHADVADLVKVLFTLGEMASANQSLDEETFQLLGGELGYVVQIVSPEDEDKELLE
+AFDIDLEAEAAGEDEADLQPRPAVVTVMGHVDHGKTRLLDAIRSSNVTAGEAGGITQHIG
+AYQVPVEHEGSERRLTFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNH
+AQSAGVPIVVAVNKIDKDSAQPDKIRGQLTEYGLIPEEYGGDTMFVDVSARNNLHIDDLL
+EAILLTADAALELSANPDKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHG
+RVRAMFDENGTPVEEATPSRPVQVLGLSSVPRAGDSFLVTDDERTARQIAEKREAADRNA
+QLAKRRKRITLEDFDQAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVI
+HRGVGAITQNDVNLATVDNAIIIGFNVRPAERVADLADKEGVDMRFYSVIYDAIDDIENA
+LKGMLKPEYEEVQLGSAEVREVFRSSKWGAIAGSLVRSGLIRRNAQARLVRDGAVVSENL
+KIESLRRFKDDATEVREGYECGIGLGNFNDIKEGDVIETFEMQEKPRV
+>GCF_023573625.1_00649
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP
+GSTPAAPGRSAAPKPAAAPSPRAAAPTSNAGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP
+AAPAEPKAPQPPATPGSAAPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR
+PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP
+GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP
+RKGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK
+VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE
+ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL
+TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI
+DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA
+NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA
+ADPSRPVQVLGLSAVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD
+QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA
+TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG
+SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSDHLKIESLRRFKDDATEV
+REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000608.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000608.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c161bee0471d9c740fa2c3145e395d1f6403dfb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000608.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00681
+MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY
+TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR
+AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSEAAAGLFPVRELTEHEAHEL
+AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA
+>GCF_003691675.1_00418
+MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGADKTY
+TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR
+AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSEAAAGLFPVRELTEHEAHEL
+AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA
+>GCF_005280335.1_02282
+MDKPQGWTSHDVVGRLRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY
+TATIRLGQSTVTDDAEGDVVQTRLANAVTPERVAEQVAALTGPILQAPSAVSAIKVAGRR
+AYDRVRAGEDVALQARPVTVHEFTVHEMRRLDGGRLVDLDVTVRCSSGTYVRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALTLEELAEGFVMTGLSEAAAGLFPVRELTEDEAREL
+AFGRAVAPTGSGEALVAGRAPDGRVVALISDVRRRGADVAKPQLVFAPAEGPGQGGTA
+>GCF_020097155.1_02143
+MNARTAHAPTPDAPGTEASGVVLVDKPAGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATG
+LLVVGVNKATRLLTAITGTDKEYTATIRLGQSTTTDDAEGEVVQTRLANAVTPERVAEQV
+AALTGDILQVPSSVSAVKVAGRRAYDRVRAGEDVQLDARPVTVHAFEVEDFRRLDGGRTV
+DLDVTVRCSSGTYVRALARDLGEALDTGGHLTALRRTAVGPFRVEDAVDLDALAERFVMT
+ELSAAAAGLFPVRELTAHEAAELSFGRAIDPSGELAAAAGASGKAADGLVAGRTPDGTVV
+ALLQDGRRSGRDVARPHLVFAPAEGQGKEEAR
+>GCF_023573625.1_00651
+MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY
+TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR
+AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSKAAAGLFPVRELTEHEAHEL
+AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000609.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000609.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95a8e63683452a9b32fd2a942dedf65046935328
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000609.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00682
+MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG
+DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG
+QW
+>GCF_003691675.1_00419
+MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG
+DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG
+QW
+>GCF_005280335.1_02281
+MILDAWFWAGLVIGAVSLAVCVAMTAIRRHPADSSILSVAAVELFLLVYAVAAAVRQLGG
+EGLNGPGWEFWGYVVTALLVPVIAVAWAVTDKTRWSNLVLAVVGPTVVVMLHRMQVIWFG
+QW
+>GCF_020097155.1_02142
+MILDAWFWTGAVVGGLSFVVCLAMTALRRHPADSSIVSVAAVELFLLVYGVVGAFRQLGG
+QPLNGPTWEFWGYVLTALLVPVIAVAWAVTDKTRWSNLVMAVAGPTVVVMLHRMQVIWFG
+QW
+>GCF_023573625.1_00652
+MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG
+DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG
+QW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000610.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000610.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1acaaedfdbada0fe82f899645dc78c86efd3be9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000610.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00683
+MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV
+ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV
+LPVVGLIWLLTHRPARPAEAGAL
+>GCF_003691675.1_00420
+MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV
+ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV
+LPVVGLIWLLTHRPARPAEAGAL
+>GCF_005280335.1_02280
+MARTRTASGAARPGAAAPARNQGLGRIIVMVYAVFALSATARSLFQILTDVEAAPVAYSL
+SAFAATVYIVATLALARSGARAWAVALGAVLVELIGVVGVGLWTVLDPGLFAEETVWSRF
+GAGYGYVPLVLPVVGLAWLLAHRPSRPTAEEMAR
+>GCF_020097155.1_02141
+MVEQHPVADDGAPARPRRNQGLGRIIVMVYAVFALSASARSLFQILDHFWVAPFAYVLSA
+FAAVVYIVATLALARSGPTAWKVAVAAVGVELAGVVGVGLLTVLDPQLFADATVWSRFGA
+GYGYVPLVLPMVGLAWLLSHRPSREGRVR
+>GCF_023573625.1_00653
+MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV
+ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV
+LPVVGLIWLLTHRPARPAEAGAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000614.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000614.fa
new file mode 100644
index 0000000000000000000000000000000000000000..629b4c0b5995a1e1eeae4aa8b0a4e0d1c42c33cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000614.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00687
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>GCF_003691675.1_00424
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>GCF_005280335.1_02270
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>GCF_020097155.1_02137
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>GCF_023573625.1_00657
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000615.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000615.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b4669548bbf9651f5f041db90f793741b4adae3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000615.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_00688
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
+>GCF_003691675.1_00425
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGGSAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
+>GCF_005280335.1_02269
+MEGPEITFAEAVIDNGAYGKRTIRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASVSTQLSGLPFSGPIGGVRMALVDDGAGKRQWVAFPKH
+SQLQDAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGASAPTEEVVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFKDYEDDAFEAVEKLATDRLTEIFSIGDKQTRESA
+SDAYHVEVMDELAGEDKPFAERRGEIAKAYGSVTKQVVRQRILKDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYLHHYNFPPYST
+GETGRVGSPKRREIGHGALAERAMVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGAFVSLTPGKDGLLHVSELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDADAETADAIESSQTEA
+>GCF_020097155.1_02136
+MEGPEITFAEAVIDNGRHGTRTVRFETGRLAQQAAGSAMVYIDEETSMLSATTVGKHPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFTKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALLDDGSGQRQWVAFPKH
+SQLEDAVFNMAVAGRVAGDDVAIMMVEAEAGENAWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLAARAGKAPVEVPVFKDYEQDAYDAVEKIATDRLTEIFSIADKQEREAA
+SDAYHLEVIEELAGEGKDFAERKGEVAKAYGSLTKQIVRRRILKDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAHVAGIAMGLVSAEVEGQTQYAALTDILGAEDAFGDMDFKVAGTSEFVT
+AIQLDTKLDGIPASVLAGALTQAREARLHILSVLEAAIDQPDELAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGAFVSLTPGKDGLLHISELRKLNEGKRVEDVEDVLGVGQKVQVEITK
+IDDRGKLSLAPVVADEDAAAGESREEDEEA
+>GCF_023573625.1_00658
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000616.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000616.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c12631ac1491d80457226daa4b2f4f954ad1d1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000616.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00689
+MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES
+PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA
+VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG
+TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTQGALP
+APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM
+SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD
+VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR
+AVAARLAAGDRARVVVAPA
+>GCF_003691675.1_00426
+MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES
+PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA
+VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG
+TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTQGALP
+APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM
+SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD
+VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR
+AVAARLAAGDRARVVVAPA
+>GCF_005280335.1_02266
+MAGMSIHREIPLDFTGVLADEGHGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSR
+DESPEGYGSTHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDL
+PMAVEVLTDMLTSSLLDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRP
+IGGTPETIRAVTREHVAGHYARWYRPDELVVTAAGNLDHDEVCRLVLAALQASGWELAPG
+ALPAPRRAVDTEGAAASRVLTGTHTVAKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLG
+GGMSSRLFQEVRERRGLAYSTYSFSAGYSDAGYWGLYAGCQPDRVDEVSALMEAELDRMA
+AEVVTEEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLERVRAVDAA
+QVRAVAARLAAGERARVVVAPA
+>GCF_020097155.1_02135
+MAGMTVQREIPLDFSGVLAEDRGAVVCRSVLPGGVRVLTESMPDQRSVTVGYWVAVGSRD
+ESPEGYGSTHFLEHLLFKGTPTRTAMDIASAFDRVGGESNAGTAKESTVYHAHVLDEDLP
+MAVEVLTDMVTSSLIDADELETERGVILEELAMDADDPVDVAHERLAAVLMDGHPLGRPI
+GGTPETIRAVTREHVVAHYRHWYRPQELVITAAGNLDHDDVCRLVLDALERSGWDLAEGA
+APAPRRTADAAGAGAVLAGTHTVAKQVEQANVIVGGQSLSTTDPDRFALGVMMSVLGGGM
+SSRLFQEIRERRGLAYSTYSFSAGYSDGGYFGLYAGCQPERVDEVAALMEAELERMAAAE
+VTAEELDRAHGQICGGTVLGMESTGARMSRLGRAELVTGEFVDLSASLARVRAVDAGRVR
+AVAARLAAGERARVVVAPA
+>GCF_023573625.1_00659
+MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES
+PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA
+VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG
+TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTPGALP
+APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM
+SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD
+VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR
+AVAARLAAGDRARVVVAPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000617.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000617.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52a5d2bb661076793c5d0a6fba61bb1948981a45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000617.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00690
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
+>GCF_003691675.1_00427
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
+>GCF_005280335.1_02265
+MTDAPAPSAVPADDAVPRVAILGAGGKMGRHAVPAVREAAALELVAELGSADPLEAILDA
+GATHVLDLTVPDVSPRNAAFAVEHGLHTVIGTSGWGPERREALAAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAKAARFFESVELIEMHHPAKLDAPSGTAVRTAELIGQARREAGVPPSP
+DATERDPDGSRGAVVDGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGIV
+LGLRTVASRPGLTYGLDGYLDLG
+>GCF_020097155.1_02133
+MTETTPRTPVPGDATPRVAILGASGKMGRHAVPAVRAAQGLELVAELGSGDPLQAVLDAG
+ATHVLDLTVPDASPENVAFAVEHGLHVVVGTSGWGAERRAALEERLAARPGVGVLIAPNF
+SVGSVLASAFAARAARWFESVEVVELHHPAKLDAPSGTAVRTAEMIAASRAEAGVGPSPD
+ATERDPDGARGAVVDGVHVHAVRLRGLEAHQEVLLGGPGEQLTVRHDAFDRQAYMPGVVL
+ALREVAGRPGLTYGLDAVLGLD
+>GCF_023573625.1_00660
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000618.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8098b856d91d1cda63519ddb6ce3eec980454572
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000618.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00691
+MDWTDTWTLAEPSRTPDDGAVGPPAPAVRARRSTVMSKVWVGFVCLLVLLFAGFALNASV
+ALVRAPQPLAKAIGAGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSP
+GGRIDREAADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG
+>GCF_003691675.1_00428
+MAEPSRTPDDGAVGPTEHAARARRSTVMSKVWVGFVSLLVLLFAGFALNASVALVRAPQP
+LAKAIGAGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSPGGRIDREA
+ADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG
+>GCF_005280335.1_02264
+MADRAPRPAEQTVADPAEHAARARRSTLMSKLWVGFVSLLVLFFASFAVYVAVAFIRAPQ
+LLAKGIGVGVIFVVLVTVAVLAREVWFGQQTERLADLLEAEGGLPEDDLPRSPGGRIDRA
+AADAQFEVYRVEAEAAPRDWRTRYRLALAYDASGDRRRAREAAREAVRLHRQG
+>GCF_020097155.1_02132
+MASTDPRPGVDREQAPRAGSSTGAKLWVLFVAALTLFFAFFVVRAAVVFIAAGGVLPAVI
+GVAVILVVLVGLGLLGREMLFGLQTERLARTLEAEGGLPADDLPRSPGGRIDRDAADAAF
+ADAADEVRAAPEDWRARYRLSLAYDAAGDRRRAREAARQAISLASRRG
+>GCF_023573625.1_00661
+MAEPSRTPDDGAVGPTEHAARARRSTVMSKVWVGFVSLLVLLFAGFALNASVALVRAPQP
+LAKAIGVGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSPGGRIDREA
+ADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000620.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000620.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d0e1464f2102add8649c725820f4cbc8b45a8ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000620.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00694
+MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRIKPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD
+EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFLSIITV
+VNRQTGAIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTV
+GTWVNRKLRRRPMIIPVVLEA
+>GCF_003691675.1_00431
+MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRIKPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD
+EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFISIITV
+VNRQTGAIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTV
+GTWVNRKLRRRPMIIPVVLEA
+>GCF_005280335.1_02260
+MTPGTRLSTPPKLKKGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRMDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRIKPRTRVVKEDEIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYKDD
+EVVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ANVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVDCGYVYVDGSSVGEISDSDLKDRRVLGEEGFISIITV
+VNRQTGSIVSGPDIHARGVAEDEKVFEDIKPKIARALEEAVQSSKDHTAHQLQQVVRRTV
+GTWVNRKLRRRPMIIPVVLEA
+>GCF_020097155.1_00464
+MTRSSRNSSSRRRGGGQSRRPRSSGAPGQLAKGGLRITPLGGLGEIGRNMTVFEHQGKLL
+IVDCGVLFPEDHQPGIDVILPDFTSIRDRLQDVVGVVLTHGHEDHIGGVPYLLKERPDIP
+LIGSELTLAFIEAKLKEHKIVPKTHMVVAEDKRHMGPFELEFVAVNHSIPDALAVAIRTE
+AGLILHTGDFKMDQFPLDRRITDLRHFARLGEEGVDVFLTDSTNAEVPGFTISERELTPA
+IDHVFRTAPKRIIVSSFASHVHRIQQVLDAAHASGRKVAFVGRSMVRNMGIAGDLGYLKI
+PKGLVVDFKKLQDMPDEKIALISTGSQGEPMAALGRMANQTHQIKLNKGDTVLLASSVVP
+GNETSITGIINKFTDMGVNVVHKGNAKVHVSGHASAGELVYCYNIVQPRNVMPVHGEAAH
+LHANAELAKKTGLPEDRVFITKDGDVLDLVDGRVSVAGKVEAGLVYVDGDTIGKVTEGTL
+EERRTMQEAGVVTVVAIVDPDTNQLAEPLEFMTKGFIQDASVFKGAAEKVKSALSRSNVQ
+DIDDIEKLERVIGDAVTRHLERAYRRAPLVTVVVVDA
+>GCF_023573625.1_00664
+MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRITPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD
+EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFLSIITV
+VNRQTGTIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTA
+GTWVNRKLRRRPMIIPVVLEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000622.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000622.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0a350a1dd8b331a8ecb55e056c4a7abdc349cdb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000622.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00696
+MSAAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPVVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRGA
+>GCF_003691675.1_00433
+MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRGA
+>GCF_005280335.1_02258
+MSTGGEAERVSAWNLPNILTSVRILMVPLFAWALWAGGPWGGDSATARWIAVALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGAALVLFSLLGELWWWVTVVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVVGGWWPWVGWTVIGAATVLTV
+LTGLEYVKDAWILRRDALAAPRGA
+>GCF_020097155.1_02129
+MNAQPERVSAWNLPNILTTVRILMVPFFVWAVWAGGPWGQDSLTARWIAVALFAAAMYTD
+KLDGDIARSRGLITDFGKIADPIADKLLTGSALVLFALLGELWWWVVIVILVREWGITAM
+RFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVLGGWWPWLGWTVIGAALALTVVT
+GVEYVRDAVRLRADWLASHPEARR
+>GCF_023573625.1_00666
+MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWSGDSLLARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVMIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000623.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000623.fa
new file mode 100644
index 0000000000000000000000000000000000000000..faa0d86c8726c58136ab8585b99d8f481085ce04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000623.fa
@@ -0,0 +1,22 @@
+>GCF_002008305.4_00697
+MAGAQDVVHALAHAGRTVATGESLTAGLLAARLADVPGASAVLHGGVVAYQNAVKTGLLG
+VPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLAVP
+DADANALDVLGGERDGAATAILLRLDGDRAAIREATVAAALQALTRLLAVRGH
+>GCF_003691675.1_00434
+MAAARDVVHALADAGLTVATGESLTAGLVAARLADVPGASAVLHGGVVAYQNAVKTGLLG
+VPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLAVP
+DADASALDVFGGERDGAATAILLRLDGDRAAIREATVAAALQALTRLLAGRGH
+>GCF_005280335.1_02257
+MAAQETVRALAGAGLTVATAESLTAGLVAARLADVPGASAVLQGGVVAYQNSVKAGLLGV
+PADLLERVGAVDPEVARRMAEGARAGLGADVGVATTGVAGPEPHQGRPVGTVWLGVAVPE
+RLTAALDGLGGERRGAATAIPLALDGDRRAIREATVAAALAALTRLGAPVGERATGEGAA
+GEPCAGA
+>GCF_020097155.1_02128
+MSTGVGAVAAEGEAADPARAAVRALTTAGLTVATAESLTAGLVAARLADVPGASAALQGG
+VVAYQNHVKAGLLGVDAGLLTARGAVDPEVARQMACGARRAAGADVGVATTGVAGPEPHQ
+GKPVGTVFVGVAVPAELAPALAGLDGEPGAGEAAPGEAGSGGSEAGVAAAAFALTLPGNR
+AEIRAATVETVLDLLAALGTTGRGMPDEAPALS
+>GCF_023573625.1_00667
+MTTAAARDVVHALADAGLTVATGESLTAGLVAARLADVPGASAVLHGGVVAYQNAVKTGL
+LGVPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLA
+VPDADASALDVLGGERDGAATAILLRLDGDRAAIREATVAAALQALTHLLAGPGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000624.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000624.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b6478c979e18163fdac14c4b5ffc161ca7de960
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000624.fa
@@ -0,0 +1,17 @@
+>GCF_002008305.4_00699
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR
+>GCF_003691675.1_00436
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR
+>GCF_005280335.1_02255
+MMRHPVQAHGITRWVDDQPRPRATTPDIKERSMPLLRHEIGDVLRDVRQLQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICQALEIPLSYLLREVSDRLVDQEGIQVPDTLPE
+DLTDAADPSLGTLAGR
+>GCF_020097155.1_02127
+MMRHPVQAHGITRWVDSQPRPSQPTPELKERSMPILRHEIGDVLRDVRQRQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICDALQIPLSFLLREVSDRLAEQEGVVVPDTVPA
+DMAEDGAADVAPLAVR
+>GCF_023573625.1_00669
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000627.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000627.fa
new file mode 100644
index 0000000000000000000000000000000000000000..567647fdd8250cf09c9b3aba978016acb43a0fcb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000627.fa
@@ -0,0 +1,33 @@
+>GCF_002008305.4_00705
+MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAS
+DAARDAAPARDAGAPAEDVPDPAPGAAPDLGALLTRASDLPSPAPGAGPRSLPWSGREDT
+RADTERRGRRRAPAKRSGRTRPREDGRAPAEPAPQTDRPRRRPGPAPLPTAPREREEAAR
+EVVLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRS
+KGLARRALGHELQQKGVDREIAAEALEAIDGEDERAAALDLVRRRLRGRTVPGGASPEAR
+AERDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE
+>GCF_003691675.1_00439
+MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAA
+RDAVPARDAGTPAGDGSDPAPGAAPDLGALLTRASDLPSPAPGAGPRALPWSGREDTRAD
+TERRGRKRATTPPRRGRPRDEGRPAVDPRPAVETDRPRRRPGPAPLPTAPREREEAAREV
+VLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRSKG
+LARRALGHELQQKGVDREIAAEALEAIDGEDERTAALDLVRRRLRGRTVPGGASPEARAE
+RDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE
+>GCF_005280335.1_02252
+MTRARRDAGGGAARRSERNGRSGAASGASAFDDARDTDAARMWLELAGVPEADAPAAARS
+VDEPPAAPTDGPDDPPLATAENGSSAAPSGPAAAPDEAGPPDLGSLLGRASDLPSPAPGA
+AARVLPWSADARPERGGRGARGTSSEARRARRRTARLAAADVASAPEAASTPEEANARED
+ARPRRRPGPAPLPAEPREREEAAREVVLRQLALGPRSRGQLEAKLADREAEPELIARVLD
+RFEEVRLVDDAAFAEVWVRSRHRSKGLARRAIGHELRQKGVDRDVAAEALEAIDGEDERA
+AALELVRRRLRGRRVPAGNGPHARAERDKVTRRLVGMLGRKGYGGGLAFAVVKEVLGELE
+E
+>GCF_020097155.1_02124
+MPEDPREREEAARQVVLRQLAMGPRSRRQLERKLADREAEPELVERVLDRFEEVSLVDDA
+AFAEVWVRSRARGKRLSRRAISRELHDKGVDRDVAEEALAAIEPEDERQAALELVRSKMR
+GRPAPAADGPEGRAERDKVTRRLVGMLGRKGYGPGLAFGVVKEVLAELDEA
+>GCF_023573625.1_00672
+MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAA
+RDAVPARDAGTPAGDVPDPAPGVAPDLGALLTRASDLPSPAPGAGPRTLPWSGREDTRAD
+IERRGRKRATTPPRRGRPRDEGRPAVDPRPAVETDRPRRRPGPAPLPTAPREREEAAREV
+VLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRSKG
+LARRALGHELQQKGVDREIAAEALEAIDGEDERAAALDLVRRRLRGRTVPGGASPEARAE
+RDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000628.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000628.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b435fe31e1f5cf76acb3dc55bba7a9120a1ee40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000628.fa
@@ -0,0 +1,49 @@
+>GCF_002008305.4_00706
+MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED
+AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW
+VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN
+NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK
+LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRS
+YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSI
+RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER
+GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD
+AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS
+>GCF_003691675.1_00440
+MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED
+AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW
+VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN
+NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK
+LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDRVLKDMRRS
+YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETAEDFAETMRVVEASRFSSAFTFQYSI
+RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER
+GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD
+AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS
+>GCF_005280335.1_02251
+MNVHDSERISGLLESTGYAPVPQDAQADLVVFNTCAVRENADNRLYGNLGNLRAVKDARP
+GMQIAVGGCLAQKDQATIQRKAPWVDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEV
+FPSTLPTKRDSTHSGWVSISVGCNNTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAV
+EVTLLGQNVNTYGVEFGDRGAFAKLLRACGQIEGLERVRFTSPHPAAFTDDVIDAMAETP
+NVMPQLHMPLQSGSDTVLKAMRRSYRSKRFLGILEKVRERIPHAAITTDIIVGFPGETEE
+DFQDTMRVVEASRFSSAFTFQYSIRPGTPAGEMADQVPKAVVQERFERLVALQDRISAEE
+MATLVGTRQELLVTADSGTKASERGRLSGRARDNRLVHFSVPAGAPTPRPGDFVTVTVTE
+AHPFFAVADPAPEDYSLRRSRAGDAWDRAQAESCGVPTPGASGGAGATSLGMPTLRPRS
+>GCF_020097155.1_02123
+MTLTDPTTHLPALGTAPDAHAGLTYEVRTFGCQMNVHDSERISGLLESTGYTPAEDGTQP
+DLVVFNTCAVRENADNRLYGNLGNLRPVKDAHPGMQIAVGGCLAQKDQATIQEKAPWVDV
+VFGTHNIGSLPALLERSRHNAEAEMEILESLEVFPSTLPTKRESTHSGWVSISVGCNNTC
+TFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAKLLR
+ACGEIDGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRSYRS
+AKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSIRPG
+TPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKATERGRL
+SGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGDAWD
+RAQAESCGAPAPGAAGGSGATSLGMPTLRPRF
+>GCF_023573625.1_00673
+MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED
+AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW
+VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN
+NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK
+LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRS
+YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSI
+RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER
+GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD
+AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000629.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000629.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7eb1c4fde87e18de2875f8b16ca24cc0989aeef6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000629.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00707
+MPAAASRPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTQAER
+EGVPHHLLDVLDVGQEASVAAFQSAVRDLFAQIRARGRTPILVGGSGLYVRAALDVLEFP
+PTDPALRAELEARAQREGLAGLRAELASLDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHRRIAARVERMLAEGLLDEVRRLDVPGPDGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAADQTVVATRRFARRQETWFRADPRVVWLDAQDEDVV
+AEALAVVAGDAT
+>GCF_003691675.1_00441
+MPAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTPAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLDFP
+PTDPALRTELEARAQREGLAGLRAELAALDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRSELHQRIAARVERMLAEGLLDEVRRLDVPGPGGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDVV
+AEALAVVAGGAA
+>GCF_005280335.1_02250
+MRAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDIGTAKVTEAEREG
+VPHHLLDVLDVGQEASVAAFQSAARGVFEDVRSRGRTPILVGGSGLYVRAALDVLEFPPT
+DPEVRAAVEAELAERGEAALRAELAAVDPESAAKVADARRLVRALEVHRITGRPFSAFMP
+RREHDPSVAPVVQIGLSLERAVLHERIEARVERMLAAGLLDEVRALDVPGPDGLRQGPTS
+ARAIGYAQMLAVLDGTLTPEQAAEQTVVATRRFARRQETWFRADPRVHWVDALAPDVVAQ
+ALAVVAGS
+>GCF_020097155.1_02122
+MSAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTQAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLEFP
+PTDPALRAELEARAQREGLTGLRAELAALDPASAERLRDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHQRIAARVERMLAGGLLDEVRRLDVPGPDGLRQGP
+TASRAIGYAQMLAVLDGELTAAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDVV
+AAALAVVAGDAT
+>GCF_023573625.1_00674
+MPAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTPAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLDFP
+PTDPALRTELEARAQREGLAGLRAELAALDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHRRIAARVERMLAGGLLDEVRRLDVPGSEGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDIV
+AEALAVVAGDAT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000631.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00b54f3764d729daf549a840818f3e049660db45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000631.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00709
+MVAVSSASHYFDADPSAPERRRTVRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPARGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNLVALRP
+EDVPEGAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVARAR
+>GCF_003691675.1_00443
+MVAVSSASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP
+EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVVRAR
+>GCF_005280335.1_02246
+MVAVTSPAHYFSPDPGTPERRRSVDVELAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA
+PPARGAFLDVGAGWGPLALTLALASPEAEVTGVEVNERSLALARDNAAAVGASNARFLTP
+EQIPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIA
+GMLQEQAPGEFTATRAATVKGFRILRISRAAESSS
+>GCF_020097155.1_02119
+MDAVTSPAHYFSPDPGTPERRRRVDVEIAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA
+PPARGAFLDVGAGWGPLALTLALTSPEAEVTGVEVNERSLALARDNAAAVGAQNARFLTP
+EQVPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIS
+GMLQERAPGEFTATRAATVKGFRILRISRAAESSS
+>GCF_023573625.1_00676
+MVAVSPASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP
+EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVVRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000632.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000632.fa
new file mode 100644
index 0000000000000000000000000000000000000000..888db0b33ba499abe9df8b1280f8d84bd4d7da56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000632.fa
@@ -0,0 +1,37 @@
+>GCF_002008305.4_00710
+MGRTQWPLTDEFAGQRVVIVGMGVSATQLLAEISTVADTLWVTRREPRWQDSAAPGALAE
+SVRGVDERTRAGLPPGSVVGATGMHRSSWVREAESRGVLVRHPMFTAVEPDGVRMPDGSF
+EPADVILWATGFRPAIRHLAPLRLRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANR
+AGRDAVRAILADLAGPASG
+>GCF_003691675.1_00444
+MGVECTGRRVWATGAPAPGPLTTRTYPAGMTASPSPAPPRPGRTGRATVVVIGAGQAGLS
+AAYHLRRRGFVGLGPNDDGAAGVPDDAPGTFVVLDAETAPGGAWQHRWDSLTMATVNHIH
+ELPGDPVPPADPAAHANTLLPAYFADYEARFALPIRRPVRVRRVERIGEPGRARGFFVRT
+DGAPGTWRADFVVNATGTWTSPRWPSVPGMRSFRGRQLHTRDYVSKDEFAGQRVVIVGMG
+VSATQLLAEISTVADTLWVTRREPQWQDSAAPGALAESVRGVDERTRAGLPPGSVVGATG
+MHRSSWVREAETRGVLVRHPMFMAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLAPLR
+LRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG
+>GCF_005280335.1_02245
+MRTILAADRRRRHPSPVGEHAPAVPTLGRMTPHPDRHVTVLVVGAGQAGLSAAHHLRRRG
+FQPVGPGEAPRPAPEGSPGTFAVLDAEDRPGGAWLHRWDTLTMGSVNHIHELPGHPVPPA
+DPAARANAVLPAYFAEYEERFDLRVHRPVRVSRVERIGEPGAAEGFRVHTDAGTWTCGFL
+VNATGTWTSPHWPAVPGRREFRGRQLHTHDYRDPEEFARRRVVVVGMGVSATQHLAEVSR
+VADTLWVTRREPRWIDDPDPGHLAESVEGVDERTRLGLAPRSVVSATGMFRSDWVREAQA
+RGVLERHPMFERIEPDGVRMPDGSLERADVILWATGFRPAVRHLAPLRLRTPDGGIRAAH
+GRALDEPRLFLIGYGPSQSTVGANRAGRDAVRAILADLRAAGAA
+>GCF_020097155.1_02118
+MTPHPDRHVTVLVVGAGQAGLSAAHHLRRRGFLPVGPGEAPGPAPGGSPGTFAVLDAEDR
+PGGAWLHRWDTLTMGSVNHIHELPGHPVPPADPDAQANAVLPAYFAEYEERFDLRVHRPV
+RVSRVERIGEPGAAEGFRVHTDTGTWTCGFLVNATGTWTSPHWPAVPGRREFRGRQLHTH
+DYRGPQEFAGRRVVVVGMGVSATQHLAEVSRVADTLWVTRREPRWIDDPDPGHLAESVEG
+VDERTRLGLAPRSVVSATGMFRSDWVREAQARGVLERHPMFERIEPDGVRMPDGSLERAD
+VILWATGFRPAVRHLAPLRLRTPDGGIRAAHGRALDEPRLFLIGYGPSQSTVGANRAGRD
+AVRAILADLRAAGAA
+>GCF_023573625.1_00677
+MGVECTGRRVWATGAPAPGPLTTRTYPAGMTASPSPAPPRPGRTGRATVVVIGAGQAGLS
+AAYHLRRRGFVGLGPNDDGAAGVPDDAPGTFVVLDAETAPGGAWQHRWDSLTMATVNHIH
+ELPGDPVPPADPAAHANTLLPAYFADYEARFALPIRRPVRVRRVERIGEPGRARGFFVRT
+DGAPGTWRADFVVNATGTWTSPRWPSVPGMRSFRGRQLHTRDYVSKDEFAGQRVVIVGMG
+VSATQLLAEISTVADTLWVTRREPQWQDSAAPGALAESVRGVDERTRAGLPPGSVVGATG
+MHRSSWVREAETRGVLVRHPMFMAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLAPLR
+LRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000633.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000633.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a6852c37418ca3fd5689a8863cf46f9ff355f60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000633.fa
@@ -0,0 +1,54 @@
+>GCF_002008305.4_00714
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADSVVADHEDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHIVDGSHPDPEGQIA
+AVRSVFAEVHAHRIPEIIVLNKADAADPAVIARIRAKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAL
+>GCF_003691675.1_00445
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADGAAAEHRDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQIA
+AVRSVFAEVDAHRIPEIIVLNKADAADPAVVARIRSKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAS
+>GCF_005280335.1_02244
+MTEEKNPTPAGGSEDEIQAVIDRILAADDARRSAAQGRADTPGRADAETAGDADAGTPDR
+TSALAGRALALAEGGDGHTAADGDQDELAARHSLRRVQGLSTELEDMTEVEYRQLRLERV
+VLAGVWTEGTAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATYLGKGKAQELAEI
+VALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQVELAQL
+EYLLPRLRGWGESMSRQAGGRAAGGEGIGSRGPGETKIELDRRRIRTRMAKLRKDIAGMK
+PAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTVRKAMTP
+DGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQISAVRSVF
+AEVDAHRIPEIIVLNKADAADPAVVARIRAKEPHTVVVSARTGEGIEELERAIAATIPRP
+DVRLELLIPFTRGELVSRLHSEDAEILAEGYEEGGTRLSVLVRQDLAPEYEDYVVDPAAS
+>GCF_020097155.1_02116
+MTEEKNPTPAGGSEDEIQAVIDRILAADDARRATEREAAGRGSADSAAADHEGAPDRSGA
+LAGRALALAEGGDGHTAADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQLRLERVVLA
+GVWTEGTAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKARELADVVAL
+TGADTVIVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHATSREGRAQVELAQLEYL
+LPRLRGWGESMSRQAGGRAAGGEGIGSRGPGETKIELDRRRIRTRMAKLKKDIAGMKPAR
+EAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVQNALFATLDPTVRKAVTPDGI
+GYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDASHPDPEGQIAAVRSVLREV
+DAQSVPEIIVLNKADAAEPDVIARIRAKEPHTVVVSARTGEGIPELESAISATIPRPDVR
+LELLVPFTDGQVVSRLHSVDAEILSETYEETGTRLTVLVRRDIAADLEGYRVDAAAGDDA
+QEAASA
+>GCF_023573625.1_00678
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADSVVADHEDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQIA
+AVRSVFAEVDAHRIPEIIVLNKADAADPAVVARIRSKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000634.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000634.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50ef63d82028171f3fe226d45bdd472aa90f1399
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000634.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_00715
+MSGGAEEVGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGMIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVVVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFSEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
+>GCF_003691675.1_00446
+MSEEEQEAGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGVIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
+>GCF_005280335.1_02243
+MSGAGTEGTTPAGEGAQPRTDHEREALRLLDAAVEATGGQQRAGQREMVLQVARALESRR
+HLLVQAGTGTGKSLAYLIPALQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDEL
+PREPVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGLLGSAADGTGGPSSLLGK
+EVMYLRAWADQTETGDRDDLDVPVTDRAWRQVSVSAIDCLGASRCPMAEECFSERARADA
+ADADVVVTNHAMLAISAFEGLAVLPAYSAVVVDEAHELQDRVTGAVTGQLSGSIVHGAAT
+SLRKHTTVAVEDLMEAGAGLDRAFTDAPSGLLAAGPDEVQEQALNAVLAAARQCLSDLGQ
+DKDKEADADGGRQMARSRVLEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGD
+ESDPPQLFVAPISVAGKLREGLFGKATTVLTSATLTVGAGERRFDSVAGDVGLAGPDAPR
+FEALDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASGGGALGLFSSRRAA
+EDAAAEMRRRLGPKATVLCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLV
+AIDRIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVHDRGVVA
+VLDSRLATERYGGYITSALPDFWRTTDRAVVLGVLGRLAETGS
+>GCF_020097155.1_02115
+MTDSTTGPAGAVPTTDREEEALRLLDVVVEATGGQQRAGQREMVLQVARALESRRHLLVQ
+AGTGTGKSLAYLIPALQHAMDQEDPVVVATATLALQAQIMKRDAPRLVQALAGELPREPV
+VALVKGRSNYLCRHKVDGGYPGDEGEETLFEVADDGGLIGSGEDGEPSSPLGKEVMYLRA
+WADVTETGDRDDLEVPVTDRAWRQVSVNAVDCLGATRCPLAEECFSERARADAADADVVV
+TNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLRRHTS
+VAVEDLAQAAAGLDRAFTDTPSGLIQGGPDDVQEQALTAVLSAARQCFSDLGKDKEGEAD
+AGRQMARSRLLEVVEVAERMLAAHPEADFPEVLWATRPGRFEPGSGWQPGDEADPPQLYV
+APISVAGRLREGLFGKATTVLTSATLTVGQGERRFDSVAGDVGLAGPDAPRFTALDVGSP
+FDYPRQGVLYVARHLPKPGRTASPESLDELEALLRASNGGALGLFSSRRAAEDAAEHMRR
+RLGRGHTVLCQGDATLSALVRQFADEPDTSLFGTMSLWQGVDVPGPSLRLVVIDRIPFPR
+PDDPLSQARTRDVARHGGNGFMRVSATHAAVRMAQGAGRLVRSVEDRGVVAVLDSRLATE
+RYGGYITSALPDFWRTTDRAVVRGVLERLAREAH
+>GCF_023573625.1_00679
+MSEEEQEAGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGVIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLSASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARNGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000636.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000636.fa
new file mode 100644
index 0000000000000000000000000000000000000000..201431bad2b01695b5ae7af63066c2475f5417c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000636.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00717
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR
+>GCF_003691675.1_00448
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR
+>GCF_005280335.1_02241
+MTLMTAQFAGSPAAARRRPAAIRLTRRGRLLLRGIPVMAAAAAATLAVAFLLGVLLSPAA
+VSADTAAPATQTVTVMPGDSLWTIATTIAPEEDVYEVIAAIDELNGLEGRAPALGEELFI
+PATR
+>GCF_020097155.1_02113
+MTAVTAVLSRTHQLTSVRARPTRAVAASTRAAARTSGVRLTRRGRLLFRGLPVILSVAAA
+TVAAAFFAGVLFSPPAVSADTPAEELQTVTVMPGDSLWTIARDVAPEADRRDTMRRIDEL
+NGLEGRDPELGQELYVPPTR
+>GCF_023573625.1_00681
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000637.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000637.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48b30ff207b58b098cb82307bf6c3c29becfe854
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000637.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00718
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAEDHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWRRLLDRGVLVRDVGIPHHLRVTAGTEAETTAFLT
+ALAEVLGETGDRS
+>GCF_003691675.1_00449
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAADHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVTDALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWGRLLDRGVLVRDVGIPHHLRVTAGTEPETTAFLT
+ALEEVLGETGHRS
+>GCF_005280335.1_02240
+MTDLSSLPLRENLRGLSPYGAPQLDVPHMLNTNENTHPVPQEVATAIAERVAAVAGGLNR
+YPDREFTALRRALARYLGHGLTEGHVWAANGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTAFVDGGRAADHTLSAERAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAENESAGGPGAMIVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+VGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLETVEDIKGQRDRIVATLR
+ELGLEPSVSDSNFVFFGRLEDAADVWRRLLERGVLVRDVGIPHHLRVTAGTEEETTAFLE
+ALEAVLAEIGHRR
+>GCF_020097155.1_02112
+MTDLSSLPLRDSLRGQSPYGAPQLDVPYMLNTNENTHPVPQAVAEAITARVAKVAGGLNR
+YPDREFTELREHLAAYLGHGITPEQVWAANGSNEVLQQILQAFGGPGRTLLSFLPSYSMY
+PLLANGTDTAFVDGGRAADHTLSAEHAAALVREHRPNVVFLASPNNPTGTALGLDVIEAI
+YAAQAQNEAEGGHGAMVVVDEAYAEFALAGTDSALTLLRGRERLIVTRTMSKAFALAGAR
+LGYLAADAAVADALRLVRLPYHLSAVTQATAIAALERVDELLETVEDIKGQRDRIVAELT
+GMGLVPAVSDSNFVFFGRLADAHAVWEALLERGVLVRDVGIPHHLRVTAGTEEETTAFLD
+ALREIVEQDPAVVSAVDAD
+>GCF_023573625.1_00682
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAEDHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWRRLLDRGVLVRDVGIPHHLRVTAGTEAETTAFLT
+ALAEVLGETGDRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000638.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000638.fa
new file mode 100644
index 0000000000000000000000000000000000000000..036aa540eb43aa8767bd0c3e6eb485e7783cbe86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000638.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00719
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
+>GCF_003691675.1_00450
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
+>GCF_005280335.1_02239
+MAAELISGRRARMTRTTSESDVHVEMDLDGTGRAEISTSVPFYDHMLTALARHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMSGVPSTKGAL
+>GCF_020097155.1_02111
+MAAELMSGRRARMQRTTSESDVYVEMDLDGTGTSEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKRGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFEAITYHASICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRVHDVPSTKGAL
+>GCF_023573625.1_00683
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKAALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000640.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000640.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef1ec092ce26d36b2db71a0ea5ba6e541c84a766
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000640.fa
@@ -0,0 +1,10 @@
+>GCF_002008305.4_00721
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA
+>GCF_003691675.1_00452
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA
+>GCF_005280335.1_02237
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVAR
+>GCF_020097155.1_02109
+MPYWSVLYLGLGGILLGAAWSMRTQKAPTWAVVIALVLAAMAVAAAFLTV
+>GCF_023573625.1_00685
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000641.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000641.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f79e9e099e84f816a05e9b77f6275f094374719
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000641.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00722
+MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA
+AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR
+VIERFGDRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG
+PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL
+AVAGGATVEQARSEQPGPVAP
+>GCF_003691675.1_00453
+MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA
+AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR
+VIERFADRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG
+PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL
+AVAGGATVEQARSEQPGPVAP
+>GCF_005280335.1_02236
+MTPNPAAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPLTAALDWQRAGAEWIHLVDL
+DAAFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPAWT
+ARVIERFGDKVAVGLDVRGTTLAARGWTQEGGDLWEVLARLEDAGCSRYVVTDVTKDGTL
+KGPNTELLAQVCARTDKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQ
+ALAVAGGATVEQARAEQPGPVAE
+>GCF_020097155.1_02108
+MTETTPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPLTAALDWQDAGAEWIHLVDLDA
+AFGRGDNRDVLRRVVDEIGVKIELSGGIRDDASLENALAMGAARVNLGTAALEDPAWTAR
+AIERFGNRVAVGLDVRGTTLAARGWTQDGGDLWEVLARLEEAGCARYVVTDVTKDGTLRG
+PNRELLARMCAATDKPVVASGGISSLEDIAALAAMVPQGVEGAIMGKALYAGRFSLEQAL
+AVAAGATVERAREQHPFQAAP
+>GCF_023573625.1_00686
+MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA
+AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR
+VIERFADRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG
+PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL
+AVAGGATVEQARSEQPGPVAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000642.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000642.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da6c74499d12dae39a8899fdd638beb061b39ff4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000642.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00723
+MTGSHDDGGLARDDGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP
+WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMSALTDGSAGEREVTEVLARIRVFA
+AVVPTLAGDEDDVHDHADHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALT
+AWNPVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQREWTPAYRD
+QEIADEIAEVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADAA
+GVRLMTATLKTLLADLPLLAERADSVEITVRRP
+>GCF_003691675.1_00454
+MTGSHDDGGLARDEGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP
+WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMAALTDGSAGEREVTEVLARIRVFA
+AVVPTLAVDEDDVHDHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALTAWN
+PVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQKEWTPAYRDQEI
+ADEIAQVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADATGVR
+LMTATLKTLLADLPVLAERADSVEITVRRP
+>GCF_005280335.1_02235
+MTHGHDDGAPAGVAGAGPIEETVAVPRPDSRELPGHIRAALDRMREKTAGPNTADTAGVP
+WEGRDLSGPGVDGSANPLHVFDEDDGTSPEEWTRVMAALTTGAAGEAEVTDVLSRIRVFA
+AVVPTLAVDEDDVHDHADHSGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTSVPALT
+AWNPIARPVAVWMPRACLSAVDEGCELVVVDAGAEHTYAVRRPAVWALAQQKPWTPSYRD
+QEIADEIAQVADLVPHLLNLGLAPGSGVATHTGSGAVMSGGGAGPELQIVAMPARDADAA
+GVRLMAATLKTLLADLPLLAERADSVEVTVRRP
+>GCF_020097155.1_02107
+MSSASSSEPAHDAEATVPVPAPGGRELPGHIRAAMERMRQKTARENTADTAGVPWAGRDL
+SGPGLEGSANPLHIFDEDDGTAPAEWARVMDALTEGTAGEAEVVDVLGRIRVFAAVVPTL
+AVDEADVHDHAAHSVHEHAQHEDAAHGDKAADVALVTMRAPDGRQALPVFTSVPALTAWN
+PLARPVAVWAPRACLSAVDEGCELVVVDAGAEHTYAVRRPAVWALAQQKPWTPSYLDQEI
+AEEIAGVADLVPNLLNLGLAPGPGVATETASGEVMNGGGSGTELTVLAMPARDADAAGIR
+LMTTTLAMLLGDLPLLAERADSVEITVRRP
+>GCF_023573625.1_00687
+MTGSHDDGGLARDDGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP
+WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMSALTDGSADEREVTEVLARIRVFA
+AVVPTLAVDEDDVHDHADHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALT
+AWNPVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQREWTPAYRD
+QEIADEIAEVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADAA
+GVRLMTATLKTLLADLPLLAERADSVEITVRRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000644.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000644.fa
new file mode 100644
index 0000000000000000000000000000000000000000..776f5842ed9f261724662becdd8d71eb62268bcc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000644.fa
@@ -0,0 +1,23 @@
+>GCF_002008305.4_00725
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR
+LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL
+C
+>GCF_003691675.1_00456
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR
+LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL
+C
+>GCF_005280335.1_02233
+MNSSSTPTPEPSETARHAWRAYFEATQMLSEMLERGLKKDSGMSLADYNLLLLLYEAPEG
+RLRMGELASGMVFSPSRITYQVKTLVARGLIERRAAECDRRGFEAVLTDEGRTAFRRAAA
+GHARQVDELFLSHLEPGEAETLERIFTRLGGRLEGLC
+>GCF_020097155.1_02105
+MTSSSTPAAEPTGPRAARHAWRAYFESTQMLQDQLERGLKAECGITLADYNLLLLLVESD
+GGRLRLGELASRMVFSPSRVTYQVKSLVARGLIERRRVECDRRGFEAVLTDAGRTAFRRA
+AVVHARQVDELFLDLLQPGEAEVLGRVFTRVGTALESRCAGRAAPSEPCGAQASNSADA
+>GCF_023573625.1_00689
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVLERR
+LKQDCGMSLADYNLLLLLYESPEDRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLVDLAPGEAESLTRIFSRLGRRLEGL
+C
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000647.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000647.fa
new file mode 100644
index 0000000000000000000000000000000000000000..701cd6dbea4bf13a4a068e39d9e889bdaf4435ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000647.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00728
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
+>GCF_003691675.1_00459
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPLAHLVRQFAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
+>GCF_005280335.1_02229
+MNTAFDAGRLGRTDVLTLQQVTSFMSNDMQVTGPDGQTVATVVTTGGGLGRMVLGSRTFD
+VVDGEDGRVLFRLADPATFGRDRYAIVDADGLPLANLVREFALFRTSVSVEVVDGTRFAV
+TGNLWDHDYTMTVGQAPIARATATFGGFMNALAGRSRYELRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRRNN
+>GCF_020097155.1_02102
+MTTFDAGRLALVNSLALQQVTSFLSNDMQVLGPDGEVVATVQTQGGGLSRMLMGSRRLLV
+CDGDDGRPLFELQDPATFGRDRFQVLDPAGLPLANLRREVAFFRTAVSVEVVDGTVFRVE
+GDLFDHDYRMIAGEVPIARAVSQWSGFGNALLGRSRYRLELDPAMPPVVRCAVLGTAIAL
+DLLRAKDARRND
+>GCF_023573625.1_00692
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000648.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000648.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3b6a4d0029fc05172dec8583f49d4d7b65974e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000648.fa
@@ -0,0 +1,46 @@
+>GCF_002008305.4_00729
+MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL
+GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS
+VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG
+GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL
+PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRTHFSWVGPEVLGVLVVSMA
+AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA
+VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVVEERRGEAMGFYGSAMTAG
+AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVMRGRRPA
+>GCF_003691675.1_00460
+MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL
+GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS
+VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG
+GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL
+PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRSHFSWVGSEVLGVLVVSMA
+AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA
+VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVEEERRGEAMGFYGSAMTAG
+AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVARGRRSA
+>GCF_005280335.1_02226
+MGFIARFPHTAAGVILTLHVALTLDLGYGQAGLAAAAMTLGIAVGSPWRGRVVDAKGLRR
+ALLPSVIAEALIWPLVPWLPFWLMLVAVFFGGVFALPIFSVVRQGLGVLTHGRDRQTAFA
+LDSIITETIFMVGPALGAVVAATWSSALGLTIVGLSSALGGVLLMWFNPPTRSSQLAVVG
+PETEDPYTEDEDREEAVAQTVHGAPMHVEMTAPSLATGALPVVTEAIPLVTGALPVIAAD
+GSGPATPTPGLTRAERLRLWRARHFAWVGPEALGVLVVSMAAGLVMVGTEVTMVAELEHA
+GMAGSVGVVYAFWCGASAVGGLFYGAWGRQVHPYLLMGLLALLTLPMAFVDGLWALALAA
+IPSGLFTAPTLASASSRLSTLVPEERRGEAMGFYGSAMTAGAAMGAPLSGVFIDAIHPAA
+GYVFAGLAGAVLVLAAALVTLARRRRVGGTSA
+>GCF_020097155.1_02100
+MDFRAYGRLLQDPRIRNLLAVGFIARFPHTAAGVILTLHVAVTLGLGYGQAGLAAAAMTL
+GIACGSPWRGRAIDRDGLRRALLPSVVAEAVIWPVVPWLPFGFLLVAVFFGGLFAVPIFS
+VVRQGLGVLTHGADRQTAFTLDSIITELVFMVGPALGAVIAATGSTALGLTVVGLSGALS
+GALLMWFNPPTRSTQLAADGPSAGDPFTEEEDREQALSQAVHTAPVRATVAAADLATGAL
+PVVTEAVPIVTGSLPVIAADGSGPVSPAPRAGRHDDGRAADGLTRDERWRLWRVRHFGWV
+TPEVLGVLVVAMAAGIALVGTEVTMVAELEHAGQEASVGVVYAFWCGASALGGLFYGAWG
+RQVHPYLLGALFALAVAPMAFVDGLWALAWASVPSGLLTAPTLAAASSRISLLVSEERRG
+EAMGYYGSAMTAGSALGAPVVGLVIDGVGPGAGYVGAAGAAVVMIGAAAILTAARRRRSP
+ARG
+>GCF_023573625.1_00693
+MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL
+GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS
+VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG
+GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL
+PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRTHFSWVGPEVLGVLVVSMA
+AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA
+VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVVEERRGEAMGFYGSAMTAG
+AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVMRGRRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000649.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000649.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c7da0266acb1557270184192d3b5c59f7d5ea4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000649.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00730
+MAQIVLFHHALGLTDGVRALAEQIASGGHTVHTPDLYDGRTFATVDEGVAHAQHLGFEEI
+GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQPHT
+ALQIHLGTRDPWALEGDLATARSYAATAEHPDRPADLFEYDTDRHLFMNSSTADFDADLT
+AVLVRRIHELLA
+>GCF_003691675.1_00461
+MAQIVLFHHALGLTDGVRALAEQIAGGGHTVHTPDLYDGRTFATVDEGVAHAQHIGFEEI
+GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGALALDAYAPLWQPHT
+ALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDADLT
+AVLVRRIHELLA
+>GCF_005280335.1_02223
+MAQILLFHHALGLTDGVRALAAQIEAGGHTVHTPDLYDGALFTDVEEGIAHVESLGGFDV
+IAERGMRAAAQHPQASVVAGISMGVVAAHKAAQAVPAFRACIDIAGIVPLDAFAPLWQPH
+TALQVHLATRDPWVMDEDLPLARSVAATEEDPDKPAVLFEYDTDAHLFMDSSTDGHDPAL
+TEVLVRRIHELLA
+>GCF_020097155.1_02099
+MAQIILFHHARGLTEGVLALAEQIEQASGHHVHTPDLFGGAVLPTVEDGLAHLQQIGQDE
+VMTRAMHACAEHKEASVVAGISMGVMPAWKAAQTAPGFRACIAMSSALPLDAYARLWQPH
+TSLQIHLAAQDPWVKDEDLPLARTYAATAEHPDRPADLFEYETASHLFMDSSTDQYDARH
+TEVMVERIRELLA
+>GCF_023573625.1_00694
+MAQIVLFHHALGLTDGVRALAEQIASGGHTVHTPDLYDGRTFATVDEGVAHAQHLGFEEI
+GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQPHT
+ALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDADLT
+AVLVRRIHELLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000650.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000650.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21636010afa5133aaea460d1f715ddeb6c87f754
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000650.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00732
+MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ
+DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML
+KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT
+PTAARFLDAAVDAGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS
+RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR
+>GCF_003691675.1_00463
+MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ
+DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML
+KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT
+PTAARFLDAAVDAGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS
+RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR
+>GCF_005280335.1_02221
+MDAVRILEDEIREVVRRQGIDPQREHARVIALIQDAAADYESRAEVSALPDLEDPAAARQ
+DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARAGRSELTGIVLTEEEVHDLVEVML
+KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFISRARRLEDLVRSGSLT
+PTAARFLDAAVDVGMNVLVSGATQAGKTTLLNCLASSIGARERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSAADALTKLCTLPLLAGENISRSFVVPTVATCIDVVVHCERDWDGRRRVLEVLTVGA
+RVEDGVIETSTLFQRDSAGDLRLNEAASLEFDAFARRGVDVHELVGLR
+>GCF_020097155.1_02097
+MDAVRMLEDELRELVRRRGVDPRVEGHRIRTMIAEATLDYESRSLVSSLPPLEDPEAARQ
+ELFDRIAGLGPLQRLMDDPTVEEIWLNAPDQVYCARAGRSELTGIVLSEEQVRDLVELML
+KSSGRRLDLSMPFVDASLPDGSRLHVAIPDITRRHWAVNIRKFISRAHRLDDLVRSESLT
+TPAARFLDAAVDAGMNILVSGATQAGKTTMLNCLSASIGARERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGTGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSASDALTKLCTLPLLAGENISRNFVVPTVATCIDVVVHCERDREGRRRVREILTVGS
+RVEGGVIETSTLFRRDAHGDLVLNPSADLEFEAFARRGLDPRDLVEVR
+>GCF_023573625.1_00696
+MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ
+DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML
+KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT
+PTAARFLDAAVDTGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS
+RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000651.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000651.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85e7ed334e2cbeb0fb6fa908a1efc41df764c047
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000651.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00733
+MAALLGLALGCGLFLLWWSLWSPPTERPGAARPDSRLRVLIAQSGIQRLSPAGVVSAMAV
+GGLVVGLLVLSLTSTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQQFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASVVCYRVMLRIGALPREKRVFA
+>GCF_003691675.1_00464
+MAALLGLALGCGLFLLWWSLWSPPTEKPGAARTDARLRVLIAQSGIQRLSPAGVVSAMAV
+GGLVVGLLVLSLTSTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQQFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASVVCYRVMLRIGALPREKRVFA
+>GCF_005280335.1_02220
+MAVLLGLLLGGGLFLLWWSLWSPPVQRPQTARPDSRLRVLIAQSGIRRLSPAGVVSAMAV
+GGVVTGLLILAVTRTWTIAACFALFGAAVPWLLLSWQARRRTTALRELWPDAVDHARSAI
+RAGLTLPEALIQLGESGPEGLREPFRQFARDYRSGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARTRAELEARQSWTVNAARLAVCAPWIVLLLLGT
+QPSAVAAYQSAAGGAVLLGGLVASVVCYRVMLRIGALPEEKRVFA
+>GCF_020097155.1_02096
+MGAVLGLGLGAGLFLMWWSLWSEPVVSAEEPRGPGRLAELIARSGIERLTPAGVVGAMAA
+GCVVAALIVLAVTRTWTIAACFGLFGAALPWALLTWQATRRTRALRDLWPDAVDHVRSAV
+RAGLTLPEALTQLGETGPEGLRAPFREFARDYRSGARFLDALERLKTRMADPVADRLVAS
+LRLTREVGGADIGLLLQSLSEFLRQDARTRAELEARQSWTVNAARLAVCAPWIVLLLLGT
+QPLAVTAYQSVAGGALLLAGLVVSALCYRIMLRIGALPQEKRVFA
+>GCF_023573625.1_00697
+MAALLGLALGCGLFLLWWSLWSPPTEKPEAARPDSRLRVLIAQSGIQRLSPAGVLSAMAV
+GGLVVGLLVLSLTGTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQHFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASIVCYRVMLRIGALPREKRVFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000653.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000653.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1c92ba7233fa82d235f57c58ee1fd1691293026
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000653.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00735
+MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALQGLFNQA
+ISQVSQGG
+>GCF_003691675.1_00466
+MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALQGLFNQA
+ISQVSQGG
+>GCF_005280335.1_02195
+MLHHHVISILTALRGLLHDDVRDDRGDVPGWVMITLMSAVLVAALLTLALPALTDLFDQA
+ISQVTQGE
+>GCF_020097155.1_02094
+MLTNAYLTVVSALTSLLHDDARDERGDVPGWVMITLMSAALVVALLGLAMPALKAMFDQA
+ITQVNNAAG
+>GCF_023573625.1_00699
+MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALEGLFNQA
+ISQVSQGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000656.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000656.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c5bba736e01a9e609f41fd902002e642e2d8f85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000656.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00738
+MRRRLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAIAGAE
+ELGFRLGEDPGVVLSDDDVAASASAHLAAVGAQEAVPGLGGMNARVADDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR
+>GCF_003691675.1_00469
+MSRRLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAIAGAE
+ELGFRLGEDPGVVLSDDDVAASASAHLAAVGAQEAVPGLGGMNARVADDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR
+>GCF_005280335.1_02192
+MRALSALRRDDGQTTVLTVGLCALLIGLMLVMLAATTVQLQHRRLQSLADGAALAGAEEL
+GFRLGEDPGVVLDDGDVAASAAAHLDAVDAASSVHGLGGMAAGVADDGATVTVRLDAEVD
+LLAAAGPFAGMLPLSVPIQATGDSRTSLSR
+>GCF_020097155.1_02091
+MTRRHRSRPQRRPDRRHGAHERGEITVLTLGLSAIVVGLLLVVLSATLVLIQARKVQSLA
+DGAALAGAEQLAFQLDADPRVVLEPGSVQASVNEHLDAVGARESVPGLESVSAQVAGDGA
+TVVVRARAKVTLVPSGAGWLADLIPASVPVSAEGSSRTVLTR
+>GCF_023573625.1_00702
+MRRPLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAVAGAE
+ELGFRLGEDPGVVLSDGDVAASASAHLAAVGAREAVPGLGGMSARVAEDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000657.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000657.fa
new file mode 100644
index 0000000000000000000000000000000000000000..865b29eec9e56d5c9604bd12623626066dd03c26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000657.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00740
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPYAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED
+>GCF_003691675.1_00471
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED
+>GCF_005280335.1_02189
+MADTDFSAEIDSLRHTLASIEQVSDIDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQADLKRITSLESRIEDLETMVELAAEEDEPSLLDDANDELASIRKSLEELEVVTLLSG
+EYDPRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHIPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLQRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGAIDAFVDAGI
+RWRAEQAKAAQED
+>GCF_020097155.1_02087
+MADTDFSAEIDALRHTLASIEQVSDVEKMTAEVAELEKEAAAPDLWDDPEAAQKVTSKLS
+HRQADLKRIKSLADRIDDLETMVELAAEEDEPSLLDDANVELTSIRKALEELEVVTLLNG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQKGWSTKVMDTSYAEEAGLKSATF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHIPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLVRKA
+EEDAKKKEMAGDIKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGAIDDFIDAGI
+RWRAEQVKAAQED
+>GCF_023573625.1_00705
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPYAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000660.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb3b09bb4c98e6670af4b38d9952b2639c47f509
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000660.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00743
+MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGATDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQAPDEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRASGEGRA
+>GCF_003691675.1_00474
+MALDKTVATPAEAVADVPDGASLAVGGFGLTGNPVQLIEALLEQGATDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQTPDEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGI
+FVHRIVEVGTDIEKRIEKRTVRASGEEQA
+>GCF_005280335.1_02186
+MALDKTVATAAEAVADVPDGASLAVGGFGLSGNPIQLIEALLEQGAADLSVVSNNCGVDG
+WGLGILLGAGRIRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDAEGNVVKSSAAKPTDTFVLGEGYVSQDPAEEQTYVLEQSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDEVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRAAGEES
+>GCF_020097155.1_02084
+MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGAMDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGIQVAEGGLPMHYDADGTVVKSSQAKPTDTFVLGEGYLNQAPGEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRASGEEQA
+>GCF_023573625.1_00708
+MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGATDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQTPDEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRASGEEQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000661.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000661.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c11932d6be962b25460c14f74b37d4370c26dfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000661.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00744
+MSEQTTGRPRGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEEAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVFKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQARALTGAPLD
+>GCF_003691675.1_00475
+MSEQTTERPQGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGAPLD
+>GCF_005280335.1_02185
+MSEQSTERPEGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNYIPAGRSVVLQSENGIL
+GTGPYPVEDEVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSSAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLRLVETAPGVSEEQVRDLTGAELD
+>GCF_020097155.1_02083
+MSEQTTGRPRGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEISAAG
+DLANWMVPGKMIKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGAPLD
+>GCF_023573625.1_00709
+MSEQTTGRPQGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGASLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000662.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000662.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c74eb5e4e9a5151e1f2770814551b3728463685
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000662.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00745
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA
+>GCF_003691675.1_00476
+MGKNSKGKATKQPAPGERQVIANNKKARHDYTILDTYEAGIVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA
+>GCF_005280335.1_02184
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDVYEAGLVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRIRNRRAGVA
+>GCF_020097155.1_02082
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA
+>GCF_023573625.1_00710
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000664.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000664.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2a776ccd7ce857c94aacaea2609d2e4e7b040fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000664.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00751
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEVGMVTTVDRGRYAVVLPERLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGEEGTLARIVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGVPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED
+>GCF_003691675.1_00481
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAQVGMVTTVDRGRYAVVLPDRLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIIRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED
+>GCF_005280335.1_02179
+MGRRVDPGAWDESDVRVRPSKRGTRPRTKERPKHEDAVVGMVTTVDRGRYTVVLPERLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARVVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALMAHYESL
+DLEVMTSGAAVFEAETGDTALDGALVARVAERLQGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTDDDGVPLADTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCAHTADSPGCGLDGWVAAGHAGPSGAARLASLRRLLGNRLGPAGAED
+SASSED
+>GCF_020097155.1_02074
+MGRSLDPSAWDESHVRVRPSKRGTRPRTKQRPQHEDAQTGLVTTVDRGRYTVVLPGRAHA
+PVTAMRARELRRTPIATGDRVDVVGDLSGDEGSLARIVRVQERDTVLRRSADDSDAVERV
+VVANADTLMVMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAELVAHYEAL
+DLEVMTSGASRFEAESGDTDLDDGLVERVAERLAGHTAAFVGPSGVGKSTLLNALTGAGR
+ATGHVNAVTGRGRHTSSSALAMSLPGPDGEPVPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+EDLAGGLEGCPRGCTHLADSPGCGLDAWVAEGHAGEAGPARLASLRRLLGNRTTAEAGGS
+ASSED
+>GCF_023573625.1_00715
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEIGMVTTVDRGRYAVVLPDRLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000667.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000667.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e58cf0fa5d6c50348cadc73a57bdd30a33b71e40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000667.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00754
+MTADQHGHECRVAQDASLERLYQYLDGALTPEDIEQVRAHVAECPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQISTTTVTWG
+>GCF_003691675.1_00484
+MTVDQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG
+>GCF_005280335.1_02176
+MTADQHGRECRDAQEDTLERLYQYLDGALTPEEIDQVRAHVEDCEDCRHQQELEQFIRTA
+VRRSCQEKAPEQLRTTILTRITQLSTTRVTWR
+>GCF_020097155.1_02071
+MSQDGDCRGCNDGEDRLEQLYQYLDGALTPEDIDQVRAHVDQCPDCHHQQELELIIRSAL
+RRSCQEKAPAQLRATIMTRITQVSTTTVRRAG
+>GCF_023573625.1_00718
+MTADQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000668.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000668.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73b7eec9781ea9189e59d6aa1481156a0256695a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000668.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00755
+MHNRRIRIAAVGDQLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER
+WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT
+PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
+>GCF_003691675.1_00485
+MHNRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER
+WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT
+PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
+>GCF_005280335.1_02175
+MNDRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPGVELENYVLAVPHETTEDLNER
+WWGEASRRYSEDTENRLVVALSDADLDLEASSTARSRLNLANVLDTASQRGIPVLVVGPT
+PTLDEERNARLAELNAAYLDVADRRSHVYVDTFTPLQGHEQWRADLAAGEGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
+>GCF_020097155.1_02070
+MQNRRIRIAAVGDHILAGAGDPRSIGWWGRVLARTAAPEVTLENYVLAVPHETTEQLNER
+WWGEASRRFSESAENRLVVALSDADLDLEASSSARSRLNLANVLDTASQRGITALVVGPV
+PTLDEARNDRLADLNTAYQDVAARRGHLYVDAFTPLRTHEQWRADLAAGDGVPGQAGHGL
+IAWLVLHRGWYQWLGVPEPTA
+>GCF_023573625.1_00719
+MHNRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER
+WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT
+PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000669.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000669.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8094e6432e6fb286424052661cfccb99b707dadb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000669.fa
@@ -0,0 +1,110 @@
+>GCF_002008305.4_00756
+MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAEAEPKAAA
+KTEPKTAAKAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADT
+ATTTADEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKVLIDNRVVINSHLART
+RGGKVSFTHFIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA
+LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH
+GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYSMAYHPDLDIREHGLTLWDLDRKWPTGGFGGAGSLTLRKILGVLRDAYCRTIGV
+EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP
+DSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVVVNNQVGFTTPPTQARSA
+VYSTDVAKTIQAPIFHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETHEDAP
+ASGGEGLRPAEDRDAAPEAPASTAISAETLRAIGQAHIDVPEGFTVHPKLAALLERRAKM
+AVDGGIDWGFAELAAFGSLLMERVPVRLAGQDSQRGTFTQRHSVFHDRITGDTWAPLRHL
+SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD
+QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREHA
+YARPRRPLIVFTPKQLLRLKAAANSVEDFTEGGFQPVIPDAGVDAKDVTRVLLVSGRLYY
+DLLARRQKSGDTSTAIVRVEQLYPLPLDEIRKALRAYPVADVTWVQDEPANQGPWPFMAL
+NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR
+>GCF_003691675.1_00486
+MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAEAEPKAAA
+KTEPKTAAKAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADT
+ATTTADEKQEKATVLKGMAKAVATNMDASLSVPTATTVRDLPAKVLIDNRVVINSHLART
+RGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA
+LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH
+GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYSMAYHPDLDIREHGLTLWDLDRQWPTGGFGGASSLTLRKILGVLRDAYCRTIGV
+EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP
+DSFSVLPILVHGDAAFAGQGVVAEVLQLSQLPGYRTGGTIHVIVNNQVGFTTPPTQARSA
+VYSTDVAKTIQAPILHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETHEDAP
+ASGGEGLRPAEDRDAAPEAPASTAISAETLRAIGQAHIDVPEGFTVHPKLAALLERRAKM
+AVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITDETWAPLKHL
+SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD
+QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREQA
+YARPRRPLVVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDAKDVTRVLLVSGRLYY
+DLLARREKSGDTSTAIVRVEQLYPLPLEEIRKALRAYPDADVAWVQDEPANQGPWPFMAL
+NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR
+>GCF_005280335.1_02174
+MLRKRRYTVPELTSDRLAQEFPGNERLVAEIYRKYRADSGSVDRQWAQIFARLEASAPAP
+AEKAPAQAAAKAAPKAEPQAEAKVTEPKAKPAPARGAQPKETSTSTGPKVKKTPAAQAVP
+SEPADPSKDAAKEEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDVPAKVLIDNRVVI
+NSHLARTRGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLP
+RPDGSRSLVVPNVKAAETLDFRGFWQAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGT
+VHSVPRLSKGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSG
+EFLKIVHGLLLGEDGFYDEVFHSLRIPYEPVRWAQDLQVNPEEQVGKVARVQQLIHAYRD
+RGHLMANVDPLEYSMPYHPDLDIREHGLTLWDLDRQWPTGGFGGASTLTLRKILGVLRDA
+YCRTIGVEYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIG
+QKRFSLEGGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYGQVFREFE
+GATPGGTSGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRL
+DLGGQRPDSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVIVNNQVGFTTP
+PTQARSAVYSTDVAKTIQAPILHVNGDEPESVMHVAELAFEYRQRFNKDVVIDLVCYRRR
+GHNEGDDPSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFA
+ETHEGSASSGGEGIRPAEDRDQAPEAPETTAISAETLRAIGQAHIDVPEGFTVHPKLAAL
+LERRAKMAVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITGDE
+WAPLKNLSEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFINGAQTIID
+EFISSAEQKWAQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPTTGANHF
+HLLREQAYARPRRPLVVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDPKKVTRVQL
+VSGRLYYDLLARRNKDGDETTAIVRVEQLYPLPLDELRAALEAYPQAEVVWVQDEPANQG
+PWPFMALNLLPQLDREVRLVSRPASASTSAGTKGRHDQELSTLLDAGFAR
+>GCF_020097155.1_02069
+MPELTSDRLSQEFPGNEDLVAQIYRKYREDQGAVDRQWAQIFARLEASQPQPEPAAAAPK
+ATSSATAEPAPAVKPAVKRGAATPADPQAAAKKSGPTDVSAPAQRKRSVSEAVPSEPARD
+AAAGASEKQDKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKLLIDNRTVINSHLART
+RGGKVSFTHLIGYAVVRALKAMPSMNTLYEERDGKPTMVEPAHVNFGLAIDLPKPDGTRA
+LVVPNIKAAETLSFRQFWEAYDDLVKRGRANKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SKGQAAIIGVGALTYPAAFQGAAESTLNSLAISKTITLTSTYDHRVIQGAGSGEFLKLIH
+GYLLGEDGFYDDVFHDLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYRMPTHPDLDIREHGLTLWDLDREWPTGGFGGADTLTLRRILGVLRDAYCRTVGV
+EYMHIQNPAERAWFQDKLERPYEKPSREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDSILGDAADEGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVARAKQDRLEAAGESG
+AAFPVLPILVHGDAAFAGQGVVTEVLNLSQLPGYRTGGTIHVVVNNQVGFTTSPAEGRSS
+VYATDVAKTIQAPILHVNGDEPESVLRVARLAYEYRQRFHKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYTLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFAETHAAET
+GQAVATTGLEPARDRDAARPAPSTTAISPDTLRRIGDVHLEVPEDFTVHPKLSQLLEKRA
+KMAVDGGIDWGFAELAAFGSLLMEGVPVRLSGQDSQRGTFTQRHSVFHDRVTDETWTPLN
+HLSESEAPFWVYNSLLSEYAVLGFEYGYSVERSDALVLWEAQFGDFINGAQTMIDEFISS
+AEQKWSQNSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSHGANHFHLLRE
+QAYSRPRRPLVVFTPKQLLRLKAAADPVEAFTQGGFRKVIGDASVDAAQVERVILVSGRL
+YYDLLARREKSGDTSTAIVRVEQLYPLPAEEIRAELAKYPGAQVRWVQDEPANQGPWPFM
+ALNLLPQLDREVTLVSRPALAATSAGTKGRHDEELSTLLDTAFGA
+>GCF_023573625.1_00720
+MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAAAAEAEPKAAA
+EAEPKAAARAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKAKKTPAAQAVPSEPADT
+ATTTADEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKVLIDNRVVINSHLART
+RGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA
+LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH
+GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYSMAYHPDLDIREHGLTLWDLDREWPTGGFGGASSLTLRKILGVLRDAYCRTIGV
+EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP
+DSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVIVNNQVGFTTPPTQARSA
+VYSTDVAKTIQAPIFHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERAFAETHEDAP
+TSGDEGIRPAEDRDAAPKAPASTAISAEMLRAIGQAHLDVPEGFTVHPKLAALLERRAKM
+AVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITGDTWAPLKHL
+SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD
+QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREHA
+YARPRRPLIVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDAKDATRVLLVSGRLYY
+DLLARRQKSGDTSTAIVRVEQLYPLPLEEIRKALRAYPDADVAWVQDEPANQGPWPFMAL
+NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000671.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000671.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9306da2e9c702c9a0ce70636c23a6e952c4d47b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000671.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00758
+MEWLLLILGLALIVGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE
+LIPKNMSIAEPMAIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVREDQALPEVLD
+LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF
+PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR
+RIERVRFDPAAEDEETRA
+>GCF_003691675.1_00488
+MEWLLLILGLALIVGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE
+LIPKNMSIAEPMAIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVREDQALPEVLD
+LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF
+PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR
+RIERVRFDPAAEDEETRA
+>GCF_005280335.1_02172
+MEWLLLILGFALVLGTGFFVAVEFSMIAIDVPTVQRMVDEGDKGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPVLLDVGVPESVVGTVSLVVAMVVATLLSMLIGE
+LIPKNMAIAEPMTIGRALARPQLLFSTVFKPAILVLNGFSNGVLARFGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDEQTATFLDRTLRFADRTAADVMTPRIRVETVGEDQPLPEVVD
+LARRTGFSRFPVIGESSDDIRGVVHVKKVVAVPRERRADLEAGSLMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDKVTPGVLQTAAGRWYF
+PAELRPDEAQAQITSLSVPEDGAYETIGGFIMARLGRLAAVGDVVSVDGGTLSVERMDGR
+RVERVRFDPAAAADKEARA
+>GCF_020097155.1_02067
+MEWILLILGLLLVLGTGFFVMVEFSLIAIDAPTVQRMVDDGDRSWEPLLTCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLVDPLILAVGLPQSVAGPVSLVVAMAAATLLSMLLGE
+LVPKNMAIAEPLRLGRALARPQLVFAAVFKPAILVLNGFSNGVLHRMGLEAKEEISGARS
+PEELSSLVRRSAQLGTLDEQTATFLDRTLRFAERTAADVMTPRIRMETVGEDDGLLDVVE
+LARRSGYSRFPVIGESPDDVLGVVHVKKAVAVPMDRRADLTAGALMTDVIRVPETVHLDQ
+LLAELREASLQLAIVVDEYGGTAGVVTLEDVVEEIVGEVSDEHDRVTPGVLQTASGRWYL
+PAELRPDEAHAQIKALDVPEDGAYETIGGFVMARLGRIPAVGDVVPLDVGTLTVERMDGR
+RVDRVRFDPRPVTEEARA
+>GCF_023573625.1_00722
+MEWLLLILGLLLIAGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE
+LIPKNMSIAEPMTIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVGEDQALPEVLD
+LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF
+PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR
+RIERVRFDPAAEDEETRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000672.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000672.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9dd537704ea3463e40d3d45271858b71d81ce8d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000672.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_00759
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMAALGVPSAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WTVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA
+>GCF_003691675.1_00489
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMAALGVPSAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WTVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA
+>GCF_005280335.1_02171
+MNEDVIGLLWLVVLLVANAFFVAGEFAVMGARRSQIEPKAEAGSRPAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVGPMTALGVPDAAADVTAFVLALLVVTFLHVTF
+GEMVPKNAAVSFADRAVMILARPLVGLSKLLHPIVTVLNWAANVVLRAFRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHTAGDVMVPLEKVVTVPEGITPHDFE
+WTVGRVGYSRFVVEDPDGGYTGYLHLKDVLTVGPSGHEEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGVLFLEDVLEELVGEINDVTQSPRRFRPA
+>GCF_020097155.1_02066
+MSQDVVGLLWLAVLLAANAFFVAGEFAVMGARRSQIEPRAEAGSRQAQVALFAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLAAPMEALGLPLAAADVVAFVLALLIVTFLHVTM
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPLIVVLNWAANTVLRAFGIEPKDEVASS
+FTLEEVQTIVAESTRSGTLEDESGVLHSALEFSSYTAGDVMVPIEKVVSVPEDVTPQQFE
+WAVGRVGYSRFVVEDSQGGYAGYLHLKDVLAGGPSRYADPVPVTRVRSLANVRVADEVED
+ALGLMQRTGSHLARVISEDGATVGVLFLEDVLEELVGEIHDVTQSPRRFRPTTGSHAAPE
+PTRMRDLPAR
+>GCF_023573625.1_00723
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMGALGVPAAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WAVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000673.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000673.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43185970586e2911acbd9d70d990801d72d03cf8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000673.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00760
+MLRRRRLPALTGALAALTLSLAACGGTSGDSAGAQAAGASADSGSGSAAGAPVAVATTTQ
+LGSVLDRVVACADARSATVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDERFAECGATVRGELEQTDAQVREILAGVPEDRRTLVTDHDAYGYFSDAYD
+FTVSGVVVPGGSTDGEPSSQEIAELARSIRDGGADAVITSVGARNSLVDTVAEEAGNLPV
+IEVYESGVGPKDTPEADYAEAMLANARTLADALEG
+>GCF_003691675.1_00490
+MLRRRRLPALTGALTALTLSLAACGGTSGDSAGEQAAGASAAAGSGSAAGAPVAVATTTQ
+LGSVLDRVVACADARSVTVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDERFAECGATVRGELEQTDTQVREILAGVPEDRRTLVTDHDAYGYFSEAYD
+FTVSGVVVPGGSTDGEPSSQEIAELARSIRDGGADAVITSVGARNSLVDTVAEEAGDLPV
+IEVYEGGVGPKDTPEADYAEAMLLNARTLADALEG
+>GCF_005280335.1_02170
+MHRTPRRRAAAALTLASALALAGCGADSGGDGQAGSGEPAAVATTTQLGSVLGDVARCAG
+ATTATVMGPGDDPHDFAPSSQQVAQMARAGLVFANGFGLEAGMASALENAAQDGAQVLEV
+APRLDPLPFGAGEGAADGHAGETADEHAAHAEEGSAGAHDGHDHGSQDPHVWMDVARMAR
+AAEVMGDALAEHTGEDRFADCGRQVRGELEATDAEVREILAAVPEDRRRLIADHDAYGYF
+AAAYGFEVAGVVVPGGSTDGEPSSQRIAELTQAVAEAGADALVTSAGGGAPTVETIAADG
+GGSTPVVELYEGGVGPADGEPAGYAEAMLHNARVLADALGE
+>GCF_020097155.1_02065
+MSRSSPTPRLAAPAVVAALGVALAGCSVADSSSPSAAEEGAVTASSSAAGPVVAVATTTQ
+LASVADRVARCGGGSVVSVMGPGDDPHDVAASSDQVAQMVHSGLVFTNGLGLEGGMDSAL
+DNARQDGAVVVEVAPRLDPLPFGEHDADHAGHEGADAHAGHEHGSQDPHVWMDVARMAAA
+ARVVGDELAAETGEQKYAECGATVEGELEETDRQVREILAAVPQERRTLVTDHDAYGYFS
+AAYGFTIEGVVVPGGSTDAEPSSRELAALTQQVKDHGAAALLTSTGTPNGLVETVAREAG
+GLPVVQLYEGGVGPVGTPEADYAQAMLHNARTLADALKG
+>GCF_023573625.1_00724
+MLRRRRLPALTGALTALTLSLAACGGTSGDSSGAQAAGASADAGSGSAVGEPVAVATTTQ
+LGSVLDRVVACAGARSATVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDEQFAECGATVRGELEQTDTQVREILAGVPEDRRTLVTDHDAYGYFSEAYD
+FTVSGVVVPGGSTDGEPSSQELAELARSIRDGGADAVITSVGARNSLVDTVAEEAGDLPV
+IEVYEGGVGPKDTPEADYAEAMLVNARTLADALEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000674.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000674.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b643c0cf5aa871db433e63150e7d241e56462651
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000674.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00761
+MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT
+GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT
+SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS
+YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQRERETPVVALPGAEVAR
+>GCF_003691675.1_00491
+MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT
+GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT
+SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS
+YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQREQEAPVVALPGAEAPR
+>GCF_005280335.1_02169
+MDWLIEPFLLGFQQRALVGGLIAAALCAVVGTWLVLRGMSFFGDAFVHGVMPGIALSVVL
+GFDAHLGAALAALVMLAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISLSDSYTGSLT
+AILFGDALGVTWEGIVRQAVIAALVLVLALVLYRPLMALSFSPAKARSLGMRPRLTHALL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRTVPQMMALAVLLGAAGVTIGLVLS
+YHLGTAASATMALVPIAMFFVVLAGRAGLRALRSRRVRADRRRAVVETPSRRSVSP
+>GCF_020097155.1_02064
+MDWLIDPFLLGFQQRALLGGLIAALMCSAVGTWLVLRGMSFFGDAFVHGVLPGIALAVLL
+GGSPHLGAALAAVLMMGGISLVHRTTTLKEDTAIGLLFVGMMALGVVIISLSSSYTGSLT
+AILFGDALGVTPENLLVQAAIGVVVVVLALVLYRPLLALSFSEAKSQALGMRPRLTHTLL
+LVLIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRTVPQMMALSAGIGALSVVAGLVLS
+YHWGTAASATMALVPVVLFFVVLLGRSAVQAAAGRRRRTRGAASAPTPAGDDDAESRRET
+EGSPAR
+>GCF_023573625.1_00725
+MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT
+GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT
+SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS
+YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQREQEAPVVALPGAEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000675.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000675.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2bffcdbe6004cc50affa4c6150ea88913ea7771c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000675.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00763
+MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT
+LQQQLDDGLVDVLRRDDGESVYRRCEDEGHHHHLVCRSCWTTVEVTAPHVEAWATAVAAE
+HGFTDADHTVEITGVCARCRTEGRTRGA
+>GCF_003691675.1_00493
+MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT
+LQQQLDDGLVDMLRRDDGETVYRRCEDEGHHHHLVCRICWTTVEVTAPHVEAWATAVAAE
+HGFTDADHTVEITGVCARCRTEGRTRGA
+>GCF_005280335.1_02167
+MSAPDPGPRVVRPRATRQKAAVDRALETIPDFVSAQELHARLQEEGERISLATVYRTLQQ
+QLEDGQVDVLRREDGESVYRRCEARGHHHHLVCRLCWSTVEVTAPPVEAWAARIAAEHGF
+TEAEHTVEITGVCADCAATRAADAG
+>GCF_020097155.1_02062
+MSETPGRPSEAPAPRGRSTRQKAAVDGALDAAEDFVSAQELHARLRDAGERVSLATVYRA
+LQQRLDEGTVDMLRREDGESVYRRCAAEGHHHHLVCRVCWTTVEVTAPGVEEWAARMAAE
+HGFSDPDHTVEITGVCAECRAAGRG
+>GCF_023573625.1_00727
+MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT
+LQQQLDDGLVDMLRRDDGESVYRRCEDEGHHHHLVCRICWTTVEVTAPHVEAWATAVAAE
+HGFTDADHTVEITGVCARCRAEGRTRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000677.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000677.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d104d317d064449b0580a63404c5bd360fd32bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000677.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00765
+MATVFSRIIAGELPARFVWQDQTCVAFLSAAPLQPGHALVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD
+>GCF_003691675.1_00495
+MATVFSRIIAGELPARFVWQDQTCVAFLSAAPLQPGHALVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD
+>GCF_005280335.1_02164
+MASVFSRIIAGELPARFVWQDETCVAFLSTGPLNPGHALVVPREEVDAWVDADPALVMHL
+MTVAQQLGKAQVRAFSAQRAGLMVAGYEILHLHVHVWPSNSLADFDLNRVDNSPDPAEMD
+DAAARLRAALRELGHGEVVPQD
+>GCF_020097155.1_02060
+MATVFSRIIAGELPARFVWQDEQCVAFLSLGPLAQGHTLVVPREEVDQWVDADPDLLAHL
+TRVAQAIGRVQVRAFGAQRAGLMVAGYEIPHLHVHVWPSNSMNDYDMARVDNAPEPESLD
+EAAAAIRAGLREDGHGDVVPQD
+>GCF_023573625.1_00729
+MATVFSRIVAGELPARFVWQDQTCVAFLSAAPLQPGHTLVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000678.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000678.fa
new file mode 100644
index 0000000000000000000000000000000000000000..403793de0146c67d320b9b35a43094579dbe19a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000678.fa
@@ -0,0 +1,121 @@
+>GCF_002008305.4_00766
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT
+TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKA
+TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII
+TSATIDPERFARHFGRPLAEGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELASEPPGDILVFLPGEREIREAADHLTGVV
+AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT
+GTARISRYSHRTKVQRLPIERVSQASANQRSGRSGRTSDGIAIRLYSEEDYLSRPEFTDP
+EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA
+GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE
+LHRRFADENSDFSAILNLWAYLRERQQELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ
+LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLAQIGAYDERRREYAGARGTRFAVFPGSA
+LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRAYNEPHWSRRAGSVVAR
+EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL
+ETRLRRRDLRIGDEDLFAFYDARIPANVVSERHFDAWWKKARQEQPDLLDLDVAALLTAD
+AEDLDTDAFPTTFSYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW
+LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPEALSAAVRR
+VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA
+GTDDPASARPGPRGTGRGGRAQADARAGAEGRRRPEGPGRSGATPAFEERHRLTSWSIGT
+VPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLAT
+LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD
+RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGSVSLALAPALSDVKAHLEQLVFPGFVA
+ATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG
+TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA
+>GCF_003691675.1_00496
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT
+TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKA
+TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII
+TSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPVPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVV
+AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT
+GTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDGIAIRLYSEEDYLSRPEFTDP
+EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA
+GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE
+LHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ
+LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLSQIGAYDERRREYAGARGTRFAVFPGSA
+LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRAYNEPHWSRRAGSVVAR
+EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL
+ETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTAD
+AEDLDTDAFPTTFAYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW
+LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPDALSAAVRR
+VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA
+GTDDPASARPGPRGTGRGGRAPADARAGAEGHRRPEGPGRSGATPVFEERHGLTSWSIGT
+VPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLAT
+LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD
+RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKDSVSLALAPALSDVKAHLEQLVFPGFVA
+ATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG
+TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA
+>GCF_005280335.1_02163
+MTETPTPPAAASSAPAIVFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKTTQLPKMC
+LALGLGEAGVIGHTQPRRIAARSVAERIAEELGEDIGRTVGYQVRFTAQTSKATRVKVMT
+DGILLAEIPHDPQLRRYSVVIVDEAHERSLNIDFLLGYLRTLLPQRPDLKVIITSATIDP
+ERFARHFGRALAEGEEHEDAVPADDGGLVVPAPVIEVSGRTYPVEVRYRPLTGEPSPDDP
+EDDSDDAAETRDPLDAIGEAVLELAAEPPGDILVFLPGEREIRDAADHLSGVVASSKRLA
+GTEVLPLFGRLSMAEQHRVFGRAAAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISR
+YSHRTKVQRLPIERVSQASANQRAGRSGRTSPGIAIRLYSEEDYLSRPEFTDPEILRTSL
+ASVILQMLSLGVAATPADVQGFPFVQPPDGRQVSDGATTLTELGALHPPRPSGAKDGHDG
+GRGRGGRAPEPGTITPIGRRLARLPVDPRLGRMILESGERGCVREVMVLAAALTIQDPRE
+RPVEQREAADELHRRFADENSDFSAILNLWAYLQEQQKELSGSQFRKLCRREHINWLRVH
+EWQDLVRQLRQLAKDVGVAVHAGPVDPVGQHEAVHRSLLTGLLSQIGSYDERRREYAGAR
+GTRFAVFPGSALFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEAAGGLVKRTYNEPH
+WSRRAGAVVAREKVTLFGVTLIPDRSVKYGRIDPELSRELFIRHALVEGDWRTRHRFFAR
+NRAALEEVDALETRLRRRDLRIGDEDLFAFYDARVPANVVSERHFDAWWKKARQERPDLL
+DLDVAALLTADAEDLDTDAFPTVFPYPLSGGDVDLDLEYTFDPTGASGTDGVTVSVPVLL
+LNQVSPGPFAWLVPGLRVELVTALIKALPKAVRKQLVPAPDVARQLVADLDAHADPLADE
+LTEALSAAVRRVRGIVVEPGLWAPDAVPAHLRMDYRVVDARGAVMGAGQDLAALQARLAK
+ANRSAIAARLAGTDDPANARPGPGRQGGRRDGGGNDGGAGRRGSGRGVRGRGRDGTGRPE
+AGAQGAGGAAAAFAERHGLTSWSIGTVPRRITTDPGARGPAITGYPALVPETTAEGGPAA
+GLTVARSAEDQAAWHRAGVIRLLLATLPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVAD
+CSQAAVDRLVGDELPFDEAAFRALFDRVRADLIDTVFAVTRLVEQVLSRAAEVRRRLKGS
+VSLAMAPALSDVKAHLEQLVFPGFVAATGWERLQHLPRYLQGILVRLDRLDAGGHLQRDG
+QHMAVVQRLEDEFDAAVQAHRARFSGVPVPADLERVRWLIEELRVSFFAQELGTAVSVSE
+KRVRQALAQAARA
+>GCF_020097155.1_02059
+MTDFPQPPAAAPVITFPAHLPVAERREEIMDAVRENQVVIVAGETGSGKTTQLPKMLLAL
+GLGGAGVVGHTQPRRIAARSVAERIAEELGEDVGRTVGYQVRFTAQTSTRTRVKVMTDGI
+LLAEIPHDPDLRKYSAIIVDEAHERSLNIDFLLGYLKRLLPRRPDLKVIITSATIDPERF
+ARHFGTEDEPAPIIEVSGRTYPVEIRYRPLTEEPSPDDPDDDADDHAETRDPIDAVGDAV
+LELAGEAPGDILVFFPGEREIREAADHLAGVVASTPRLAGTEVLPLYGRLSMAEQHRVFG
+RAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERISQASAN
+QRSGRSGRTSDGIAIRLYSEEDFLSRPEFTDPEILRTSLASVILQMLSLGVADTPREVMD
+FPFVQPPDSRQVTDGAATLTELGALHADAPTRGGGRGRGKGAGNRSAAGTITDIGRRLAR
+LPVDPRLGRMILESGRRDCTREVMVLAAALTIQDPRERPVEQRQAADELHARFADDRSDF
+SAYLNLWEYLREQQRELSGSQFRKLCRREHINWLRVHEWQDLVRQLRQLSKDVGVSVHPG
+PVDPVGKHDDVHKSLLTGLLSQIGAYDERRREYQGARNTRFAVFPGSALFKKRHPFVMAA
+ELVETSRLWARAVARIEPEWIEEVAGDLVLRSYAEPHWSRKAGAAVAMEKVTLFGVTIVP
+ERSVRYGRIDPVLSRELFLRHALVEGDWRTRHRFFARNRRLLEEVDELETRLRRRDLRVG
+DEELFAFYDARVPANVVSERHFDAWWKKARQETPDLLDLDLDALLTQDADELDTDAFPTA
+FRYPLPGGDADLALDYTYDPTGASGTDGVTVAVPILLLNEVAPGPFAWLVPGLRGELVTA
+LIKALPKAVRKNLVPAPDVARLLVEDLDAHADPLRDELPAALSSAVRRVRGAVVEPELWR
+LDAVPDHLRMDYRVVDARGAVMGAGQDLPALQARLAKANRSAIAARLAGTDDPRNARPGQ
+GAGRGRGKTEPKGGDGGARGPAADTGRPGPSRTADGAPAFRERHGLTSWTVGEVPRQITT
+APGDRGPAITGYPSLIPETTADGSPAAGLVVARSAQDQAAWHRAGVIALLLATLPSTHRY
+VLDHLDNKEKLTFTQNPHGSVESLVRDATHVAVDRLVGTDLPFTEVGFRALFDRVRADLI
+DTVFAVTALVEQVLSRAAEVRRRLKGGVSLAMAPAKSDVQAHLEQLVFPGFLAATGWQQL
+QHLPRYVQGMLARLDKLDAGGHLQRDGQHMAVVQGLEDEFDAAVTAHRSRFPGTPVPAEL
+ERVRWLLEELRVSYFAQELGTAVSVSEKRVRQALAQARQG
+>GCF_023573625.1_00730
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT
+TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTTQTSKA
+TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII
+TSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVV
+AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT
+GTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDGIAIRLYSEEDYLSRPEFTDP
+EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA
+GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE
+LHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ
+LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLSQIGAYDERRREYVGARGTRFAVFPGSA
+LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRTYNEPHWSRRAGSVVAR
+EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL
+ETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTAD
+AEDLDTDAFPTTFTYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW
+LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPDALSAAVRR
+VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA
+GTDDPASARPGPRRTGRGGRAQADGRAGAEGRRRPEGPGRSGATPAFEERHGLTSWSIGT
+VPRTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSADDQAAWHRAGVIRLLLAT
+LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD
+RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGSVSLALAPALSDVKAHLEQLVFPGFVA
+ATGWERLQHLPRYLQGILTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG
+TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000682.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000682.fa
new file mode 100644
index 0000000000000000000000000000000000000000..950f0cea6563e91cb219a5aca245803c50a3fd79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000682.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00772
+MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLSITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMATVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGLVI
+IVMLVVTWIVERSTVRRRAARAARA
+>GCF_003691675.1_00503
+MSHVTESSPAHPGRAEESTPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAALTVHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWAIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI
+IVMLIVTWIVERTTVRRRAARAARA
+>GCF_005280335.1_02158
+MSPVTESSPAHRGRAEESAPLRPTSRLGIAATFIGTTIGAGYASGNEILQYFVSFGFWGG
+TLALVIAGALFFLLSAIVLKMAQKLRTTDIHRLVNPTTSRVPTWFADLCITASLLGTLVI
+MLAGAGAAVNTSFGLPTMVGSLLMAAVCVLSVLAGISGLVRVQAVVVPLIIVVAVGVAWW
+GLANPGAPVEDVASLVTSSPLINQWWMSGILYVAFNFQLAYAVLAPIGRDSSSSGRTLVA
+GAGLGAVGLVVMAGAIMFAMAAHAHLIGRADLPMVELAAMIGGWAALVYTVILLLAQFTT
+AVSCLFGGVERIALLSPLRRVPGWAIAVATALAATLLSSVGFSDLVGTVYPVLGYAGIAI
+IVMLIITWIAERTLVRRRAARAARA
+>GCF_020097155.1_02053
+MSHVAQSTHENRPAQDGGNGLRPMSALGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGVLFFLLSAIVLKMAQQLRTTDIHRLVNPTSSRIPTWFADLCITASLLGTLVI
+MFAGAGAALDTWLGLPAWAGAALMAAVCVLTVLGGISGLVKVQGLVVPLIILVAVGVAWW
+GLTHPGAGADDVASLVTSSPLINTWWMSGILYVAFNFQLAYAVLAPIGKGSSSPGTSLVA
+GAGLGAIGLVVMAGAIMAAMGAHATLIGRAELPMVELAGMVAPWVAAVYTVILLLAQFTT
+AVSCLFGGVERIALLSPLRDVPGWLIAVVTAVVAVLLSSVGFSDLVGIVYPVLGYAGIAI
+VAMLIATWILDRTLVRRRAARADRA
+>GCF_023573625.1_00739
+MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI
+IVMLVVTWIVERSTVRRRAARAARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000683.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000683.fa
new file mode 100644
index 0000000000000000000000000000000000000000..979503700d49edb47ccf0bab076c8000f705d961
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000683.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00773
+MTSAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD
+VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA
+VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG
+GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS
+WDDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG
+>GCF_003691675.1_00504
+MTPAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD
+VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA
+VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG
+GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS
+WEDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG
+>GCF_005280335.1_02157
+MLSIAGSDSGGGAGVQADLKTIAVWGGYGMTAITAITAQNTQGVQAVHPLPVDVVRAQLD
+SIAADIAVDAVKIGMLGTAELMGAVAGWLEETRPAVVVLDPVMVASSGDALTAVGDDDGR
+AAWSRLLRAAHLVTPNLPELARLTGRDSTDWEAALDAAGGLAAEHEVTVLLKGGHLDEAA
+AAEVPDAVVRVAGAVHEVRGPRVATRASHGTGCTLSSALATLAGAGLSWEDALERAKPWL
+ADAMRAGEALAVGDASRPTWHGPVDHGHARRG
+>GCF_020097155.1_02052
+MAPSPSTPPSSSPAAEGPAVPRVLSIAGSDSGGGAGIQADLKTIAEWGGYGMTAITAITA
+QNTQGVQAVHPLPAEVVRAQLDSVASDIAVDAVKVGMLGTAELMRVVADWLEEARPAVVV
+VDPVMAATSGHALTPVGDAEAHAAWGRLLRAAHLVTPNLPELARLAGRPLDSWAAALDAA
+RELAAAHAVTVLAKGGHLADLTRADPEGAEAGDDPDAEGGVPDALVRPDGSVHEVRGPRV
+ESGATHGTGCTLSAALATLAAGGLGWEDAIERAKPWLAQAMVAGEALAVGDRTRPTWHGP
+VDHGHARRG
+>GCF_023573625.1_00740
+MTSAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD
+VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA
+VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG
+GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS
+WEDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000684.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000684.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23cb9f6631cfecc119ffb5d9546ff14daa2faf7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000684.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00775
+MHSPDPLLMTAAGRDDGGTGPGARRRARLAASRLYVCTDLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVAVELAAFATLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPDVVLGRSCHTEAQVRGARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPTLAARLDAEDPAGARPWFAIGGVDADRLPEVRAAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG
+>GCF_003691675.1_00506
+MHSPDPLLMTAAGRDDGGTGPGARRRARLAASRLYVCTDLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVAVELAAFATLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPDVVLGRSCHTEAQVRGARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPTLAARLDAEDPAGARPWFAIGGVDADRLPEVRAAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG
+>GCF_005280335.1_02155
+MHSPDPLLMAAAGRDDGDTGPGTGRRARLAASRLYVCTDLQRFLRPDGTLDTVAFADFCA
+AAFRGGVDLIQVRDKAVDVAVELAAFAVLVPLARAHEALSAANDRADVAALAGVDVFHTG
+QTDLTTVQCRALLGPDVVLGRSCHTEAQVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPSHAARLDAEDPAGARPWFAIGGVDADRLTEVRAAGADRIVVVRAVTQAEDPEAAART
+LRAGLPG
+>GCF_020097155.1_02050
+MHSPDPLLMTAAGRDDGDTGPGAGRRARLAASRLYVCTDLQRFLRPDGTLDTAAFGGFCA
+AAFRGGVDLIQVRDKAVDVAVELAAFAVLIPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPNVVLGRSCHTPDHVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+GLPTLAARLDAEDPAGARPWFAIGGVDAERLPEVRAAGAGRIVVVRAVTQAADPEAAARE
+LRAGLPA
+>GCF_023573625.1_00742
+MHSPDPLLMAAAGRDDGGTGPGAGRRARLAASRLYVCTGLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVALELAAFAVLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPNVVLGRSCHTEAQVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+GLPSLAARLDAEDPAGARPWFAIGGVDADRLPEVRTAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000687.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000687.fa
new file mode 100644
index 0000000000000000000000000000000000000000..848ab8f5dd2a1c106bcc47a079a58438aee35457
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000687.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00778
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
+>GCF_003691675.1_00509
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
+>GCF_005280335.1_02152
+MAEHRTPPATPAIPPLRIGGYDLAARLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATELLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
+>GCF_020097155.1_02047
+MAPHDTTERRRAREASTAVPPLRIGGYELSSRLIMGTGGITDLAALEGALVASETTLTTV
+ALRRWSTDARDGLIALLDRLGIDVLPNTAGCRTARDAVLTARLGREALETELVKVEVIAD
+DRTLLPDVVETLDATEQLAAAGFTVLAYTSDDPAMALRLEHAGAAAVMPLGSPIGSGLGI
+LNRTNLELIVSRAGVPVVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACR
+LALEAGYHAHRAGRIPRRLHALASSPMAGRIGGAEERA
+>GCF_023573625.1_00745
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000688.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000688.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ee1f01865b2deeac16e0be6921c03add23d1c13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000688.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00779
+MTAALDPAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV
+LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH
+RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP
+GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSV
+DALTMRFRELRLVPDPERTPVTDLSAHADQAPRPDDAGAPGSAEACGAAGGEIAPAALAA
+LLADPARVASLTLLDVREDWERRLRRVEAPAAVADRHVPLEAVLAEPAALAPGRDRVLVV
+YCAAGARSARARDAVVGADPSAGGRVLSLAGGLAAWPA
+>GCF_003691675.1_00510
+MTAALDPAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV
+LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH
+RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP
+GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIVGSLMAAEAIKLLSGVGEPLVGRLLSV
+DALTMRFRELRLVTDPERTPVTDLSAHAAQAPRPDDAGAPGSAEACGAAGEEIAPAALAA
+LLADPARAASLTLLDVREDWERRLRRVEAPAAVADRHVPLEAVLAEPAAHAPGQDRVLVV
+YCAAGARSARARDAVVGADPSSGGRVLSLAGGLAAWPA
+>GCF_005280335.1_02151
+MTAAPDPADREPRDLTALSDTQLQRFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV
+LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH
+RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP
+GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSV
+DALTMRFRELRLVADPERTPVTDLSAHADQAPGSDDAGAPGSAEACGAAGGEIDPATLAA
+LLADPARAASLTLLDVREDWERRLRRVEVPAAVADRHVPLDAVLAEPAAHAPGPDRVLVV
+YCAAGARSARARDAVVAADPSAGERVLSLVGGLAAWPA
+>GCF_020097155.1_02046
+MSRPAGEPLVPEDRAPHSLDELSDTQLQRFARHLGLDGFGPEAQLALLRSRVLVVGAGGL
+GAPVLTYLAAAGVGEVHVVDDDVVDRSNLHRQVIHVETDLGRPKTASAAETMRGLHPEIR
+VVEHRQRLAAANALELVGAVDLVVDGSDNYATRYLVADAGEITGVPVVWGAILRFAGQVS
+VFAPGGPLYRDVFPEEPEPGDVPTCAQAGVLGVLPGIVGSLMAAEAVKLLAGVGEPLTGR
+LLSVDALTMRFSTLRLVPDPERTSVTDLSAHTVPRGGADPVESGEITPAGLAALLADPER
+AAALTLLDVREDWERGLARISAPAAAEDRHVRLDEVLADPAAHSPESGRTVVVYCAAGAR
+SARAREAVVAAAPEAADRVLSLAGGHAAWADRN
+>GCF_023573625.1_00746
+MTAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPVLTYLA
+AAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEHRERLT
+ATNALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAPGGPLY
+RDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSVDALTM
+RFRELRLVPDPERTPVTDLSAHADQAPRPDDAGAPGSAEACGAAGGEIAPAALAALLADP
+ARAASLTLLDVREDWERRLRRVEAPATVADRHVPLEAVLAEPAALAPGQDRVLVVYCAAG
+ARSARARDAVVGADPSAGGRVLSLAGGLAAWPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000689.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000689.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89e92859ec0368aaf0b6a0a942e6861ea47fb20d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000689.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00780
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTDKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLREQGHVEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM
+>GCF_003691675.1_00511
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTGKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLRAQGHIEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM
+>GCF_005280335.1_02150
+MKPEDLSALLSAVLTDAVDAGDLPAELREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTGKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPDYGRNA
+ALVGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPEGGYPGAYVQELADAVALEHPDVRELTDEAARPVVRQAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHESGAIEQAVERLREQGHIEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVDTLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM
+>GCF_020097155.1_02044
+MKPEELSALIHAQLLAAVDAGELPAELREQLSADRVKVERPRSREHGDWATNVALQFAKQ
+AGMNPREFASALASRVGEQPGVATVDVAGPGFLNITLDAAAAGELARQIVEAGEAYGRNE
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIVRLLRASGADVTAEYYINDAGNQMNV
+FADSVLARMAGRDVPEGGYPGAYVKDLADAVATDHPQVRELTDDAARPVVRQAAYELQMQ
+DIKDTLAAFDVHFDVFTSETRLHESGAIQAAVDRLREQGHVEDREGAVWLRTTDFGDDKD
+RVMIRANGEPTYFAADAAYYLDKRDRGFEEKVYLLGADHHGYVGRLKAIAAAAGDDPEEN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVQWLGKDALRYDLARYPADSPITIDPELLRS
+QTNDNPVYYVQYAHARACGAARTAAAHGVDRCAFDASLLTDPTESELLAQLAEFPAVVAS
+AARLREPHRVARHLEVIAGAYHSWYAAQRIVPVPLEDGTPAPVEDVNRTRLWLNDAAAQV
+LRNGLGLLGVSAPETM
+>GCF_023573625.1_00747
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTDKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKNTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLRAQGHVEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVGA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVTAPEKM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000690.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000690.fa
new file mode 100644
index 0000000000000000000000000000000000000000..978f3ebb6359856792af7e4b3ec70ec71b0bc2f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000690.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00781
+MRTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFRKGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGIDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASTDRDGNVAGRSPAAVAVAAALAA
+ESIELLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDVDA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSGGQARVIIRRETQEDLF
+ARETDPRLAR
+>GCF_003691675.1_00512
+MRTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFRKGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGIDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASTDRDGNVAGRSPAAVAVAAALAA
+ESIELLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDVDA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSDGQARVIIRRETQEDLF
+AREADPRLAR
+>GCF_005280335.1_02149
+MTTPQPAPASPLAPAWLPAPGDPDALAPGLWAAGVDRAADGELTVQGLRASALAVEFGTP
+LLVVDEDDFRARARAFREGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGVDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELEHLAALAAEAGH
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPATTDRDGNVAGRSPAAVAVAAALAA
+ESIDLLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDADT
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSAARTSDAQAVLTRVVGKHCESGDVLV
+RDVYLPEDLGRGDLLAVPATGAYTHVMASNYNALTRPAVVAVAGGRARVIIRRETQEDLF
+AREADPRLGR
+>GCF_020097155.1_02043
+MNAGSVNLEETVTETAPQSAHPLAPAWLPAPADPDALAPLVWSSGVARDAAGELAVQGVP
+ASVLAERFGTPVLVLDEDDFRARARAFREGFDAAFESLCGGADVYFAGKSMLTLSTARWA
+AEEGLRVDTASGGELAIALRAGVLPEHIGLHGNNKSAAELATALDAGVGRIIVDSVDELE
+FLAALAAERGQIAPVMLRVTPGVHAHTHDFIATAHEDQKFGLSLTPSATGRDGNEAGVAP
+AAVAVRTALQADSIRLLGLHCHIGSQIFEADGFGLAAERVLGFLAEVKDEHGVELPELDL
+GGGHGIAYTAVDEPRPAAEIADALADDVQKAVERLGLTCPRISIEPGRAISGPAGLTLYS
+VGVTKTVDVDAPDDGTASRRYVAVDGGMSDNPRPVLYDADYTAALASRTSDAAPALSRVV
+GKHCESGDILVRDVWLPEDVARGDLLAVPATGAYTHSMSSNYNALLRPAVVAVRDGEARE
+IVRRETLDDLLRREVDPQNPA
+>GCF_023573625.1_00748
+MTTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFREGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGVDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASSDRDGNVAGRSPAAVAVAAALAA
+ESIDLLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLRCPRVSLEPGRAISGPAGLTLYTVGVTKTVDADA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSGGQARVIIRRETQEDLF
+AREADPRLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000692.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000692.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8385bd4ce6e6072403eb025399d2ec1f29dedabe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000692.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00783
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
+>GCF_003691675.1_00514
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
+>GCF_005280335.1_02147
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVDQGAKAVVCASTGNTSASAAAYAAQAGLTCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDALGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDEELPAVSTKTPVMWGFQAAGAAPI
+VLGHPVTEPDTIATAIRIGNPASWEQAEAARDGSGGMIDSVTDEEILAAHRWLSAKEGVF
+VEPASAAGVAGLIKHHAAGNVPAGKSWVITVTGHGLKDPQWALRDADGEDVTPRTVPFDV
+VTVAQALGLA
+>GCF_020097155.1_02041
+MAHVWRGVIREYAGRLPVTEDTRVVSLGEGGTPLIRAPHLSELVEGEVYVKFEGMNPTGS
+FKDRGMTMAITAAVENGAKAVVCASTGNTSASAAAFAAQAGLTCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDNCLDIARKLSENYPVFLVNSVNPARIEGQKTAAFEVVDLLGDAP
+DYHLLPVGNAGNITAYWKGYQEYSRPYVNPHPGTSDEELPAVATKTPVMWGFQAAGAAPL
+VLGHPVTEPETIATAIRIGNPASWDQATAARDASGGMIDSVTDEEILAAHRWLSSKEGVF
+VEPASAAGVAGLIKHHAAGNVPAGKTWVITVTGHGLKDPQWALKGADGDDVTPRSVPFDV
+VTVAEALGLT
+>GCF_023573625.1_00750
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000693.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000693.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa5df08b989fc410ba266ce50a0335a7fa9faca7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000693.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00784
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA
+TLPRDGAHLILRLAREQLRGRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATVRLRLHERVVPVV
+AIPDTELSTHVARGVLPADVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA
+VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL
+VPCVAVDGVRVESLHHG
+>GCF_003691675.1_00515
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA
+TLPRDGAHLILRLAREHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV
+AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLLAATRDWLHQEPRA
+VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL
+VPCVAVDGVRVESLHHG
+>GCF_005280335.1_02146
+MPAPRTLAAGTAVVVAVPATSANLGPGFDSMGLALELRDEVSLTVVDGPDVAEVTGEGAD
+VLPRDGSHLILRLAHEHLRARGVRAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAADRRPPEALLEAATDFEGHPDNVAPALVGGATVSWTRDDDARPATAPLRLHERIVPVV
+AIPDTELSTHAARGVLPESVPHAVAAAQAGRAALLVHALAERPELLMAGTRDWLHQGPRA
+AAMPASAALVAGLRVRGHAAVVSGAGPTVLALCDGAEAAEQAAAAARALTADDVLAWRVL
+VPAVAADGVRVEPLHHG
+>GCF_020097155.1_02040
+MRELRDLTPGTGARVLAPATSANLGPGFDALGLALELRDEVTLTVVDGPDTAVVTGEGAA
+ELPTDGEHLVLRLAHAHLTRRRFRAPGLALTAVNRIPHARGLGSSAAAVVTAVLAAEALL
+PADERLSAAELLDVTARREGHPDNVAPALSGGASVSWHRDGGPGWATAAVALHPQITPVI
+GIPDVTLSTHAARAALPESVPHAVAAEQAGRAALLTLALASRPDLLLPATRDWLHQDARA
+SAMPPSAALVRGLREQGHAAVVSGAGPTVLVLAPTPADAERAAEAMRALAPETGAAWRVL
+VPGVAAEGARVEPLHHG
+>GCF_023573625.1_00751
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVVGEGEA
+TLPRDGAHLILRLAHEHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV
+AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA
+VTMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAAAWRVL
+VPCVAVDGVRVESLHHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000694.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000694.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f80e93b326880fe5c848c816905b23bdfa9d4f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000694.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_00785
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR
+DAAERAAQAPAAPAAEAAPAAASSQDAAPAAERPARRRSRRADADTSAPAAAQDGQPQAE
+AREDQTEQAPRETASDQDRSEGSETRDEGEGRPQSERRSRGRRAGDDDAQQGQDRRSDGA
+QGEDGADRRGDREDRDDNGRENGRGRNGRNGRDRDNGRDRENGRENNRDRENGRDGSREQ
+RGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETELTE
+DDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDG
+EKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIG
+PRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVTD
+MQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAA
+PASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGT
+GNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLEQQQALDL
+LTNKIKDTASNAEFLMLVSKTTLGSKGDD
+>GCF_003691675.1_00516
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR
+DAAERAAQAPAAPAAEAAPAAASSQDAAPAAERPARRRSRRADADTSAPAAAAQDGQPQA
+EAREDQTEQAPRETASDQDRSGGSEARDEGEDRPQSERRSRNRRRAGDDDAQQGQDRRSD
+GAQGEDGADRRGDREDRDDNGRENGRGRNGRNGRDRENGRDRENGRENNRDRENGRDGSR
+EQRGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETEL
+TEDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPR
+DGEKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKL
+IGPRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEV
+TDMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNL
+AAPASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFK
+GTGNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLDQQQAL
+DLLTNKIKDTASNAEFLMLVSKTTLGSKGDD
+>GCF_005280335.1_02145
+MTESTEQTTPTTGGGLAALKLAQLQALASQLGIPGGSRMRKADLVTAISDHQRGGSVADR
+AAAERAAKAAAAPAAEAAPAADKAAEQPAEAAERPARRRSRRADADTSAAAQSAESGKDQ
+AERRAEQPAEGRDAEGSQDSGDRAQDSGDRTQGERRSRGRRRAGDDDARGQDRRRQDGED
+AGQDQAHDSAEDRGGDREDGGRENGRGNRGRNGRDNGRDRENGNGRDRDNGNGRDRDGSR
+EQKQDKSEDGGRDGGRNDRNRRDDRDDEGGRGRRNRRNRNERGRNRRGRGGPDVDETELT
+EDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKHGLRKGDAVVGAIRAPRE
+GEKPQHQGGGSNRQKFNALVKISSVNGQPAVEHPERVEFAKLVPLYPQERLRLETDPKQV
+GPRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVT
+DMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLA
+APASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKG
+TGNMELRLSRHLAERRIFPAVDVNASGTRREEALLSPEEVKIMWKLRRVLSGLEQQQALE
+LLTNKIKDTGSNAEFLMLVSKTTLGAKGED
+>GCF_020097155.1_02039
+MTESPDQTTAGGGLASLKLAQLQALASQLGITGGSRMRKSDLVAAISDHQRGGSVADRDA
+AAQAAAAPAAQAEAAEAPAAEQAPRSRRRSRRADSDGAVAADQPAEATQAPADEQPAAET
+EDAPARAEASAESGAQEAGSGRSRRRRGDRAARDEQQDGAQDEKQESGRGAGEETRREQD
+GDEERAEGRSRSRRGRGDRDRGERQNADRQNGERANGERANGQGEDRSQGGRREDREEES
+GRGQGGDGQKRSDRGNGRREDRDEDGRRGRNRRNRNDRGRNRRSRGPEVDDVEVTEDDVL
+QPVAGILDVLDNYAFVRTSGYLPGEKDVYVSLAMVKKFGLRKGDAVVGAIRAPREGEKPH
+SGGGRNQKFNALVKVTTVNGQPAEENPQRVEFGKLVPLYPTERLRLESDHKLVGPRVIDL
+ISPIGKGQRGLIVSPPKAGKTMILQSIANAITRNNPEVHLMMVLVDERPEEVTDMQRSVA
+GEVIASTFDRPAEDHTTVAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAAPASGRI
+LSGGVDSAALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELR
+LSRQLAERRIFPAVDVNASGTRREEVLLSPEEVKIMWKLRRVLSGLDTQQALELLTNKIK
+DTASNAEFLMLVSKTTLGSKGDD
+>GCF_023573625.1_00752
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR
+DAAERAAQAPAAPAAEAVPAAASSQDAAPAAERPARRRSRRADADTSAPAAVAQDGQPQA
+EAREAQTEQGPRETASDQDRSGGSETRDEGEDRPQSERRSRGRRRAGDDDAQQGQDRRSD
+GAQGEDGADADRRGDREDRDDNGRENGRGRNGRNGRDRDNGRDRDNGRDRENGRDGSREQ
+RGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETELTE
+DDVLQPAAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDG
+EKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIG
+PRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVTD
+MQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAA
+PASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGT
+GNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLEQQQALDL
+LTNKIKDTASNAEFLMLVSKTTLGSKGDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000695.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000695.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e49d8cd2b69a6c49074e5b0394d7a73126b0b49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000695.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00786
+MFDSEQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYADSRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA
+>GCF_003691675.1_00517
+MFDSEQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYADSRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA
+>GCF_005280335.1_02144
+MFDSEERREAVDRLLAEHRELTARLSDPAVHQDPVLARRLNRRFAELGAVVTAHAAWREA
+AAELADARELAAAGDDDAAAFAAEVPCLEEAETAAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYAESRGWKTEVLSATHSDLGGYKDVHVAIRAGATDPAEGV
+FARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVRIDPNEVKTDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAAMRVLRSRLLERRRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVVASCLALDEER
+RLAALGGDA
+>GCF_020097155.1_02038
+MFESVERLLAEHRELAGQLSDPALHADAARARRVGRRYAELGAVVAAHREWEQAVADRDD
+ARELAAAPGEDAAAFAAEVPALEAAADEAAERLRRLLIPRDPDDGRDVILEIKGGEGGEE
+AALFAGDLLRMYLRYAESRGWRTEVLSATHSDLGGFKDVHVAVRGSAQDPAEGVYARLKH
+EGGVHRVQRVPVTESAGRIHTSAAGVLVLPEADAPDEVQIDPNDLKTDVFRSSGPGGQSV
+NTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAERDAEDSAARSAQ
+VRTMDRSERIRTYNFPENRIADHRTGFKAHNLDAVLDGALDPVIDSCVALDEQRRLARLG
+EEAR
+>GCF_023573625.1_00753
+MFDSDQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYAESRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000696.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000696.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1125967474fdf0a6af96721a971ed6f4ac02cac7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000696.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00788
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAADRIAAEDAAAARPAD
+REA
+>GCF_003691675.1_00519
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAADRIAAEDAAAARPAD
+REA
+>GCF_005280335.1_02143
+MSAADESEPWGQALRRATGLLAEAGVDSPRVDAELLLAHVLGLGRGELLARVFAGAAGTA
+GEAERFAALVARRARREPVQHLTGVAFFHGLDLAVGPGVFLPRPETELLVDAVLAELTAR
+PAAATVVDLCTGSGAIAAAVSAWAQEHGRDVAVIAVELDDEAAGWARRNLEPRGVYMRQG
+DALVALPELEGRVDVVVSNPPYVPEAETPVQAEARLDPARALYGGDAAGLRIPQAIAHRA
+TELLVPGGLFAMEHHETQGPALLGALDADPRFTGVCVHQDLTGRDRFLTARRSCEAAAAA
+EDGRMADVSDFIDVSDPAALEDAVARAREVLGDCGCVVLPTDTVYGIGADAFSPRAVAVL
+LAAKGRGRTMPPPVLISDRRVLAGLAYDVPDEAEALAERFWPGALTLILKSQPTLTWDLG
+ETRGTVALRVPDDAVARELLYAVGPMAVSSANRTGMPAATTAEEARGMLGESVDLYLDAG
+PREDRAPSTIVDCTVTPFRVARQGAVPLEALRELVPDLLAEGEEPPVPADRLAAEPVAEA
+PAPTPAPDGDDAADRAGREA
+>GCF_020097155.1_02036
+MSEFIDVSDPSDLTAAVERARAVLADRACVVLPTDTVYGIGADAFSPTAVAVLLAAKGRG
+RTMPPPVLISDRSVMAGLAYDVPEAAEELAERFWPGALTLILRSQPTLTWDLGETRGTVA
+LRVPDDAVTRELLYAVGPMAVSSANRTGMPAATTARGAEEMLGESVALYLDGGERATQEP
+STIVDCTVTPFRVARQGAVSLEALRAVVPDLVAEGEEPPVPAELTTPPAAPEA
+>GCF_023573625.1_00755
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAAERIAAADDAAAARPA
+DPEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000697.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000697.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ddad7326b33a23f0dacd06fd75295b0e036272e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000697.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00789
+MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE
+RRRADRNDAAAHPDERGDA
+>GCF_003691675.1_00520
+MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE
+RRRADRNDAAAHPDERGDA
+>GCF_005280335.1_02142
+MRAYLVLVVVTALACGALTPLMRRIGLRARVFTPVRQRDMHRRPIPKLGGVAMAAAVLVG
+LAVGGTVPFLQGIYADDAAMVGLLVAVAVVFVVGIADDLWDLRWWVKMAGQVCAGLAVAL
+GGIRIEAMPVGWIPVGSEAMQIALTVFAVVLTMNALNFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACLGFLPFNRFPARIFMGEVGAMLLGLLMAAAAV
+AVTADVKALDGMRFRNVPAYMPILLPIAVLALPLLDLALAVVRRTARGASPFSADRGHLH
+HKLVDGGYTHAQAVWLLWLWAFLVAWGAVSLNFVDDMIVLPVLGLALLGAGYLTLRTPVR
+RRRAGAPAAGPALDPEEGA
+>GCF_020097155.1_02035
+MRAYLLVAAVTALTCLALTPWVRRVGVRARAYTPHRDRDVHRAPVPKLGGVAMVAAVLAG
+LAVAGTVPFLGGIFTDASAMRGLLAALGIILVLGVVDDLVDLRWWAKLGGQSLAALAVAL
+GGIRIAALPVGWIHVGSEAVQVALTVFVVVLTMNAINFIDGLDGLAAGVALIGGSAFFVY
+SYLLTRTIDQFDYSNLATLLMALLIGACAGFLPYNRHPARIFMGESGALLLGLLLSTAAV
+AVTADLDALEGFRFRNVPAYMPVLLPIAVLALPLADLTISVIRRAAHGESPFGADRGHLH
+HRLVDGGFTHAQAVRVLWLWSFIVAWGVLSLNFADDAVVLLLAAAGLAVATWLTVHPLRA
+RAARPASRPDAQPKDQP
+>GCF_023573625.1_00756
+MRAYLVLVVVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVALLWLWAFLVAWGAVSLNFVDPMIVLPVLAVALAGAGYLTLHPIVE
+RRRAVRNDAAAHPDERGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000698.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57a86a7fbfd7d8fb6b3f72d7bb85a6ba9ce369a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000698.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00790
+MTGAGGRRRRRRWENRRGWWGILGWSLAAAGVALAITCAAWLLSVGGEAAGSALLGGGAV
+LALSALTGVTTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL
+VTILVWQAAEVLVFARTRRGIYAD
+>GCF_003691675.1_00521
+MTGAGGRRRRRRWENRRGWWGILGWSLAAAGVALAITCAAWLLSVGGEAAGSALLGGGAV
+LALSALTGVTTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL
+VTILVWQAAEVLVFARTRRGIYAD
+>GCF_005280335.1_02141
+MSPRTAPDAAPRSARARRRPRRRRWENRRGWWGILAWSLAATAAAVAVVCAVALAAGGPD
+AAASALLGGGAVLVLSALTGATTALVWDRAREAALPVSVGLFVLKIAVFAVLLGTVPRPD
+WILPDAAAIAALVAILVWQGVEVLVFARTRRGIYAD
+>GCF_020097155.1_02034
+MTASARPARRRWENRAGWWGILRWCCAATAVGVLACGAVAAVLHGGPAGLSALTGGGAVL
+VLSALTGATTAVAWDRARAAALPLSVGAFVVKLVLYALLLATLRMPEWMSGTAVAVGALV
+GVVVWQAVEVLVFARTRRGIYAD
+>GCF_023573625.1_00757
+MTGAGGRRRRRRWENRRGWWGILGWSLAAAGAALAITCAAWLLSAGGEAAGSALLGGGAV
+LALSALTGATTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL
+VTILVWQAAEVLVFARTRRGIYAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000699.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44417326289087f82328329c737d974f353d7b76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000699.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00791
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
+>GCF_003691675.1_00522
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
+>GCF_005280335.1_02140
+MLTLVLANASFVPPTISDGNLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+QLVPGKAQWLAESGYSFVRNGIAKDILGEKNFRQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PSFSHAGAAYGIALIVYAIWIGVGLKRHGIRYLKLAVVPSGVPSWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVIIGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
+>GCF_020097155.1_02033
+MLPLVLANAEFVPPSVSDAHLPDLLPWGAEYGTGFGKQMLLVLLSVVLITGFFAWAMRKP
+KLVPGRAQWIAESGYAFVRNGIGRDVMGEKHFKQWVPLLFAIFFFVLLNNLFGAIPLLQM
+PSFSHAGSAYAIALIVYAIWIGVGVKHHGVKYFKLAVVPSGVPGWILPLLVPLEFISNFI
+VRPLTHSLRLMAVMLAGHMIVMLAGAGAAFLITQTGNPLLAGTGVLVILASVALYLLEIL
+LMYLQAFVFTLLTALYIQGAIDANDH
+>GCF_023573625.1_00758
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFSIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000701.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000701.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca35e5f800cd8587f7265963c2147e662703d603
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000701.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00793
+MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG
+LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEARRISE
+QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA
+GVAE
+>GCF_003691675.1_00524
+MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG
+LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEARRISE
+QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA
+GVAE
+>GCF_005280335.1_02138
+MISNGLILAAGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGGLA
+KAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAESTRISEQA
+QAQIAAERQQAASQLKGEVGTLATTLASKIVGESLEDDARSQRVVDRFLADLDRHQSAGV
+AE
+>GCF_020097155.1_02031
+MISNGLILASAEGANPLVPNPWEILVTTVGFAVLMFIVVKFVVPALEKSYTDRVEAIEGG
+LEKAEKAQAEANKMMADYEGQLADARQEANRIREEARTEGAQIVAEARERAAAEAARITE
+QAQTQIAAERTQAAAQLKGEVGTLATTLASKIVGESLDDDARSQRVVDRFLADLDRHQSA
+GVSE
+>GCF_023573625.1_00760
+MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG
+LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEATRISE
+QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA
+GVAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000702.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000702.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e5b35f19035c2acfcb77939f96f6588f614063b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000702.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00794
+MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAVHAAAAEAARGGHAGLAAL
+LGELLAFNRTVEDSHELQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG
+LKPSAAIRKAADAVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH
+VVGGVRVQVGDDVVDGSMASRLHDLQRRMAG
+>GCF_003691675.1_00525
+MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAVHAAAAEAARGGHAGLAAL
+LGELLAFNRTVEDSHELQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG
+LKPSAAIRKAADVVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH
+VVGGVRVQVGDDVVDGSMASRLHDLQRRMAG
+>GCF_005280335.1_02137
+MMTGASRDSLTASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVIKDLAGRRWSAERDLGDALETVAAHAAAAEAGRGGHAGLAAL
+SGELLAFNRTVEDSHEVQRALTDQHAPVEARAALARRLLGESASPAGQLLVERAVAAPRG
+VKPAAAVRQAADVVAERQRQWIAEVTVARPLGAEQQERLALGLRRAFERDLVMDVTVDPH
+VVGGIRVQVGDDVVDGSMASRLNDLQRRMAG
+>GCF_020097155.1_02030
+MMTGASGDSLTASLESVRTVLDEGGVALARELFAALDVVDQQGALRRALTDPAWSTERRH
+GVLDSLFGGRVSPGALQVLKDLAGRRWSAERDFGDALEAVAADAAAGEAARGGHAGLAAL
+SGELLGFQRVFQDSHEVERALTDQRAPRESRSGLARRLLGAQASPAAVLLVERAVTDGRG
+VKPATALRSYADVVATRQRQWIAEVTVARPLEDGQRERLAAGLRRAFGRDLVLDVNVDPT
+VVGGIRVQVGDDVIDGSMASRLNDLQRRMAA
+>GCF_023573625.1_00761
+MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAAHAAAAEAARGGHAGLAAL
+SGELLAFNRTVEDSHEVQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG
+LKPSAAVRKAADVVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH
+VVGGIRVQVGDDVVDGSMASRLHDLQRRMAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000707.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000707.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9eae775c640a4c1b06e16a295cca2897d0ea038
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000707.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00799
+MQGPVLIASATVAAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL
+RLTGRWRLSRERWSADRSRLQIDRLPADEAGRTVLELSAGARPVRVVVDPDDAGALRAWS
+EAGPSAASSFWRR
+>GCF_003691675.1_00530
+MLIASATVVAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRLRLTG
+GWRLSRERWSADRSRLQIDRLPADEAGRAVLELSAGARPVRVVVDPDDAGALRAWSEAGP
+SAASSFWRR
+>GCF_005280335.1_02132
+MLIALAGVLAVFALSASALAVRRRALLRTSAAFPAVLQGHGRPRERVIGVYDETRLLFTG
+RWMIRRERWSVGRCDLQIDRLPVAEDGRAVLELDGGRGSVTVVVDPDDAGALRAWSEAGP
+SAASSFWRR
+>GCF_020097155.1_02025
+MRGPVLLLSGALAVFALLALAGWARHRALVRGPGRFAGVLVTDGGRRCRVVGCFRSHELV
+LSHHLLPERRLWSAERWRLEVDRLPAAEAGHTRLRITDASGRSDDAVDLEVEDDVAGAVR
+AWTEAGPSQAGQSWWRPPGAA
+>GCF_023573625.1_00766
+MEGPVLIASATVVAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL
+RLTGGWRLSRERWSADRSRLQIDRLPADEAGRAVLELSAGTRPVRVVVDPDDAGALRAWS
+EAGPSAASSFWRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000708.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000708.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7d1c1682d137d917cb5a27db061fe0a0bae5ec2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000708.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00800
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
+>GCF_003691675.1_00531
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
+>GCF_005280335.1_02130
+MRLVIARCSVTYEGRLNAHLPPATRLLMVKADGAVLVHSDGGSYKPLNWMSPPATLHTTA
+PTAEQAEQGVVEVWRVQAAKSDDRLMILIEEILADQSHELGADPGLVKDGVEADLQRLLA
+EQIGLLGDGHTLVRREYMTAIGPVDILARDPEGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
+>GCF_020097155.1_02023
+MRLVIARCSVTYEGRLNAHLPSATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PTEEQAAAGVTQVWRVQAKKSDDRLLVLLEEVLADETHELGVDPGLVKDGVEADLQRLLA
+EQIGLLGDGHTLVRREYMTAIGPVDILAKGPGGQTVAVELKRRGDIDGVEQLTRYLDLMN
+RDPLLAPVTGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDADARLF
+>GCF_023573625.1_00767
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PFPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000710.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000710.fa
new file mode 100644
index 0000000000000000000000000000000000000000..047ef0f3b4c1ac370184ecf0dfe777291aba71cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000710.fa
@@ -0,0 +1,43 @@
+>GCF_002008305.4_00802
+MEEKEPASGPDAPSVADVRAPAEPEGAEQQPVGGIPVEPAGAAAAPPSHGPTPAGRRRRL
+RLGSVLRRRRPFLEEDRVDPEPDPADGAEDPAVAAVALESPVLTGFLLAVGVTLAIGIVS
+VLRTNGQLIVWIAAALFIALGLDPLVRRVESWGAPRWVGVLTAALGLAAVAGAFVALLVP
+TVIEQSTQLVQDLPAIIDGVMRAEWFVQLDEEFHLQEAVRAQTERLAADGVAITDLFGGL
+LGLGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAYRLAPRSRRPRIEALSEQITSSVGH
+YVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAAFMAFIPLVGAAIGGTLLTLVSLLT
+SWQTAAVFAAIYFVYLQIEAYVISPRVMARAVPVPAAVAVIAVIAGGALLGVLGALMAIP
+LAAALALLVREVFIPRQDAR
+>GCF_003691675.1_00533
+MSLGPTVASRARRGQAGALTYAERVEEKETASGPDVAGVADVRGPAEPEGAEQPPVAGVP
+VEPVGVAAAPPSHGPTPAGRRRLPRLGSVLRRRRPFLEEDRVDPESVPVDGAEDPAVAAV
+ALESPVLTGFLLAVGVALAIGVVSVLRTNGQLIVWIAAALFIALGLDPLVRRVESWGAPR
+WVGVLTAALGLAAVAGAFVALLVPTVIEQSTQLVQDLPAIIDGVMTAEWFVQLDEEFHLQ
+EAVRAQTERLAADGVAVTDLFGGLLGFGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAY
+RLAPRSRRPRIEALSEQITSSVGHYVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAA
+FMAFIPLVGAAIGGTLLTLVSLLTSWQTAAVFAAIYFVYLQIEAYVISPRVMARAVSVPA
+AVAVIAVIAGGALLGVLGALMAIPLAVALLLLVREVFIPRQDAR
+>GCF_005280335.1_02128
+MEPVDPTAAPASAAPAPLPASGRVPRRRRRRGRLIPLRGVLRRRRPVFLAEDRVDPDPEH
+PEPEPTGEPPVTAVTVESPVATGFLLTVGVALALAVVWVLRTNGQLLVWIAAALFIALGL
+DPLVRRVESWGAPRWAGVLTAALGLAAVASAFVALLVPTVVEQSRQLVEGLPGTIEDVMT
+SAWFIELDQEFHIQEAVRAQTDRLTTDGAAVTDLFGGLLGIGQTVLNAFFSVFVVVVLTL
+YFLASLPHMKYWAYRLAPRSRRPQVERLSEKITSSVGHYVMGQSFVAALNGTVAFTALAV
+AGTPFAVLLAAFAAFMAFIPLVGAVIGGTVLTLLSLLTSWQTAAVFAAIYFVYLQIEAYV
+VSPRVMARAVAVPAAVAVIAVIAGGALLGVLGALMAIPLAAALSMLVREVFIPRQDAR
+>GCF_020097155.1_02021
+MDHIEDSPAPSGPSRGARRLRLGSLVRRREAFLPNERVDPLPPGSPDAAPAEPEVPELAL
+RAPVAAGFLLTMGVCLAAVLVWVVLENTQLLVWIAAALFIALGLDPVVRLVERWGAPRWV
+GVLLAALGLAAVAGAVVGMLVPAVVQQSTQLITGLPDTITQIMATPWFREVDRQLQIQHA
+VQSWLDGLTKDGAAVTQLFGGLVGIGQTVMNAVFSTIVVVVLALYFLASLPHLKYWGYRL
+APRSKRLRVEALGEEITLSVGHYVMGQTVVAVLNGTVAFIALSVAGGPFPVLLAFVAAVM
+AFIPLVGALIGGTILTAVCLLESWQAAALFAAIYFVYLQIEAYVVSPRVMARAVAVPAAV
+GVIAVIAGGTLLGVLGALMAIPTAAAVLLIVREVLIPRQDAR
+>GCF_023573625.1_00769
+MSLRPTVASPARRGQAGALTYAERVEEKETASGPDAAGVADVRAPAEPEGTEQPPVAGIP
+VEPVGVAAAPPSHGPTPAGRRRLPRLGSVLRRRRPFLEEDRVDPESVPVDGAEDPAVAAV
+ALESPVLTGFLLAVGVALAIGVVSVLRTNGHLIVWIAAALFIALGLDPLVRRVESWGAPR
+WVGVLTAALGLAAVAGAFVALLVPTVIEQSTQLVQDLPAIIDGVMTAEWFVQLDEEFHLQ
+EAVRAQTERLAADGVAVTDLFGGLLGFGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAY
+RLAPRSRRPRIEALSEQITSSVGHYVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAA
+FMAFIPLVGAAIGGTLLTLVSLLTSWQTAAVFAAIYFVYLQIEAYVISPRVMARAVSVPA
+AVAVIAVIAGGALLGVLGALMAIPLAAALLLLVREVFIPRQDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000711.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000711.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc1f5797bc50668c3dcb5b61d4ae35a1d0fa75ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000711.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00803
+MTDVTAQPPSDAPSHLRGAVDLSSLGTPASAGRTAPGADAGAGGGSWVIADADQGLLQQL
+VQLSAQVPVLLHLHVPGDAASEALYRQFADAVDAQAGRLVLARLDVAKEPAVLQALGLGA
+GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPAVAPARQDAGAAAA
+EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAS
+AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFDRLVRFIALHPGDDRETARAHLVDLYT
+VVGTDDPRVQASRRQLAAALF
+>GCF_003691675.1_00534
+MTDVTAQPPSDAPSHLRGAVDLSSLGTPAPAGRTAPGADAGAGGGSWVIADADQGLLQQL
+VQLSAQVPVLLHLHVPGDAASEALYRQFADAADAQAGRLVLARLDVAKEPAVLQALGLGA
+GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPPVAPARQDADAAAA
+EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAA
+AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFARLVRFIALHPGDDRETARAHLVDLYT
+VVGTDDPRVQASRRRLAAALF
+>GCF_005280335.1_02127
+MIPDADQRLLQQLVQLSAQVPVLLHLHVPGDASSDALYRQFADAVDAQAGRLVLARIDVA
+ADPSVLQALGLGAGPAVMAVVAGQPVPLVNQEVPAETLEQLMGEILEVARQNGVAGTVPA
+VAPARADAAEPAPAAPPVPPLHRAAHAALAADDLPGAVAAWEEALKDTPADPVAQQGLSA
+ARLMLRTRDADAAAVRSAAADAPDDAAAQLAVADLDVLGGHVEDAFARLVRFIALHPGED
+RETVRAHLVDLYTVVGVDDPRVTASRRRLAAALF
+>GCF_020097155.1_02020
+MTSQPSSPSLRGAVDLSSLRTPRPAPGAQGAGAQGAGAPGEPASWAVLDADSRLLEQLVQ
+LSTQVPVILVLHVPGDATSEALSTQFADAADAQAGTVVMARLDVVAEPQLLQAFGIGAGP
+AVVAVVAGQPVPLANQELPQEALDGLMGQLLEVARQNGVAGRVPALAPARDGAAAPQPAP
+VPPLHRRAHEALAADDLPGAVAAWEDALKESPADETARQGLSAARLMLRTRDMDAAAVRA
+AAAERPDELAAQTAVADLDVLGGHVEDAFARLVRFVAAHPGEDREAARAHLVDLYIVVGS
+EDPRVHASRRRLAAALY
+>GCF_023573625.1_00770
+MTDVTAQPPSDAPSHLRGAVDLSSLGTPAPAGRTAPGADAGAGGGSWVIADADQGLLQQL
+VQLSAQVPVLLHLHVPGDAASEALYRQFADAVDAQAGRLVLARLDVAKEPTVLQALGLGA
+GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPPVAPARQDAGAAAA
+EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAA
+AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFARLVRFIALHPGDDRETARAHLVDLYT
+VVGTDDPRVQASRRRLAAALF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000712.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000712.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2323b46ffe7c0ade9471d139f555afacc4fae4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000712.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00804
+MTPHASEPAPTHLAAATRRRAVDAPDPDLALVTRGLTQRFGDKLALDALDLDVPAGSFFG
+VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG
+AQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRTLVADYSAGMTKKVSLAAAMVHAP
+DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR
+AAGTLEEVRDGRDLEDRFVELVGGRHGSEGLAWL
+>GCF_003691675.1_00535
+MTPHAPEPAPAHLAAAARRRAADAPDPDLALVTRGLTQRFGDKLALDALDLDVPAGSFFG
+VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG
+TQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRKLVADYSAGMTKKVSLAAAMVHAP
+DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR
+AAGTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL
+>GCF_005280335.1_02126
+MSEHPAEPHRTAPSSAEAPHAGPAPAEAPAVVPSAAARRRAVDAPDPDLALVTRGLTKRF
+GDKTALDGLDLDVPAGSFYGVVGPNGAGKTTALSMATGLLRPDLGQAWIHGVDVWAQPLE
+AKRRVGVLADGVRTFDRLTGAQLVTYAGLLHGVDADTVAARTEDLLRVMDLADAGRKLVV
+DYSAGMTKKISLAAAMVHAPDVLVLDEPFEAVDPVSAANIRDILHDYVGRGGTVIVSSHV
+MDLVQRMCSHVAVIAGGTLRAAGTLEEVRAGRDLEDRFVDLVGGRHEQEGLAWL
+>GCF_020097155.1_02019
+MRAQDAPDPNLALVTRGLAKRFGEKVALAGLDLEVPAGSFFGVVGPNGAGKTTALSMATG
+MLRPDAGRVWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTGAQLITYAGLLHGLDRDTV
+DVRTADLLRVMDLEEAGRKLVVDYSAGMTKKVNLAAAMVHAPDVLVLDEPFEAVDPVSAA
+NIRDILHDYVGRGGTVIVSSHVMDLVQRMCSHVAVIAGGVLRAAGTLEEVRAGRDLEERF
+VDLVGGRHTGEGLAWL
+>GCF_023573625.1_00771
+MTPHAPEPAPAHLAAAARRRAVDAPDPDLAFVTRGLTQRFGDKLALDALDLDVPAGSFFG
+VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG
+AQLVTYAGLLHGLDADTVAERTTDLLRVMDLEDAGRKLVADYSAGMTKKVSLAAAMVHAP
+DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR
+AADTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000714.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000714.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c19767448521f0e607a27094b82266fc4af78af2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000714.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00806
+MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGGGKRGGWFGGRGRG
+>GCF_003691675.1_00537
+MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGGGKRGGWFGGRGRG
+>GCF_005280335.1_02124
+MSVTGEPDLTDPFSPAGGGTSVLEREQQLQDVEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPQKFPVCPTCQEIYEGLREPQDGDDAGAGGGRRGGWFGGRGRG
+>GCF_020097155.1_02017
+MSISDPFQNDPLSPSGGGTSVLEREEQLQDVEPGDHERFAHYVRKEKIMESALSGEPVIA
+LCGKVWVPGRDPNKFPVCPLCQEIYDGLRDPQDGDDAGSGGGRRGGFFGRGRG
+>GCF_023573625.1_00773
+MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGKRGGWFGGRGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000717.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000717.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8444a67c3c99f8eeb7c8973326abb559b0788a01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000717.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00810
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
+>GCF_003691675.1_00542
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
+>GCF_005280335.1_02120
+MSQNPVTSAPQTPDDWRIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTSL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTQTGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDRRGRATAEVVGVNRGAAPDADDRPLLHRFVHAGELAAGWTGPEAVTRAAE
+RHAASLRELPATVGRLQPGDPAIPTIFLED
+>GCF_020097155.1_02011
+MTQNASAPAPSAAPWHVPTSLMTDHYELTMLCAARRAGTAERRSRFELFSRRLPDGRRYG
+VVAGTGRILEGLSRFRFSTAEVDFLADHSVVDDATLQWLADFRFSGDITGYAEGEVYFPH
+SPVLQVESTFAEACILETYLLSILNYDSAVASAASRMASAAQGRPCIEMGARRIHEEAAV
+AAARAAVIAGFAATSNLEAGRRYGVRTVGTAAHSFTLLHDSERAAFEAQVAALGRDTTLL
+VDTYDVEQGVRTAVEVAGRALRNVRLDSGDLVQQAHEVRELLDSLGNTETGIMVTSDLDE
+YAIASLRSAPVASYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASHGG
+RKDAVRRRDARGRAVAELVGVNRAPAADADDRPLLHTFVKDGELQEGWTGPEAVTRAAER
+HAASLAELPRAAARLQPGEALIPTIFQED
+>GCF_023573625.1_00779
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000718.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000718.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25acb14d5cd9c4393fc21b8c68f76d690731337a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000718.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00811
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
+>GCF_003691675.1_00543
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
+>GCF_005280335.1_02119
+MSVLTSHDPTAPRAAGPAPGEAVPGGATDTAVLERPREDLALDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSESRAHRLMLEVHERGRSVVATGTREKAELHVGAMHGYGLWATLEQAED
+>GCF_020097155.1_02010
+MPHPAPPAPGADTALLERPREDLAAARPWHVVVWNDPVNLMSYVAYVFRSHFGYSAARAQ
+SLMLEVHERGRSVVFTGSREVAEGHVTAMHGFGLWATLEQAED
+>GCF_023573625.1_00780
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000720.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000720.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81cf121fb76ffa44c2163ab536caa6f31594eed3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000720.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00813
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSTAFV
+PLGAEQEGVT
+>GCF_003691675.1_00545
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSAASV
+RPGPEQEGVT
+>GCF_005280335.1_02117
+MSAPPQARPEVSASSPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTAHAPYGPRPIAQ
+VRALALGIMDELVDAGVKALVIACNSASAAVLRDARERYTGRHGIPVVEVIQPAVRRAVA
+ATRSGRIGVIGTQATVGSRAYDDSFSAAPHLQVTSAACPRFVEFVEAGITTGPELLATAQ
+EYTEPLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEH
+PHSAAGSGQDTRHRFAATGDPEHFQALARRFLGPEVGAVRRLDTVRERYPTAALAQLTPD
+LIARLGAEQERET
+>GCF_020097155.1_02008
+MSATADTAQTGAGPSSPIGVFDSGVGGLTVARAIMDQLPHEPIIYVGDTAHSPYGPRPIA
+QVRALALGVMDELVEAGVKALVIACNSASAAVLRDARERYTGRLGIPVVEVIQPAVRRAV
+AATRNGRVGVIGTQATVGSRAYEDSFSAAPHLQITSVACPRFVEFVEAGITTGPELLETA
+EEYVAPLKAAGVDTMVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRALVRHGLE
+HPHSAAGSAAAPEHRFAATGDPEHFAALARRFLGPEVGPVRQIQEIRERYPTAALTALTP
+DVLARLRAEMEEDGAR
+>GCF_023573625.1_00782
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSAASV
+RPGPEQEGVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000721.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000721.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f70d20b15f3c2a045ed10c1a8ff47b7a0649a152
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000721.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00814
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWDRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRTERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEARAVYDGPLAVAVSGLSYGV
+>GCF_003691675.1_00546
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWGRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRPERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEARAVYDGPLAVAVSGLSYGV
+>GCF_005280335.1_02116
+MKLTVIGASGSFPGPGSPASCYLVTAQGVAEDGVTPRTWRILLDLGNGSLGVLQRYIELE
+ELDGILLSHLHPDHCMDLCGMHVAIRWNPEGWHRDRMPVYGPTATADRIAEAYGMDPEPG
+MHEDFDFRVWRPGRTERFGPFRLTPVPVRHPIDEAYAIRVEADEPDGEGGTVTRVLTYSG
+DTDACEGLVEAARDADLFLCEAAFHEGRDDGIDGVHLTGLRAGQTAAQAGAKKLLLTHLP
+VWNDPQRAVLEAREAYEGPMAVAVSGLSYGV
+>GCF_020097155.1_02007
+MKLTVIGASGSFPGPGSPASCYLVTADGPDGNGGTRPWRILLDLGNGSLGVLQRHIELEQ
+IDGVLLSHLHPDHCIDLCGLHVAVRWNPEGWDAGRIPVYGPAATATRIAEAYGMDPEPGM
+QEDFDFRAWEAGRTEGLGPFRLTPFAVRHPIDEAYAIRVETTEPGPDGEPVTRVLAYSGD
+SDTCDGLVEAARDADLFLCEAAYHEGRDDHIDGVHLTGRRAGQMAAEAGARKLLLTHLPV
+WNDPQRCAQEAREAYVGPLAVAVSGLSYGL
+>GCF_023573625.1_00783
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWGRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRPERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEAREVYDGPLAVAVSGLSYGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000722.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000722.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e065879a0fbcbe1a3f491271c03db780627b0937
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000722.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00815
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+IQAETLAAATEDRA
+>GCF_003691675.1_00547
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+VQAETLAAATEDRA
+>GCF_005280335.1_02115
+MTSPASTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGDTRVLCTASFTQGVPRWLK
+GEGTGWVTAEYAMLPRATNERNQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILRKDAEVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGVPFSRAELDTLLDLALTGTGELAR
+IQAETLAGAAGSAEAQA
+>GCF_020097155.1_02006
+MTESSPSTSPSVTRQDGRAVDELRPITITRGFSRQAEGSALIEFGGTRVLCTASFTEGVP
+RWLKGEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALG
+ENTIVLDCDVLDADGGTRTASITGAYVALAEAVAWAQGRGILKKDARVLTDSVSAVSVGI
+IDGVPMLDLPYVEDVKAETDMNVVVTGSGDFVEVQGTAEGVPFRRAELDVLLDLALAGTA
+ELSRIQAETLAGDVAGRA
+>GCF_023573625.1_00784
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+IQAETLAAATEDRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000724.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df346f46f826ea2a24029e3001ff973720a83247
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000724.fa
@@ -0,0 +1,39 @@
+>GCF_002008305.4_00817
+MSGGRVPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG
+LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP
+PADADVLPGLTDAPAGRGVDRLMRAQGLGVSVLAPRAAGAGAESKATRQARRTEGVFDAR
+VPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQRAKTRAAAHG
+AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRG
+>GCF_003691675.1_00549
+MSGGRAPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG
+LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP
+PADAEILPGLTDAPAGRGVDRLMRAQGLGVSVLAPRAAGSGAESKATRQARRTEGVFDAR
+VPLRDERAMPDFMRWPDEGVNPPPNPTADPGHPLFGQTVVFTGGIGMSRQSAKTRAAAHG
+AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRGQAI
+ALVSEGEFLQMLDGNWPDAAR
+>GCF_005280335.1_02113
+MSGVLAPVPGLDFTAIDFETANGFRGSPCALGAVRVRDGVMVERAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAARFADVYDELAGFVGADVLAAHNAGFDVGVIESGLEVSGRDVPR
+LDFVCTLVLARRVYDLASYALPSAAREAGFAPGPHHDALADAEACAAILVDVARRVLGTE
+AGDGAAVAPAGARGLPEPFDVPRLMRAQGLTVNTLAQRAAGEGPESKATRQARRAQGVFD
+ARVPLKDERAMPDFLRWPDEGTNPVPNPDADPGHPLHGQTVVFTGGIGMSRQTAKVRAAR
+LGAQTANRVGAATTMLVVGDGFEAADLDRPAPAPGTREAVTTALAHRKTRDALRRRERGQ
+HISLVSEGEFLQMLDGNWPDAAR
+>GCF_020097155.1_02004
+MTAGIAPVRQPGLDFTAIDFETANGFRGSACQLGAVRVRDGLPASRAVWLMRPPAGFDRF
+DPRNVRIHGIHADRVVDAPRFAEVYDAFAAFAGDDVLVAHNAGFDLGVIESGLEVSGRDV
+PAHDYACTLTLARRIYDLPSYSLPSAAREAGFVPGRHHDALADAEACAAILVDLARRVCP
+PGEATVDALLASQGLRRSRLTARAAGTGRESRATRQARTMPGLFDATIPLADDRTLPDLM
+RWPDEGVNPEPAADADPGHPLYGQVVVFTGGIGMSRQEAKNRAAQRGAATANRVNGRTTM
+LVVGDGVDPAELVGAPEVHGVVVDPGATDPAGRGVDPGGAVTHRKTREALQRRAKGQAIA
+LVSEAEFLQMVDGAWPAGAR
+>GCF_023573625.1_00786
+MSGGRVPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG
+LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP
+PADAEILPGLTDAPAGRGVDRLMRAQGLSVSVLAPRAAGSGAESKATRQARRTEGVFDAR
+VPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQSAKTRAAAHG
+AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRGQAI
+ALVSEGEFLQMLDGNWPDAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000725.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000725.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30fc7b140ecca989b17b0057021730ec8bcb93d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000725.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00818
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQEGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLTGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAAAYALVIAALLRGLDLAAAVAHAR
+AWLDTLGEEAEETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAAHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGAAHGTAVFGAHDPADRAAAEA
+SVPGWIAEREVVLEAARRWSAATT
+>GCF_003691675.1_00550
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQQGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLSGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAAAYALVIAALLRGLDLAAAVAHAR
+AWLDTLGEEAEETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAAHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGAAHGTAVFGAHDPADRAAAEA
+SVPGWIAEREVVLEAARRWSAATT
+>GCF_005280335.1_02112
+MTETPAAPSLPGPEHATRVAALLAAGAAGDALGYTVEFDADAAVRARHGAEGLTTGEAAL
+AVVGGEALPISDDTQMTLYVLDGLLEWIEWQNDGQAADPAACVWLACLRWWATQHGGALP
+DGAPPVPPRWLEDHPELRARRAPGNACLSGLDSAAMGLPGDPRNPDSKGCGTVMRSAPYG
+MVPGLEDVHVVSFARQGAVLTHGHPTAWVAAAAYSLMIAALLRGAGLEDAVAHARVWVDS
+LDPAEGGETAAALASAVELAASPADDAGRPGTLPAALGEGWVAEEALAIAVHAALVAQAR
+HEDPADMLALALRIGANHAGDSDSTASLAGQLLGAAHGPAVFGADAAADGPAGLVPAWVA
+EREVVAEAARRWSAATT
+>GCF_020097155.1_02003
+MTDAAPSPRTDVSYPSRVLGLLAAGAAGDALGYAVEFDSVDRILGRLGAAGVTDGPALAA
+VSGVSALPVSGDTQMTLYVLDGMLEWIEWQNAGQASDPAACVWLACLRWLRTQDGALPDG
+APPAQDRWIDAHTELHAQRAPGMACLSGLRSSGMGVVPDPKNPDSKGCGAVMRSAPYGMV
+PGLEDHHVASFARQGAVLTHGHPTGWTAAAAFALTVSALFDGAELRGALEHPRTWLDSTG
+EDGAETRAALDGALAEAARAVEAGDDVGAPGTLPASLGEGWVAEEALAIAAYAALVAEAR
+AEDPAAALGLALRIGANHDGDSDSTAALAGQLVGARHGMAVFGSRGQDADSVPAWITERE
+VVAEAARRWIAATT
+>GCF_023573625.1_00787
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQEGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLTGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAGAYALVIAALLRGLDLAAAVAHAR
+AWLDGLGEEAAETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAVHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGVAHGTAVFGAHDPADRAAAEA
+SVPGWVAEREVVLEAARRWSAATT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000727.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000727.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9be088e70c373691c7b7e861bb7330eaa096acfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000727.fa
@@ -0,0 +1,91 @@
+>GCF_002008305.4_00820
+MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR
+SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS
+LRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLLPQGQFAQFLTAKSDERRALL
+RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP
+DTDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR
+DHDAEAETAAARRRAVDAHERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAA
+AWLAAARADGAADAPASRQALGEAERAAEAVARAVQDRARMGELEQEAAAAAERRAEIGR
+DRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEA
+ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT
+ADTAVTEADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERA
+EAERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR
+DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETDQALTAALAEQHF
+DDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQ
+TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL
+DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE
+LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA
+DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA
+>GCF_003691675.1_00552
+MRIHRMRLEGLGPYAQAQDVDFDRLNAAGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR
+SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS
+LRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFIQVVLLPQGQFAQFLTAKSDERRVLL
+RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP
+DTDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR
+DHDAEAETAAARRRAVDAHERAGRVLAAAQRASAAADAAGTASEAVTEALAHVEDEPTAA
+AWLAAARADGAADAPASRQALGEAERAAEAVARAVRDRDRMRELEQEAAAAAERRAEIDR
+DRAALVESRPEREAAVAAHRAVVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEV
+ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT
+ADTAVTEADVRDAEQARTAADRAATDAETALRAAEQTLRSAGEAAAGLAPEAAREALERA
+ETERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR
+DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETGQALTATLAEQRF
+DDVDAARAARLEETEAADRTAAVQEWDAERARLAELEASEPVRRGRALAEAGVEPPTEEQ
+TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL
+DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE
+LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA
+DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA
+>GCF_005280335.1_02110
+MRIHRMRLQGIGPYAEAQDVDMDRLNDAGLFLLDGPTGAGKSTVLAALCYALYGSVPGGR
+SPESLVTTLRPPGAVVPEVLVEFTVQGRRFEVVRSPRHERLKKRRSASGKDTTPTPAAVS
+LREHVDGAWQEPLTRNDEVGVQVADVMHLDAAQFMQVVMLPQGRFAEFLTARSDERQRLL
+RRLFGTQRFDGVEEHLKAEAERLGSRAAADAKVAASAREQLREAVAAELGEDWHAPEPFP
+ATDEELVERTAERTREAVDAARAGRDAAAAEEAAARGTQAELRATGEALAAAAAWTERER
+AHREGAEAAAGDRTAVAAHERAGRVLGAADRSESARAAEDRAREADGTAQAAAAEDPLSA
+GWLEQARRDAAETPADDAAETSADAAALPRDAVALAERAVEEVVRAVRDRAAAERLEETE
+RTEAARRTQIVAEREAAEAERSGREEGLAAVREAVEAASARLGAQADVDRRVAEAEQGLA
+AAREAERHALAADAADRAREAARTGRDAAAQHRLGLLRSRYEQAAADLAADLEDGTPCAV
+CGSPEHPDPAPRVGTAVTEADVAAAEEGLAAAEAVLADAETARTAAHERVRASSAAAGGR
+TPAQAEEALAAARTEHAELAAVRKALAADRRRLRALETERDEAAAAETARTAEDARLQEA
+ARQRHERLLELRAGIERARGDAPDLDARGALVRAARGRLEALAGAVEVRERAVAVAADAD
+RALAAALREQEFEDVGAARAARLPAEDAAARTARVRAWDDEQARLAELAQSDAVRRGREL
+QDQQATAPTPEDLEAAAARLLEAERSRREQDEALGRRTAVAAAVERQAALLRGVLDRSAA
+LLAEHERVTGLLALVRGGGENRLKMPLASYVLAGRLEEVAAAATERLLAMTDGRYSIEYS
+DDSAGRGNKGLELVVRDHYVDETRHPSTLSGGETFMASLALALGLADTVQAEAGGVELDT
+LFVDEGFGSLDSDTLDDVLDVVDGLRSGGRTVGLVSHVERMKQEIPVRLAVTKEREGSSL
+AVHVDA
+>GCF_020097155.1_02001
+MRIHRMRLEGIGPYAEPQDLDLDPLNDAGLFLLDGPTGAGKSTVLAALCFALYGSVPGGR
+TPESLVTTLRPPGAVVPQVLVEFTVQGRRFEVLRSPRHARPKKRGGGTTATQASVSLRER
+VDGAWTAPLTRADEVGRQVAEVLRLDAAQFMQVVSLPQGRFAEFLTARSDDRQRLLRRLF
+GTQRFDGVEDRLKECAEALGTRVAADAAEAAGARAQLLEQARLELGEDWHAPDPAPEEGE
+DERLVELTRTRADAALAEARTAQQAADAAEAAARAAQDRLTADTEALRALAAWEGREREH
+RQAADHVAADRSAVALHERASHVLGAATRAEQTRAAHASTAERARAAAEAVAADALAAAW
+LDEAEDADAARRRADRETDALARAVRDRDALTRLEAEGTQADAERERLEDEARSAREKGK
+RRAAQIAELHDTVDAAAARLGAEDEVARRLAEATERAAAAGQAAERAVAQERARAARDER
+RDAQRGAAQARLDLLRSRFEQAAAELAAGLEDGSPCPVCGSAEHPDPAPRADGAVTEADV
+AAADRALEAADAALAEAEQALAAASEEHRAARERAGGQDVAAAEEALSAVRAEHEALAAA
+RTALATDRRALARRESEQRTADEAATARTAALARLSEAQARRTERAAELTAAVAAAQGDA
+ADLDARTAHVRTATRALSALVEAGDAAARAAAVAEDAAQALAGALAEQDFADVAAARAAA
+LPPDDAAARAARVRSWDVEEARLAEAAASEPLVRGRALREAGTSEPTAEEFAAAQETLRE
+ATAARTARAAVVGRREALVASLERQARRLRAVLERSSELLAEHERATGLLALVRGQGENR
+LKMPLASYVLAGRLEEVAAAATERLLAMTDRRYSIEYSDEATGRGNKGLELVIRDHYVDE
+TRHPSTLSGGETFMASLALALGLADTVQAEAGGVELDTLFVDEGFGSLDADTLDDVLDVV
+DGLRAGGRTVGLVSHVERMKQEIPVRLEVTKSRAGSTLAIHDGG
+>GCF_023573625.1_00789
+MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR
+SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS
+LRERVDGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLLPQGQFAQFLTAKSDERRVLL
+RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP
+DTDDRLLGLAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR
+DHDAEAETAAARRRAVDAHERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAA
+AWLAAARADGAADAPASRQALGEAERAAEAVARAVQDRARMGELEQEAAAAAERRAEIGR
+DRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEA
+ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT
+ADTTVTEADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERA
+EAERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR
+DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETDQALTAALAEQHF
+DDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQ
+TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL
+DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE
+LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA
+DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000728.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000728.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75333dccc57add3323b9305933bc9160ec660cb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000728.fa
@@ -0,0 +1,98 @@
+>GCF_002008305.4_00821
+MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD
+ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR
+GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR
+DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV
+TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR
+TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI
+VPVLCWWFLRSPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA
+LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV
+QWTAGTAAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ
+GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA
+ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP
+VPLADLAEVSRVSVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA
+AVGGAAEQQAQTFRDLGLALLAAVATVYVVLVATFNSLRQPLVLLVSIPFAATGVFLALL
+ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMPLDEAIEVGALNRVRPVVM
+TALATVLAMTPMALGVTGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR
+LQEERRVAAAWEAQRVAAERAAKQERRAEQGSAAPSELDAGRLGRLRQRLRRRWRRA
+>GCF_003691675.1_00553
+MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD
+ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR
+GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR
+DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV
+TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR
+TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI
+VPVLCWWFLRSPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA
+LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV
+QWTAGTAAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ
+GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA
+ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP
+VPLGDLAEVSRVPVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA
+AVGGAAEQQAQTFRDLGLALLAAVATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALL
+ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMTLDEAIEVGALNRVRPVVM
+TALATILAMTPMALGITGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR
+LQEERRVAAEREAQRVAAERAAEQARRAEERWAAPSELDAGRLGRLRQRLRRRWRRA
+>GCF_005280335.1_02109
+MGALARFSLRRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DSLVGEPLETALQAVEGLESSGSTSQASFNSIQLQFAYGTDLNRARSQVDRVVSNLASQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNELRRRAEAVLAPRLQKLEGVRGADVLGGTE
+EHVSVVPDPEALAAAGLSTQDITTALEENAGLFPVGQVTEGESTYPVQAGAAVEDLEGLR
+GIVVTPAEGGQGAAPQDRTADGGPVGGGGGPPADAEATPAAPAEPAGDGEPRTLGEVAEV
+SLQAAEPTSVTRTDGADTLSVSVTATPDADLVAVSEAVREALPELESVVGGGADLTVVFD
+QAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSLRSTLVTAVSIPLSLLAALIGVAVFGY
+SLNTLTLGALTISIGRVVDDAIVVVENIRRHLDLGADRRTAILIGTREVATAITASTLVS
+VAVFLPIAFVGGLAGELFRPFAVTATIALLASLVVALTIVPVLCWWFLRTPRRPAGDESP
+ADAAEGGAPAVPAGEHGHDAHPSAAGGWLARAYRPVLRWTQRHTVATLAGAVAVLAGTAA
+LVPLIPTNLIGDTGQNSFVVTADQEPGTSLEATAAAAGVIERTLLETEGVETVQWTAGTA
+GGPAGAFGGSSADRARFTVVTDENADQTALQDGVRADLAALEGVGEVSVSTQQGPGGGQD
+IEVSVSAPDPQALATAADEVAGALRGVEGAREVTTPAADVRPTFQVDVDTEAAARLGLTE
+EAVAGQAAAALQAVPVGDVRFGFEQFQVRLGDPDPVESLEALRQVAVQTGSGPVPLEELA
+SVERVDVPARVTSSNGERTAVVTVTPDDQDLGAVSRRVTEAVDGLALPEGVTATVGGAAE
+QQAATFRELGLALLAAIATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALLATGTALG
+LSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMGLDEAIEVGALNRVRPVVMTALATIL
+AMVPMALGLTGHSGFISQPLAVAVVGGLLSSTLLTLVLVPVLYRLTEARGERRIQAERAE
+QARRDEEARRRAAEAEQAAAEQAESARAGLLARRRTGGAPAASAAAGMADDGGRRPGPLG
+RLRARLGGLVGRARRA
+>GCF_020097155.1_02000
+MGALARFSLSRRALVALVTAFIAVFGVLSAGLLKRELIPSLELPVISVSTTYPGASPEVV
+DAEIGQPLEQALQAVEGLDSSASTSATSFNSVQLRFRYGTDLTRARSQVDRVISNLASQL
+PEEAQTTSFAGSVSDFPVVFLALSGDEDLNALKRRAEDVLVPRLQRIDGVRGAQVLGGTE
+EYVSVVPDAAKLAAAGLTTQDVTTALEENAGLFPIGQATSGTVTYPVQAGAPVGSVADLE
+QVTVTPGGGQSSTGAADQGAGAGAGGGPGAATGTPARLGDVAAVSMQAADPTSVTRTDGA
+PTLSLSVTATPDADLVAVSHAVADALPELESLAGSGAKLTVVFDQAPFIEQSIRTLFVEG
+LLGLAMAILVIAVFLLSARSTMVTAVSIPLSLLTALIGVAVFGYSLNTLTLGALTISIGR
+VVDDAIVVVENIRRHLGLGADKRTAILEGTREVATAITASTLVSVAVFLPIAFVDGLAGE
+LFRPFAVTTSIALLASLVVALTIVPVLCWWFLRAPRAAAAPGGAEGVSSPVEDAAQDTWL
+ARAYRPVLRWTQRHAVATLAGAAALLAGTVALAPLIPTNLLGDSGQNSFVVTAQQAPGTS
+LEATTAIAGRIEAALRDTPGVRTVQFTAGSAGGAMGAFGRGSADRATFTVVTDPDADQTA
+LQDEVRGRLAGLGDVGEVDVSAQQGPAGGQDITVSVTAPDPEALADGIDRVAEALRGLDG
+VLQASTPSSDVRPTFQVDVDTLAAAERGLTEKAVSGQVAAALQAVPAGTVRFGFQEFTVR
+LGDPDPVESLGALRAVPISTPSGPVPLSELADVRRADVPAQVTSSNGQRTAEVTVTPDPA
+DLGGVSRRVSDALEGVALPDGVEATVGGAATEQAKTFRDLGLALLAAIAAVYVVMVATFN
+SLRQPFVLLVSIPFAATGVVLALLASGTALGVATMIGLLMLVGIVVTNAIVLIDLINQYR
+RRHGMALDEAIERGALHRVRPVVMTALATVLAMTPMALGITGHAGFISQPLAVAVVGGLA
+SSTVLTLVLVPVLYRLTEARGERRIQAERAAREAEERELAEREARERELAEREAAARAVA
+GPAAAAHPAPAGRLSRRRGWRGWIRRATS
+>GCF_023573625.1_00790
+MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD
+ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR
+GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR
+DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV
+TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR
+TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI
+VPVLCWWFLRAPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA
+LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV
+QWTAGTTAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ
+GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA
+ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP
+VPLGDLAEVSRVPVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA
+AVGGAAEQQAQTFRDLGLALLAAVATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALL
+ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMTLDEAIEVGALNRVRPVVM
+TALATILAMTPMALGITGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR
+LQEERRVAAEREAQRVAAERAAEQARRAEERWAAPSELDAGRLGRLRQRLRRRWRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000729.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000729.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d3d5edec58b80a78e4c17819432cb10c7730b9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000729.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00822
+MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG
+HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS
+FVWGDDHADYLRTRYEAMSAQPLFAGMEHSEDPEQIRAWAPLLIEGREPGQRLAASRNTG
+GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF
+VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM
+SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT
+KYLVTEVLKSRDKKIDALHEFYPEADGGEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT
+HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL
+DEVRTVTDAALKLA
+>GCF_003691675.1_00554
+MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG
+HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS
+FVWGDDHADYLRTRYEAMSAQPLFAGMEHSEDPEQIRAWAPLLIEGREPGQRLAASRNTG
+GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF
+VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM
+SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT
+KYLVTEVLKSRDKKIDALHEFYPEADGGEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT
+HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL
+DEVRTVTDAALKLA
+>GCF_005280335.1_02108
+MPTPSSATTHDVVLIGGGIMSATLGVLLQRLEPTWSIALYENLDQAGLESSDPWNNAGTG
+HAALCELNYAPLGKDGTVDVTKALGINEQFWTSRQFWSSLVKDGTLQDPKTFINPLPHMS
+FVWGDAHADYLRTRYEAMSAQPLFAQMEHTEDPATIAEWAPLLIEGREDAGRIAASRVVG
+GTDVDFGSLTRQLVTAMAGAGADVRFGHKVTGLSRGTDGRWEVSVKNKAAGTEVVDRARF
+VFVGAGGGALSLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNRHMAKVYGQAAVGAPPM
+SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSIRPHNLTTMLDVAKDNMDLT
+KYLVAEVVKSQNKKVESLKEFYPEAEGGDWELITAGQRVQVMKRKGRFGGVLQFGTEVVT
+HGDGSIGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGALKELIPSLGRTLNDDPALL
+AEVSASTDAALKLA
+>GCF_020097155.1_01999
+MWIPPDGVRRCTILALEHQEHIVSTPTSTTHDVVLIGGGIMSATLGVMLQKLEPSWSIAL
+YENLDQSGLESSDPWNNAGTGHAALCELNYSPLGKDGKVDTAKAKGINEQFWITRQFWSS
+LVKDGTLADPKNFINPLPHMSFVVGDAHADYLKTRYEAMSAEPLFADMEHTEDPDVIGEW
+APLLMDGRTGTERLAASRVPTGTDVDFGSLTRQLVTALAAGGADVRFGHKVTGLSRGTDG
+RWDVTVKNKAAGTEVRDRARFVFVGAGGGALGLLQNSGIPEIKGFGGFPVSGQFLRCTDE
+KVVNQHMAKVYGQAAVGAPPMSVPHLDTRFVNGKRSLLFGPYAGFSTNFLKSGSYLDLPL
+SIRPHNLPTMLNVAKDNMDLTKYLVTEVLKSNEKKVDTLHEFYPAADGSEWELITAGQRV
+QVMKKKGKLGGVLQFGTEVVSHADGSIAGLLGASPGASTAAPIMVKLLERCFPAKMAGWD
+AALKDMIPTLGRTLNDDPSLLAEVRSATDAALQLG
+>GCF_023573625.1_00791
+MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG
+HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS
+FVWGDDHADYLRTRYETMSAQPLFAGMEHSEDPEQIRAWAPLLIEGRASGQRLAASRNTG
+GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF
+VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM
+SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT
+KYLVTEVLKSRDKKIDALHEFYPEADGAEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT
+HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL
+DEVRTVTDAALKLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000731.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000731.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a24ca77df4e162cde4047da17d74f8ff8333fd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000731.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00825
+MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGISPDPIGKIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT
+FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA
+>GCF_003691675.1_00557
+MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGISPDPIGKIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT
+FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA
+>GCF_005280335.1_02097
+MSDTTQNRLQPGDIAPSFTLQDQDGRPVSLRDSAGKSTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGVSPDPIGKIIRFAQKEGLTFSLLSDEDHAVAEAYGAWGEKKNYGRT
+YEGLIRSTVVVGPDGRVTHAQYNVKATGHVARLRRTLGLDEA
+>GCF_020097155.1_01996
+MTENTAAPARLSPGDVAPEFTLQDQDGRPVSLRDSAGKSTIVYFYPAASTPGCTTQACDF
+RDSLASLTAAGYRVLGISPDPIGKIIRFAQNEGLTFSLLSDEDHAVAAAYGAWGEKKNYG
+RTSEGLIRSTVVVGPDGKVTLAQYNVKATGHVARLRRELGLDD
+>GCF_023573625.1_00794
+MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGISPDPIGRIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT
+FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000732.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4447d104ff4e13352ac4a8643a5e4b6a20164c81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000732.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_00827
+MTRADGSAYVGPMDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLE
+MLLCPFDPTSTPDDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQ
+VETVTGFRTWFDVPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPE
+TDATDVTPPDLHGV
+>GCF_003691675.1_00559
+MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQVETVTGFRTWFD
+VPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPETDATDVTPPDLH
+GV
+>GCF_005280335.1_02095
+MDSPTLQRRLRGVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDAPADAPAADAPEEDPHGPVAEPSSHGTDVVGVALGNVATVADTGSGYQVETVTGFRTW
+FDVPEHARVPVGDLTEDGTAGLDQAEDAVDFHAFMTAFMDELDRLYAAPEAGGTDVTGPD
+LHAR
+>GCF_020097155.1_01994
+MDSPTLARRIRGAFDARVFNHGDYNLVYGQRSGGSLPLVIGYRHSPLEMLLCPLDPVEAV
+AAVPEEVALANVATVADTGSGYQVETVTGFRTWFEVVDRPRVPVGEASEDGLAELDQADD
+AADFHAFMTAFMDELDRLYAEPADPDLHPPQKSV
+>GCF_023573625.1_00796
+MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQVETVTGFRTWFD
+VPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPETDATDVTPPDLR
+GV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000735.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000735.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e7579f3012a094c97ab4b7109b0aa5629ba876b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000735.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_00831
+MSTTPRDARAAVPQVPTPASRPTESARVQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAVADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAERTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGDVKEIIPDLVAELATDTEALPDLADWWAVLRRLQDTYPMGWTETEDGL
+LAPQEVISRLSALSGPEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>GCF_003691675.1_00563
+MSTTPRDARAAVPQVPTPASRPTETARVQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLVREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLVAELATDTEALPDLADWWAVLRRLQETYPMGWTETEDGL
+LAPQEVISRLSALSGTEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGYDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>GCF_005280335.1_02093
+MSTTPRDARAAVPPVPTPASRPEEQARPQERRPAVRPDTVEPRVPGEGNRVKPTLMTGSE
+GIIRALEELGVTDVFGLPGGAILPTYDPLMDSDQIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGSDAFQEADIVGITMPITKH
+SRLVTRPEDIPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRVDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDA
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPCARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLAAELATDTEALPDLADWWAVLRRLQDTYPMGWTETEDGL
+LAPQEVISRISALSGPEAAYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>GCF_020097155.1_01992
+MSTTPRATAPAASAGRDQRGPTRTETVEPRVPGPAAVVEPTVMNGAQGIIRSLEELGVED
+VFGLPGGAILPTYDPLMDSSRIRHILVRHEQGAGHAAQGYHLAGGRVGVAIATSGPGATN
+LVTAIADAHMDSQSVVFITGQVSSAAIGSDAFQEADIVGITIPITKHSRLVTRAEDIPAA
+LAEAFHIASTGRPGPVLVDVTKDAQQSEFEFSWPPRLDLPGYRPVLRGHPRQIREAARLI
+REARRPVLYVGGGVARGEAHEELRALAALTGAPVVTTLTARGVFPDSHPQHLGMPGMHGG
+VPAVAALQQADLLITLGARFDDRVTGHLPSFAPGAKVIHADVDPAEISKNRLADVPIVGS
+VKEIIPDLVAELGAGADLPDLAPWWATLERLRETYPLGFTAPDDGLMAPQQVISRISALS
+GPEAVYVAGVGQHQMWASQFVEYERPRQWLNSAGLGTMGFSVPAAMGAKVAQPQRTVWAI
+DGDGCFQMTNQELATCVINGIPIKVAVINNSSLGMVRQWQTLFYDQRYSNTDLNTGHGTA
+RIPDFVKLADAYGAAGLRCEREEDLDDVIRQALEIEDRPVVVDFVVSRDAMVWPMVPAGV
+SNDAIQIARGMTPDWDHED
+>GCF_023573625.1_00801
+MSTTPRDARAAVPQVPTPASRPTETARAQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLVAELATDTEALPDLADWWAVLRRLQETYPMGWTETEDGL
+LAPQEVISRLSALSGPEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000736.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000736.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36f6b6b5c3c40db4fbed11c5a3a0396e8a12123f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000736.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00832
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ
+VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES
+LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR
+>GCF_003691675.1_00564
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ
+VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES
+LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR
+>GCF_005280335.1_02092
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ
+VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES
+LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR
+>GCF_020097155.1_01991
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTQVPGISRMTVVVDADAHLLEQ
+VTKQLNKLINVIKVVELAGDSSVQRDHLLVKVRADASTRGQVVQAADLFRAHVVDVAPDS
+LTFEATGTREKLEAFLEMMEPHGIRELVRSGTLALARGPRSMTDRALAR
+>GCF_023573625.1_00802
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ
+VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES
+LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRAVAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000737.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9a156390ebb56d5807fcfffa62bfd0814bb1b0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000737.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00833
+MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQKGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV
+IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAQRFMDDQKAGA
+PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR
+>GCF_003691675.1_00565
+MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV
+IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAKRFMDDQKAGA
+PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR
+>GCF_005280335.1_02091
+MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV
+IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAQRFMDDQKAGA
+PEFKELRAKGEAHPIEKTGRELREMFSWLKDADDDYTEGTAAR
+>GCF_020097155.1_01990
+MTAQKFYDDDADLSIIQGRTVAVIGYGSQGHAHSLSLRDSGVDVRIGLAEGSKSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDEHIAPNLQEGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEQDASGQAEALALSYAKAIGGTRAGV
+IKTTFTEETESDLFGEQAVLCGGASQLIQYGFEVLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEFGDYVSGPRVITPEVKDHMKEVLADIQNGAFAKHFMDDQKAGA
+PEFTELRAKGESHPIEKTGRELRQMFSWLKDTDDDYTEGTAAR
+>GCF_023573625.1_00803
+MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSRSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV
+IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAKRFMDDQKAGA
+PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000738.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000738.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bca568be75fc3ea397849a8ddf1b4e2584277332
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000738.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00834
+MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATQMDAE
+AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA
+AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR
+AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE
+DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS
+VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIS
+EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA
+TAQGAQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ
+GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSV
+>GCF_003691675.1_00566
+MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE
+AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA
+AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR
+AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE
+DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS
+VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIA
+EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA
+TAQGTQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ
+GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSA
+>GCF_005280335.1_02090
+MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE
+AIAAAPQLKVIARAGVGLDNVDVPAATAAGVMVVNAPTSNIISAAELTCGHILATARNIA
+AANRSLKAGEWKRSKYTGVELYGKKLGVIGLGRIGALVAERMRAFGMEILAYDPYVTTAR
+AQQLGATLVELDQLLERADFVTIHMPKTPETVGMIGDDQFARMKDTAVVVNVARGGLVDE
+DALARALDSGAIAGAGIDVFSTEPATDLAFFAQDSAVVTPHLGASTAEAQEKAGVAVAGS
+VRLALSGELVPDAVNVAGGVIHEDVRPGLPLAEKLGRVLTSLVGEQSLTAVEVEIAGEIA
+EHDVSAMRLAALKGVFTDIVSDQVSYVNAPMLAEQRGVECRLTTTPVSESYRNTVTLRAA
+TAQGTQVSVTGTLTGPRQIQKLVGVDRHELEVPLADHLLVFTYEDRPGVIGVLGQALGVQ
+GVNIAGMDVSRDDEGEALAVLTLDGALSGDTATALAAAIGASRVAEVDLSA
+>GCF_020097155.1_01989
+MSAAKPVVLIAEELSPATVEALGPDFEIRHTDGADRARLLADLPGVDAVLIRSATTMDAE
+AIAVAKDLKVIARAGVGLDNVEVPAATAAGVMVVNAPTSNIVSAAELTCGHILSVARNIA
+PANRALKAGEWKRSKYAGVELFEKKLGVIGLGRIGALVAERMKAFGMEILAYDPYISAAR
+AQQLGATLLDLDELLAQSDFITVHMPKTPETVGMISDAQFATMKDTAFIVNVARGGLIDE
+DALDRALESGAIAGAGVDVFSSEPATDLAFFRHDTAVVTPHLGASTAEAQEKAGVAVAKS
+VRLALAGELVPDAVNVAGGVIHEDVRPGLPLAEKLARVLRALAGERSLASVDVEVAGEIA
+VHDVKALRLAALKGVFTDVVSDQVSYVNAPVLAEQRGVGGQLTTAAEAGSYRNTVTVAAV
+TDEGERLSVTGTLTGPKQVEKLVGVGRHEMEVALAEHMLLFRYADRPGVVGVLGQSLGEQ
+GVNIAGMDVSRDEQGSALAVLTLDAALAPGTAPTLAAAIDADRAAEVNLAD
+>GCF_023573625.1_00804
+MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE
+AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA
+AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR
+AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE
+DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS
+VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIA
+EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA
+TAQGTQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ
+GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000739.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000739.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ec938a8eb226a925776c057d8cfc8d28ecd716b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000739.fa
@@ -0,0 +1,54 @@
+>GCF_002008305.4_00847
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPAEDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D
+>GCF_003691675.1_00569
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPADDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D
+>GCF_005280335.1_02088
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIATDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQREGVTALELATRNAAVFKEMDDEVLDISYDRFIRTTDADHAEAVQEIWRRMEANGD
+VYLGSYAGWYSVRDERYFGEDETAVGEDGVRRAVETGTEVTWTEEESYFFRLSKYQEPLL
+EHYRRNPEFAAPRYRFNEVIRFVEDGLEDLSISRTSFDWGVPLPAPVDPDAEVADRRADH
+VTYVWVDALTNYLTGAGWPGRDPEAFGRYWPADLHVIGKDISRFHCIFWPAFLMSAGIEL
+PKRVMIHGFLNNNGAKMSKSLGNVVHPRDWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VGRKNADLANNLGNLAQRSLSMVAKNCEAAVPQPGPLTAEDEAVLAQVDALLERSRTAYA
+VQDFHDALEETWRVLGEVNAYFADQAPWVLRKTDEARMRTVLYVTLQAVRRVALLVQPVM
+PASASRLLDLLGVPAEGDAGRTGASGQGPRSFAAFHEDLVPGTALPKPEGVFPRHEEPAE
+A
+>GCF_020097155.1_01988
+MTDTRAPYYVTTAIHYPNGEPHIGHAYEVVGADALARFMRLDGRDVFFLTGTDEHGQKMA
+QTAERLGVTPMELATRNSAAFKAMDDEVLGVSYDRFIRTTDEDHHRASQEIWRRMEANGD
+VYLDRYAGWYSVRDERFFDEDETEVREDGQRYAAETGTEVTWTEEESWFFRLSKYQEPLL
+ALYRDDPEFAAPRSRFNEVIRFVEGGLEDLSISRTSFDWGIDVPAPADGAASDAHHVMYV
+WVDALTNYLTGVGFPDESSESFRRFWPADVHVIGKDISRFHCVFWPAFLMSAGIELPKRV
+MIHGFLNNNGEKMSKSLGNVVAPRDWVARYGLDAVRFFLLREFPFGADGSYSHEAVVGRK
+NADLANNLGNLAQRSLSMVAKNCGGGVPEPGSLTEADTAVLAQVDALLEHSRAAYTVQDF
+HGALEETWRVLGEVNAYFADQAPWVLKKTDEPRMRTVLYVTLQAVRRVALLVQPVMPASS
+SRLLDLLGVPAEGDAGATAASNAGPRSFAAFGEDLMPGTALPRPEGVFPRHEDPAEG
+>GCF_023573625.1_00806
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPAEDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000744.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000744.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ca5a322bc1dd6feb3b60807cba2b4e76239db7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000744.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00852
+MRIARFVDQAEPTYGIVEGPADADPAELTVTALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPAGGLRITSRLDGETRQDGTTTDMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG
+TVQEGQRVEAEVEGIGVLATVFRR
+>GCF_003691675.1_00574
+MRIARFVDQAEPTYGIVEGPADADPAELSITALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPTGGLRITSRLDGETRQDGTTADMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG
+TVQEGQRVEAEVEGIGILATVFRR
+>GCF_005280335.1_02082
+MRIARFVDQAEPTYGVVEGPADADLSELTITALQGDPFFHGIQPTSTVHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNETPASPQFFLKPNTSVVGPGEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPAGGLRITSRLDGQTRQDGTTADMVFGVRELVAAASEAFTLLPGDVILTGTPAGVG
+TVAEGQRVEAEVEGIGVLATVFRR
+>GCF_020097155.1_01977
+MRIARFVDQAEPTYGVVEGPADADLSALTVTALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPSSPQFFLKPNTSVVGPDEPVTLPSWSEEVSYEAEL
+AVVIGTICKDVPLSRVDDVVFGYTVANDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEQAGGLRVTSRLAGETRQDGTTADMVFGVKELVAAASEMFTLLPGDVILTGTPAGVG
+TVEAGQRVEAEVEGIGVLGTHVRR
+>GCF_023573625.1_00811
+MRIARFVDQAEPTYGIVEGPADADPAELSITALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPTGGLRITSRLDGETRQDGTTADMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG
+TVQEGQRVEAEVEGIGILATVFRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000745.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000745.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d86feac4cdeb018ec1f475bb75379960e1eda470
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000745.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00853
+MTDATAPVSENAPAPFADVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGYIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALHAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMQILTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEDEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQGRPTDA
+>GCF_003691675.1_00575
+MTDATAPVSENAPAPFVDVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALYAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMEVLTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEEEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQDQPTDA
+>GCF_005280335.1_02081
+MDAETPVRVRFCPSPTGTPHVGLIRTALFNWGWARHTGGTLVFRIEDTDAKRDSEESYQQ
+LLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGEIYAEVIEKLKAGGHIYPSYSSPEETEAR
+HRAAGRDPKLGYDGFDRDLTDEQVAAFEAEGRAPVWRLRMPDTDITFTDLVRGEITFKAG
+TVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLLSSTPRQIALYRALHAVGVAAY
+MPVFGHLPYVMGEGNKKLSKRDPQANLFLHREHGFIREGLLNYLALLGWSLSADEDIFTP
+EQFVEHFDVHKVLANPARFDEKKAIAINGSHVRMLDADDFRERLVPYLHAAGLVDAEPTE
+REREILAAAAPLVQERVQLLGEAVEMLAFLFTADADVATSEGALKGMPADLGAAVAAARD
+ALAALPEDGFTTERIEEALRAALIDGLGLKPRQAFGPVRVAVTGRKVSPPLFESLEILGR
+DSALARLDRFAAEQGLDQGLPTDA
+>GCF_020097155.1_01976
+MTEPTTASDTAAENAPAVFADVPQVDADTPVRVRFCPSPTGTPHVGLIRTALFNWGWARH
+TGGTLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGEIYAE
+VIEKLKAGGHIYPSYSTPEETEARHRAAGRDPKLGYDGADRDLSAEQVEAYEAEGRRPVW
+RLRMPDADITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGE
+DLLSSTPRQIALYRALHAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQSNLFLHRDRGFI
+PEGLLNYLALLGWSLSADEDIFTPEQFVEHFDIHKVLANPARFDEKKATAINGTHVRMLE
+PADFRARLVPYLQAAGLVGERLTEREERILDAAAPLVHERVALLGEAVDMLAFLFTPDAE
+IATAEGALKGMPADLPTAVAAAREALAGIDEAEFTTAAVEEALRAALIDGLELKPRQAFG
+PVRVAVTGKKVSPPLFESLEILGKESALARLDRFAAEQAAA
+>GCF_023573625.1_00812
+MTDATAPVSENAPAPFVDVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALYAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMEVLTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEEEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQDQPTDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000746.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000746.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6bb6215f1904c65363ae4e845c67977a871ec6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000746.fa
@@ -0,0 +1,52 @@
+>GCF_002008305.4_00859
+MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAVVRAAGERQALSAEHTVVGFFGA
+TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA
+ALLDWLGVRRRHLLDEAPVLDDGRPGFLGFGRRDGADATGLILLDLPDIDSVERGNREIT
+SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS
+LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA
+ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA
+DPLRRLHLMPESAAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGAGAS
+EPWAAAIRRAGREHAEELPGAVDQAIAATDLGAGRGSWWHPVLDVLQWLALLTAVVGAGW
+LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRHAR
+RRLEEATTDVGRRLVVDPVRAEVDRFRAFRDALARASGAPVRRGRR
+>GCF_003691675.1_00581
+MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAVVRAAGERQALSAEHTVVGFFGA
+TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA
+ALLDWLGVRRRHLLDEAPVLDDGRPGFLGLGRRDGADATGLILLDLPDIDSVERGNREIT
+SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS
+LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA
+ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA
+DPLRRLHLMPASTAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGTGAS
+EPWAAAIRRAGREHAEDLPGAVDQAIAATDLGAGRGSWWHPVLDVLQWLALLTAVVGAGW
+LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRRAR
+RRLEEATTDVGRRLVVDPVRAEVERFHAFRDALARASGVPVRRGRR
+>GCF_005280335.1_02076
+MELSNREITSRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSV
+RDRDTVLASLRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQIAAIVERRGAAAERLGADV
+AARARDLDAASGEGEPAGVGPGDEQRLGRDLATAGGVPAVVRAVEGSYRLRSAKQTSWPV
+LRWMHSFRADPLRRLHLMPDRPAVRRDRDEVGRDPALHRTSLPERTGTQKAVVDGAVRTL
+VTAAAAGAPEPWAASVRRAGRAHAEQVPDAVDQAIAATDLGAGRGSWWHPVLNVLQWLAL
+LTAVVGAGWLGVLALAAYLQFPLPPAPVVEGFPIPTLLLVGGLALGVLLALLAIPLTRIT
+AASRGRRARRRLEEGTTDVGRRLVVDPVRAEVDRFHAFRDAVARAAGATARRGRR
+>GCF_020097155.1_01970
+MSRPAAPTLAQRLDALGTAAELARDRLPDAVVADAQAAVRAAEERQSLSAEHTVVGFFGA
+TGSGKSSLFNALTGRELAGVAATRPTTSEPLAAVWGVGRGENLDGEGGGAAALLDWLGVR
+RRHLLDDAPVLDGGRPVFLGLGHREGADATGLILLDLPDIDSVQRSHRDVTARLAGHVDV
+LVWVVDPEKYADAVIHRDFLATMASHAAVTLVLLNQVDRLTVTDRDAVLASLRRMLSGHG
+MGDVRVLPVSARTGEGLEEVGRQIAAIVSRRGAAAERLGADVSARARALDEASGPGEPAG
+AGDDDAVRLGRDLAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRADPLRRLHLL
+PERAVARRDRDPVDRDPALHRTSLPERTQTQRAVVEGAVRTLVTSASAGASEPWAASVRR
+AGREHLDELPAAVDHAIAGTDVEAGRGSWWWPVLDVLQWLALAVAVAGAGWLGAYALAAW
+LQFPLPPAPTTQGFPIPTLLLIGGLALGLLLALLAVPLTRLTAASRGRRARRRLEEAAVR
+VGRELVVDPVNAEAARHREFRSALAAAQGSGVRSRSRR
+>GCF_023573625.1_00818
+MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAAVRAAGERQALSAEHTVVGFFGA
+TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA
+ALLDWLGVRRRHLLDEAPVLDDGRPGFLGVGRRDGADATGLILLDLPDIDSVERGNREIT
+SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS
+LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA
+ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA
+DPLRRLHLMPESAAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGAGAS
+EPWAAAIRHAGREHAEELPGAVDQAIAATDLGAGRGSWWHPVLDMLQWLALLTAVVGAGW
+LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRRAR
+RRLEEATTDVGRRLVVDPVRAEVDRFHAFRDALARASGVPVRRGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000747.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000747.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba376f1be2bbdd2f87946010f6268435a28c89d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000747.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00860
+MTVRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGSASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLCRTPAAA
+DRDRVLAEGADLVHAQAVPDGPRAAAPPGPGWAAAGLAVLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAQAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARAPAGHRPLPGSGWDPFAG
+>GCF_003691675.1_00582
+MTVRDPAAAAGATVGDLTESELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLPRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLCRTPAAA
+DRDRVLVEGADLVHAQAVPDGPRAAAPPGPGWAAAGLTLLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARPPAGHRPLSESGWDPFAG
+>GCF_005280335.1_02075
+MTPAGGRPADGRTVGEVTEAQLLRVVLDGLAPAVRPGHWPPGTVAPGDDAALVPAPRGGT
+LVSTDAMGEGTDFLHRWPAGVRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PLAWVRSFAAGVVGAVDRLGAPGCRVAGGDLGTGERVHAAVTVLGDPHPAGVLRRAPAPA
+ARERVLAEGADLVHAQDAPGSSGAARSGALRPSAARPGPGWAAAGLALLLTDRDELARRA
+AALPPEDRPGARDLARAVRAQLRPRPPLALGPAAVEAGILTLMDVSDGLGRDAHRMAAAT
+GAAASAEAPPPVPWIDAAWLAEAAAPLRGVAALAGVSAESLVTGGGEDYGLLGLAWPETA
+LPAGFVRIGRLEPAGAPAPAGHRELPEAGWDPFGG
+>GCF_020097155.1_01969
+MSTPASTASAGGRPAPARTVGEASEAELLDLIQDALAPVARDVPWPAGTVPPGDDCAVVP
+APRGLVAVSTDAMGEGTDFLRRWPAGVRTRGHDVGWKAAAQNLSDVNAMGATPSALVTAL
+ALPAPTPLDWVASLAGGFTAAVRALGADRCRVAGGDLGAGESVQVAVTALGDPDPAGALR
+RAAGGERGARIARRGADLVLAAGSPRAAAAGEGQDSAWGPAGPGWAAAGLALLLTDRAVL
+TRRWADLAAHERPSARELARAVRGQLRPRPPLAAGPAAARAGLAALMDVSDGLGRDGHRL
+ARASSAPGAPLVPWVDRRWLAEAAEPLRRVASLAGTTPEALVLGGAEDYGLLGLAEPGLA
+LPSGFRRVGRLAPAGETPDGHVRLPEAGWDHFDAGRG
+>GCF_023573625.1_00819
+MTMRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLRRTPAAA
+DRDRVLAEGADLVHAQAVPDGPRAAAPSGPGWAAAGLTLLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARPPAGHRPLSESGWDPFAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000749.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000749.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10813110f9e86160a285a23b0fb5e855a20fb87b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000749.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00862
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
+>GCF_003691675.1_00584
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
+>GCF_005280335.1_02073
+MTAEPARAQADDDVLGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL
+HRLAAALTHHRLVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRNHAD
+AVVAAATRLTELIRAGEA
+>GCF_020097155.1_01967
+MTTTPLPDAGADIGPALHVHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTLHR
+LAAALTHHRLVAKDLQGRYVLGSRLAELASAAGEDRLTSAAGPVLQWLRDACGESAQVFR
+RQADSRVCVASAERPWGLRDTIPVGTRMSMKAGSAAQVLLAWEDNERLVDGLVGAVFTPT
+VLAAVRRRGWAQSLAEREPGVASVSAPVRGPNGKVIAALSISGPLERLSRQPGRLHAGSV
+VAAADRLTELIRAGEA
+>GCF_023573625.1_00821
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000750.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000750.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b10e4e10b742d7389d565940d0e4d95200993fc2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000750.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00863
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA
+>GCF_003691675.1_00585
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADPTSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFTDPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+LQEA
+>GCF_005280335.1_02072
+MTSETTRPRTLAEKVWDEHVVVRGEGEGSSRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLEIDKPIADPTSRTQIETLRANAAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAIT
+VDGTLRPGVTAKDVILAVIAKIGTGGGQGFVLEYRGEAIRSLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADELEPFVT
+WGTNPGQGVSLNGAVPAPEDFDDPVAQESARKALGYMDLTPGTPMKEVAVDTVFMGSCTN
+SRIEDLRAFAEVVKGRKKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA
+>GCF_020097155.1_01966
+MSTQTQTPRPRTLAEKVWDEHVVVRGEGEGARRTPDLLYIDLHLVHEVTSPQAFDGLRLA
+DRPVARPELTIATEDHNTPTLEIDRPIADETSRVQIETLRANAEEFGVRLHSLGDREQGI
+VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLRLKPFRTMA
+ITVDGTLRPGVTAKDVILAVIAKIGTGGGQGYVLEYRGEAIRSLSMEGRMTLCNMSIEAG
+ARAGMVAPDDTTFEYLKGRPHAPQGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF
+VTWGTNPGQGVSLNDAVPAPEDFSDPAAQEAARKALSYMDLTPGTPMKDVAVDTVFMGSC
+TNSRIEDLRAFAEVVKGRTKADGLRVMVVPGSARVRLQAMDEGLDKVFEDFGAEWRFAGC
+SMCLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPLVAAATAVLGRLASPSDLPA
+LENQEA
+>GCF_023573625.1_00822
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000751.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000751.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dfc21ae8350d67f030817e61bfeb84a963024df7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000751.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00864
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTPVTVDLVTRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG
+>GCF_003691675.1_00586
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTTVTVDLVTRTVECGDVTAPFQIDDDTRRRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG
+>GCF_005280335.1_02071
+MEKFTTHTGIGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+AGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTTVTVDLVSRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLDHQDEI
+DAYERARPSYKPTTLPARTAG
+>GCF_020097155.1_01965
+MDKFTTHTGIGVPLRASNVDTDQIIPAVYLKRVSRTGFEDALFAGWRQDPDFILNTEPYS
+AGSVLVAGPDFGTGSSREHAVWALKDYGFKVVVSSRFADIFRGNSAKQGLVAAQVEPEDV
+ERIMKQLENQPGAAVTVDLEHLTVECGGVTAAFEIDEDARHRLLHGLDDIAITLSHADAI
+AAYEAGRPSYKPTTLPARTAD
+>GCF_023573625.1_00823
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTPVTVDLVTRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000754.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000754.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ed0a20f0a2b9acb76d35e5767232691821830f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000754.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_00867
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPESARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLRTVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDTDTMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
+>GCF_003691675.1_00589
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPESARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLHAVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
+>GCF_005280335.1_02068
+MSDPQTVAVLGAGSWGSAFARVLGTSTSPEGARARDVVIWSRRPEVAEVVNRDHANPEYL
+PGIELPACVRAVTDAFEAVRGAGVVVVAVPAQHVRETLRTLREDLAPDAVVVSLVKGLER
+GTDARMSQVCTEELGLTPDRFAVVSGPNLALEIARGEPTATVVASGSSATAERIAALTAG
+PTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGMSAEEAVAAMSQTAEGIKSVSAVV
+HVARAHGVEMPISELMDRVVAGDVAVHRLAELLLARDLKSEGRTA
+>GCF_020097155.1_01962
+MSPAPSAGPEPAFASASAGDRAGDPTRVAVLGAGSWGTAFACVLGSSTSPAGRRAREVVV
+WSRRAEVARAITEDHANPEYLPDVALPECVRAVTDAREAVAEAGVVVVAVPAQQARTVLE
+GLADALAPDAIAVSLMKGLERGTDARPSQVCQEALGIGPERFAVLSGPNLALEIARGEPT
+ATVVASASRATADRVAALTAGPTFRPYTNGDVVGVEIGGIVKNVIALAVGICDGQGLGDN
+SKASVITRGLAETTRLAVALGGEASTLAGLAGLGDLVATCASPLSRNRSAGRLMGTGLSA
+DEAVAAMKQTAEGIKSVSAVVHVARAHGVEMPISEAMDRVVAGTLDVDRLAGLLLARDLK
+SEGRHA
+>GCF_023573625.1_00826
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPEPARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLRTVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000755.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000755.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c4a212a3acaf69aa562e9bf7d0baff4442ab498
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000755.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00868
+MTATPAPEAAADARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW
+SHDELDVASFRLDGDALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP
+WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD
+PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR
+EIECAVLDGHGSAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGTTQLSCPAELPEEEI
+ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY
+DDLISELLDLALERGVGLH
+>GCF_003691675.1_00590
+MTATPAPEAAADARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW
+SHDELDVASFRLDGDALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP
+WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD
+PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR
+EIECAVLDGHGAAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGSTQLSCPAELPEEEI
+ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY
+DDLISELLDLALERGVGLH
+>GCF_005280335.1_02067
+MLLLFGGRSSEHPISCVTAAGVLHAADPQRWDVVPVGVARSGLWSHDELDVAAFRLDGET
+LPEVPEPEAPVSLRTLPDGTVELTAEDGSSLGRVDVVFPLLHGPWGEDGTLQGMFESLGL
+PYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITDRDWARDPEAALARAGALAFPLF
+VKPARGGSSFGITRVSDPADLRAAVEEARRFDPKVVVEAGIVGREIECAVLDGHGSDAPR
+ASLPGEIVVKHDEGDLQFYDFQAKYQDDDAAQLSCPAELPEEQTRRLRELAVRAFEAVDG
+SGLGRCDFFHTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSYDALISELLDLALERGV
+GLH
+>GCF_020097155.1_01961
+MTQPPETAPGRRPRVLLLFGGRSSEHPISCVTAAGVLHAADRERWDVVPVGVAHSGLWSH
+GEVDAAAYALGDGELPSVPEPERPVSLRARADDAVELVGADGEDLGVVDVVFPLLHGPWG
+EDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAGGLEVGPWETITDRQWRNDPE
+AALERAGALDYPLFVKPARGGSSFGITKVDAPEDLRAAVEEARRFDPKVVVEAGILGREI
+ECAVLDGHGAESPRASLPGEIVVKGAESGHQFYDFEAKYQDASAAQLSCPAELPEEAIER
+LREQAVRAFEAVDGAGLGRCDFFYTPDGRWVVNEINTMPGFTSISMYPAMWERTGLPYGE
+LISELLDLALERGVGLH
+>GCF_023573625.1_00827
+MTAIPAPEAAAGARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW
+SHDELDVASFRLDGGALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP
+WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD
+PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR
+EIECAVLDGHGSAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGTTQLSCPAELPEEEI
+ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY
+DDLISELLYLALERGVGLH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000756.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000756.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c95f3cabad0012fd697f224db7c4f365718da49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000756.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00869
+MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT
+DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVVRDEDENWRITTYGRDPAVEV
+LFGKDQASSDTVMVGLSSAVAQIEPSGGCVGVQDATPVG
+>GCF_003691675.1_00591
+MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT
+DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVVRDEDENWRITTYGRDPAVEV
+LFGKDQASSDTVMVGLSSAVAQIEPSGGCVSVQDATPVG
+>GCF_005280335.1_02066
+MESRPLRPLRRLVPLLTAIALGATACSGRVATVEAAPDAANPECAPAMVAMPDALGDAAL
+RPTDSQATAVWGDPAAVVLRCGAPVPGPTTDRCISVDGVDWVIRDEDENWRIVTYGRDPA
+VEVLFGKDKASSDTVMVGLASAVAQIDADGGCVNLQDATPVG
+>GCF_020097155.1_01960
+MPRLPRPVILAPALAAAALGLTACSGPVVSVEAAPGAADPACAPAMVAVPDVLGGQDRRE
+TDSQATAAWGEPAAVVLRCGVPTPGPTTDRCVSVDDIDWVVRDEDDHWRITTYGRTPAVE
+AVFGKSEVSSDSVMTGLGSAVAQIPSQRRCVNIEDATPVG
+>GCF_023573625.1_00828
+MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT
+DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVIRDEDENWRITTYGRDPAVEV
+LFGKDQASSDTVMVGLSSAVAQIESSGGCVSVQDATPVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000760.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000760.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0f25bef17f4bafd56c7272c4ee4dfcbd7463de9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000760.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00873
+MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC
+EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAAPVDLI
+LADPPYPVAGPPLEAVVEAAAERLAPGGLLVLERAARDAAPRRPRGLEEVEVRVYGETAL
+YLWQDER
+>GCF_003691675.1_00595
+MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC
+EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAAPVDLI
+LADPPYPVAGAPLEAVLEAAAGRLAPGGLFVLERAARDAAPRRPRGLEEVEVRVYGETAL
+YLWQDER
+>GCF_005280335.1_02062
+MSRIIAGAAAGRPLTSVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLFAGSGALGC
+EAASRGAASVLLVERERRAVAACRANAALVNRARGADVVQVRAGTVEQALAAGGEPADLI
+LADPPYPLAGPALEAVLEAAAARLTPGGLIVLERAARDAPPRRPAGLEEVEVRAYGETAL
+YLWQDER
+>GCF_020097155.1_01956
+MSRIIAGAAAGRPLRSVPGTGTRPTTDRTKEALFSWLQARDWLDGTRVLDLYAGSGALGC
+EAASRGAAHVTLVEKARRAAEVCRANAAALNAVLGAPVVQVAASSVEQALALPGDSADLI
+LADPPYPESGPAFHAVLAAAAARLAAGGLLVLERSARDPAPERPAGLEQVEVRTYGETAL
+YFWQDEG
+>GCF_023573625.1_00832
+MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC
+EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAASVDLI
+LADPPYPVAGPPLEAVVEAAAGRLAPGGLLVLERAARDVAPRRPRGLEEVEVRVYGETAL
+YLWQDER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000764.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000764.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fb279b60c3841188528acf16285430a89c5c248
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000764.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00877
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>GCF_003691675.1_00599
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>GCF_005280335.1_02058
+MDTTQRQDADSSWVIPVRDLTRGAGVQRELTAQWPAPAGVTTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECSRCLLPLHEGITVDLQELYLTGASEDEAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>GCF_020097155.1_01952
+MATTVPSGAPSPWVLSVRDLARGAGVQRELTTRLPAPAAVSMPMLGIPEGDPVDLELRLE
+AVHEGVLVTGTAHADLTGECSRCLLPLHEGITVDLQELFLADPPAEGDDEQPLVEHETVD
+LEPVFRDAVVTALPFQPLCRPDCEGLCADCGIRLEDAPAGHAHERVDPRWAALAALADTT
+EETSITETEKR
+>GCF_023573625.1_00836
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWRAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000765.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000765.fa
new file mode 100644
index 0000000000000000000000000000000000000000..623460b59b9f2674ccebb48f41e9bf7ce41dd946
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000765.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00878
+MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA
+>GCF_003691675.1_00600
+MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA
+>GCF_005280335.1_02057
+MAVPKRKMSRANTRARRSQWKATAPTLVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA
+>GCF_020097155.1_01951
+MAVPKRKMSRANTRARRSQWKAEAPSLVKTVENGRVSYRLPHQAELKTDAAGTPLFYEYK
+GRKVADA
+>GCF_023573625.1_00837
+MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000766.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000766.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a75d9ec3ddf4fc17126924aaf8f98be654964708
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000766.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_00879
+MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV
+AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEADLPAAGR
+>GCF_003691675.1_00601
+MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV
+AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEAGLPAAGR
+>GCF_005280335.1_02056
+MHVTAETLERALTHRSYAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVHPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGEGRTGGADKDSILADTLEALIGAVHVDHGLV
+AASALVHRHVVPLLDEPDLVRESTDWKTVVAEAANRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEADLPAAGR
+>GCF_020097155.1_01950
+MASPQTRTGSVPVPESSALLERLGVHITAGTLERALTHRSYAYEHGGLPTNERLEFLGDS
+VLGFVVTDHLFTAFPDLPEGDLARRRAAIVSTRALAKVARRIGVGPHVRLGTGETRTGGA
+DKDSILADTFEALIGAVYRDHGAVAAAALVHRHVVPLLDEPGLLRESTDWKTVVAEAASR
+HGLGEVRYDIEGQGPAHDPRFRATLTVGGRAFGSAVASSKKQAERDAAAEGWPELSATLP
+AAGS
+>GCF_023573625.1_00838
+MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV
+AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEAGLPAAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000768.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000768.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d70befc73836bfad14f6ad88ce4c32f3314f9ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000768.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00881
+MSHPPAASWTPEPLPRPEPPRDDAPPVARRRRRWPWVVGLLAVLLAALLGLGAWYTSSLG
+RTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYTLAVDTVELLLGVSIHHVLEVDFQGFRGV
+TNALGGVEVCNPRAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVENQQR
+YLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPTKEKKAQAAGGPAP
+VLTLLTGTTPAPVLGEDPCDD
+>GCF_003691675.1_00603
+MSHPPAASWTPEPLPRPEPPRDDAPPVARRRRRWPWVVGLLAVLLAALLGLGAWYAGSLG
+RTFDDHRQTVDVGALEQAAGDGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVDTVELLLGVPIHHVLEVDFQGFRGV
+TNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVKNQQR
+YLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPEKEKKAQAAGGPAP
+VLTLLTGTTPAPALGENPCDD
+>GCF_005280335.1_02054
+MSQPPAASWTPEPLPRPARSPEPPRPARRRRWPWVLGVLAAVLVVLLALGAWYAVSLART
+FDDHRQTVDAGALEQAGGGEPVNVLVLGSDSRGGEGEEDMGERSDAMMLVHLPADRSQVF
+VMSVLRDSWVEIPGHGEAKVNAAFDLGGYPLAVDTVEQLLGVPVHHVVEMDFQGFRGVTN
+ALGGVEVCNPVAFSSGQTSPSYYPRGPVLLQDTAALRYVRERHAFDDGDVSRVQNQQRYL
+AGAVERFLSPQILGNPARTTEVVATFSDHLGVDAGLTSGVVASLAWQLRGVRAGDVEMFT
+VPRAGFGYSPDGDSIVELDEAKLADLRSALKDDDVQRYVAEHESEDGQDASAAGADPAPV
+LALLAQPAPTPAVGEDPCAD
+>GCF_020097155.1_01948
+MTQPPQQPWIPPERPGGAADPLEGLRGPAPAAPPTSTPPATRRSGGGRARRRRPLRRFLA
+VLGVLALLLVVALGAYGLLLARTFDGHRQTVSAAAFADPGNDGPVNFLVLGSDSRAAEDS
+AETSQRSDTMMLVHVPADRRHVYVISVLRDSLVEIPGRGQRKANAAYELGGPELTAAMLD
+KLLGVPVHHLAELDFQGFRGMTTALGGVEVCNPHAFSSGQKNPSFYPRGRIELKDTAALR
+YVRERHAFPEGDVMRVQNQQRFVRGAVAAFLDPAVVLNPPRAVDVVAGLSDHLTVDEGLD
+SATLASLAWQLRGVDRSALTMFTVPRAGYGTSPDGQDVVLLDADRMAALRDALQRDDVES
+YLRAHDPEALAAGEDVQPALAAAPGATPLLTELAAAPPAGEGTLLGEDPCGG
+>GCF_023573625.1_00840
+MSHPPAASWTPEPLPRPESPRDDASSVARRRRRWPWVVGVLAVLLAALLGLGAWYAGSLG
+RTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVDTVELLLGVPIHHVLEVDFQGFRGV
+TNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVKNQQR
+YLAGAMDRFLSPEILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPTKEKKAQAAGGPAP
+VLTLLTGTTPAPALGEDPCDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000769.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000769.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9b765500fa24aff91e3813bd3313d5e3561e3d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000769.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00882
+MTTESRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAVPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGAAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VRVVRTLGNGVDLARLAVAPRRERAAGELHVLYLGNMGESQGLERLIDAAATLRRTRPGV
+RVRLVGEGTRRPALEARNAELGSPAEILGPVHGAAVAEQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGLVTGEAARTLEAAGGADVIGPDVDDLVRHLTALADDPHRTDVG
+AGGRDWVRRHADLPAVARRYERVLRRVAGR
+>GCF_003691675.1_00604
+MTTEPRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAIPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGVAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VRVVRTLGNGVDLARLAVAPRRERDAGELHVLYLGNMGESQGLERLIDAAATLRRTRPGV
+RVRLVGEGTRRPALEARNAELGSPAEILGPVHGAAVAQQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGLVTGEAARTLEAAGGAEVIGPDVDDLVRHLTALADDPHRTDVG
+AGGRDWVRRHADLPAVARRYERLLRRVAGR
+>GCF_005280335.1_02053
+MPTEPRRPRVLLITHSYRPERTPPARRWAAVVAALRAGGWDVDVVAPGGLRAVAGDDGER
+ILRTPRLPAGRSGRNGRFLEAAVHAVLAVPRGLAARRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGVAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VERVETLCNGVELAGLARAPARRREPGDLHVLYLGNMGESQGLERLVEAAAELRQSRPGV
+RVRLVGAGTRRGELEARNAELGSPAEILPACYGEEAAAQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGMVTGEAARTLEDAGGADVIGSRVADLVAHLTALADDPARTDVG
+EGGRPWVRLHADLPSVARRYVRLLGQLVPDYRRHA
+>GCF_020097155.1_01947
+MGERRTRAGGRAPRLLLVTHSYRPERTPPARRWAAVVQALRAAGWEVDVLVPGGLRTRVG
+EHGERLRPTPRLLGSGDGRNGRFAAAAVHAVLAVPRGLVLPRPDVVVATLPALPVVVAGR
+ALAVLRRRPLVVEMRDAWPDLAREAGVHPGLLGTLMERVVTGGQRAADLVVTVTEGFAAT
+LRGRGMRRVEVLANGVDLERVPVAPPRDRTAGELHVLYLGNLGESQGLERLVEAAARQRA
+THPGVHVRIVGDGTRRAALEALNAELEAGVEFVPPVSGAALTEQYAWADTLVVCLRPDWP
+SFRHTIPSKTYEALAVGRHVTGQLSGEAALMLERSGAADVVGPGVEDLVAHLDALADDPA
+RTRVGDAGRRWAAAHGDLPTTARRYEALLRRVAARPSRRTRTETTA
+>GCF_023573625.1_00841
+MTTEPRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAIPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGAAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VERAETLCNGVELAGLAWAPARRREPGDLHVLYLGNMGESQGLERLMEAAAELRQSRPGV
+RVRLVGAGTRRGELEARNAELGSPAEILPACYGEDAAAQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGMVTGEAARTLEDAGGADVIGPRVADLVAHLTALADDPARTDVG
+EGGRPWVRRHADLPSVARRYVRLLGQLVPDYRRHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000770.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000770.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78f5f5da71297048bb05dc5acf744751301fa3f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000770.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_00885
+MKKIETVAVIGLGYIGLPTAAILAENGVRVLGVDVSDRTVDAVNAGTVPFVEPDLAGFVA
+RGVEKGLLSASTTTPAADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLTGDELVILES
+TSPPGATEYMAEVIFAERPELREAELDFAHCPERVLPGRVMVELVTNDRIVGGSTRRAAE
+RARDLYRTFCEGEILLTDTRTAEMAKLVENSFRDVNIAFANELSVICAEQGIDVWELIEL
+ANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARLIRAAREINDGKPQWVIDQVKAA
+AFDVQQATGRAPVVAALGLAFKPNIDDLRESPALNIAAELAGQFSGSDVLVVEPHVTELP
+AALQGKDNVRLVAVDEALEAADIVVLLVDHSAFADLGDRVADKRVIDTRGQWRTDPSL
+>GCF_003691675.1_00607
+MKKIETVAVIGLGYIGLPTAAILAENGVKVLGVDVSDRTVDAVNAGTVPFVEPDLAGFVA
+RGVEKGLLSASTTTPAADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLTGDELVILES
+TSPPGATEYMAEVIFAERPELREAELDFAHCPERVLPGRVMVELVTNDRIVGGSTRRAAE
+RARDLYRTFCEGEILLTDTRTAEMAKLVENSFRDVNIAFANELSVICAEQGIDVWELIEL
+ANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARLIRAAREINDGKPQWVIDQVKAA
+AFDVQQATGRAPVVAALGLAFKPNIDDLRESPALNIAAELAGQFSGSDVLVVEPHVTELP
+AALQGKDNVRLVAVDEALEAADIVVLLVDHSAFADLGDRVADKRVIDTRGQWRTDPSL
+>GCF_005280335.1_02051
+MTTQIKDVAVIGLGYIGLPTAAILAENGVRVHGVDVSQRTVDAVNAGTVPFVEPDLADFV
+ERNVKAGRLSASLKTPQADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLRGGELVILE
+STSPPGATEHMAAVIREARPDLDGATLDFAHCPERVLPGRVMIELVTNDRIVGGSTPEAA
+QRAKQLYETFCQGEILVTDCVTAEMAKLVENSFRDVNIAFANELSLICSDLGIDVWELIE
+LANHHPRVDILQPGPGVGGHCIAVDPWFIVDAAPQTARIIRAAREINDGKPKWVVDQAKA
+AAFDVQQATGRAPVVAVLGLAFKPNIDDLRESPALNIATEVAQQFTGSRILVVEPHVEEL
+PAALAGRDNVELVPAEDGIREADVVLLLVDHDAFASLGTTTEGKKVIDTRGQWR
+>GCF_020097155.1_01945
+MMGTPPALRCRDVNARMGIQNVTQIKTVAVIGLGYIGLPTAAILAENGLTVHGVDVSPRT
+VDAVNAGKVPFVEPDLADFVERNVAAGRLDASLETPKADAYIVAVPTPFQGDHAPDLSYI
+EAAARGLAPQLTGDELVILESTSPPGATDHMADVIREVRPDLKDAPLDFVHCPERVLPGR
+VMVELVTNDRIVGGSTPAAAERARDLYRSFCEGEILLTDCRTAEMAKLVENSFRDVNIAF
+ANELSLICAEQGIDVWELIGLANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARII
+RAAREINDAKPQWVIERAKAAAFDVQQKEGRPAVVAALGLAFKPNIDDLRESPALNIAAQ
+LADEFSGSTVLVSEPHVDELPAKLQGKENVRFVPAEQAVAEADVVLLLVDHDAFAGLGEQ
+TAGKRVIDTRGQWR
+>GCF_023573625.1_00843
+MTTQIKDVAVIGLGYIGLPTAAILAENGVRVHGVDVSQRTVDAVNAGTVPFVEPDLADFV
+ERNVKAGRLSASLKTPQADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLRGGELVILE
+STSPPGATEHMAAVIREARPDLDGVTLDFAHCPERVLPGRVMIELVTNDRIVGGSTPEAA
+QRAKQLYEAFCQGEILVTDCVTAEMAKLVENSFRDVNIAFANELSLICSDLGIDVWELIE
+LANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARIIRAAREINDGKPKWVVDQAKA
+AAFDVQQATGRAPVVAVLGLAFKPNIDDLRESPALNIAIEVAQQFTGSRILVVEPHVEEL
+PAALAGRDNVELVPAEDGIREADVVLLLVDHDAFASLGATTEGKKVIDTRGQWR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000772.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000772.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2f8d937399183a3543df26f5526d3ea91a526e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000772.fa
@@ -0,0 +1,29 @@
+>GCF_002008305.4_00896
+MSDTGDPRVPSGTAVLTVDGATLRRVGARPGLARYLASLWEYRSFILFDSRSRIAGANSV
+NALGRVWMVLNPILDGAAYFLVFGLLLGTGRGVPNFLGYLIIGVFLFRYTSSAITAGSRS
+ISTNLSIVRAFRFPRATLPIATNIRELMLFGPTLVVMLVLVLAIPPMEQITWRWLLLIPL
+LALQTLFNVGASLLLARYVARWSDLSNLIAFGTRIWLYVSAVFFSADRFADFPPMMTAMH
+LNPLFCVLDIARQSLLYASDADPMRWVVLAAWTAALLVVGTVVFWRAEETYGEER
+>GCF_003691675.1_00618
+MADTGDPRVPSGTAVLTVDGATLRRVGARPGLARYLASLWEYRSFILFDSRSRIAGANSV
+NALGRVWMVLNPILDGAAYFLVFGLLLGTGRGVPNFLGYLIIGVFLFRYTSSAITAGSRS
+ISTNLSIVRAFRFPRATLPIATNIRELMLFGPTLVVMLVLVLAIPPMEQITWRWLLLIPL
+LALQTLFNVGASLLLARYVARWSDLSNLIAFGTRIWLYVSAVFFSADRFADIPPLMTAMH
+LNPLFCVLDIARQSLLYASDADPMRWIVLAAWTAALLVVGTVVFWRAEETYGEER
+>GCF_005280335.1_02043
+MSGTGMAASGPVNTVVVDAAPLGVVGARPSLRDYVLSLFRYRSFILFDSRSRISGANAVN
+TLGRLWMVLNPILDGGAYFLVFGVLLGTGRGIPNFIAYLIIGVFFFRYSSQAITAGSKAV
+SSNLTLVRAFRFPRATLVLATNLRALLEFVPTLAVMVVLILAIPPLEVFTWRWLLLVPLL
+ILQTLFNVGLSLVLARFVAHWPDLANMIAFGMRIWLYLSAVFFSVERFDGQPIVQTAMHL
+NPLYCVLDIARQSLLYGQDAEPHRWLVLAGWAALVAVVGLVVFWRAEETYGEER
+>GCF_020097155.1_01941
+MTDRVEATSPPVELRVDESRLERVGRRPSLGDYVTRLWRLRHYVRYDAVAAVQAQNRRHR
+LGNVWLLLNPILNGATYFLVFGVLLRTSLGVENFIGYLTVGVFMFTFTTRAVTALSRSLT
+ARNNVADAFQLPRAVLPLTALAREVLAYGFTLAAMLLAVLILPPHAQVTWWWLLFPVVVA
+LQLMLVAGVGLLLARAVSRVRDLSQIVGFGIRLWMYGSAVFYSFDRFVSQPNVLAVLQLN
+PMYQVLDISRDLLLYGRSPSPVAWGILAAWSVGLLVVGVVVFWLGEERYAKDLNR
+>GCF_023573625.1_00847
+MLDAIFYWLIFGLLLRFDHGMDNFVAFVIVGVFMFQMTSAALTSGTRTIASNLSLTRAFR
+FPRMALPLADLVYDVLQRLPAIAVMFILVIAIPPHETPEWSWLVFPGVLGLHVILNFGIM
+LLLARLSTLLPDVSRMVPFVSRLLMYGSGVIFPITRFTDNHPALHAIIQLNPLYVLITMY
+RQVIIEGVTPPASSWAMLAAYAVCLTIVGGIVFWLGEESYGRDQYR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000773.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000773.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82e08bcc7c4d3ab28dd2ef1bf642d25ee8c7a910
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000773.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00897
+MPKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLN
+IIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAG
+LRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALLE
+AVGHQVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLP
+AHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPV
+LVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGDGRAAER
+TVSAIAELLGVGERLPAFDGGDPA
+>GCF_003691675.1_00619
+MPKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLN
+IIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAG
+LRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALLE
+AVSHQVPFEDERLAGLEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLP
+AHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPV
+LVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYSAMSQAVNPYGDGRAAER
+TVSAIAELLGVGERMPEFAPDDRG
+>GCF_005280335.1_02044
+MKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLNI
+IQPRQTLNGVFARTLDGLDAILEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAGL
+RSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALLEA
+VGHQVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLPA
+HRNPVVREAILPEIEGRANVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPVL
+VMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGDGRAAERT
+VSAIAELLGVGERLPAFDGA
+>GCF_020097155.1_01942
+MPLKIMPIYGTRPEAIKMAPIVNALRADDRFECFTTVTGQHREMLDQVNAIFGITPDADL
+DIMRPNQTLNGIMSVMLEGLDELLVRERPDAVVVQGDTTTSTAGAIAAFYRGIPVVHAEA
+GLRSGDLFSPFPEEANRKITSQIASLHLAPTSVSRANLEREAIDSAAITVTGNTVIDALL
+ETVAQQLPFTDPRLAELAERRAADPQSRVLLVTTHRRENQGEAMRGVGRALARLAQSHPN
+LTIVLPAHRNPVVREAVLPTLEGIDSVIVTEPLPYGEFTRMMDLADVVLTDSGGVQEEAP
+SLGKPVLVMRDNTERPEAVHAGTVRLIGTDEERLVEETSLLLTDPDAYAAMAHAVNPYGD
+GRAGLRTVAAIAQLLGVGDRLDEFGA
+>GCF_023573625.1_00848
+MPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLNIIQP
+RQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAGLRSF
+DILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALLEAVSH
+QVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLPAHRN
+PVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPVLVMR
+ENTERPEAVTAGTVRLIGTDEEVVVTEVTRLVTDEAAYTAMSQAVNPYGDGRAAERTVSA
+IAELLGVGERLPAFDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000774.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000774.fa
new file mode 100644
index 0000000000000000000000000000000000000000..caa02863c94c24ca8e6759aad3e1365153190042
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000774.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00900
+MPSSPPAARVPLPTEIKVMVAAAFVIAIGFGIIAPLLPQYAEMFASDFANPATAVAAVVS
+AFGLTRLLFAPVSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQDYTQLLLYRALGGVGS
+TLFTVSAMAFLASKSPPTIRGRVSGAYASAFLIGNIVGPIVGSVLAVFGFRVPFLIYGTS
+LVIAAGIVFVMLRDTRLQDRARGETRPVMPLRAALGHRSYRAALTSMFANGWATFGVRNA
+ITPLFAASAFTGTALLGWGITEENRQLMAGLALSVFAAGNVLAVASSSRLSDLHGRKPLI
+LVGLAVMAVFTGAIGWLESPLLFLVSCALAGAGTGTLNAPQQAAVADLVGQDRKAGPVMS
+AAQMSGDLGAILGPLLVGLVVDAAGYGWGFVVTGAVIAVGALAWARAPETNLPVAPGGPR
+TGSLPKVDPDVDPCRMEGRELG
+>GCF_003691675.1_00620
+MAVMPSSSARSSRVPLPREIKVLVAAAFIIAIGFGIIAPLLPQYAATFDASAVGVAAVVS
+AFGLTRLLFAPVSGKLTNRLGETPVYMTGVLIVAASMFLVAFAQTFPQLLLFRALGGVGS
+TLFTVSAMAFLARKSPPTMRGRISGAYASAFLIGNIVGPIVGSALSVFGYRAPFLIYGSS
+LVVAAALVFFLLKDTRLADRAVRDVRPAMPVREALSNPSYRAALVSFFANGWATFGVRNS
+VMPLFAATAFAGTGLLGWQVDGAMMAGLALSVFALGNVVAVSFSSRLSDVHGRKPLILTG
+LLVMAVTTGAIGWVGTPSLFLIACLVSGAGTGILNAPQQAAIADVVGQDRRSGSVMSSAQ
+MSADLGAIVGPLAAGLVVDVAGYGWAFVVTGAVILLGAIAWWRAPETNLPVVPGGPRTGA
+LPKIEPEDARPPHREDG
+>GCF_005280335.1_02041
+MPSSSSRTARAPLPREIKVLVAAAFIIAIGFGIIAPLLPQYAASFNASATAVAAVVSVFG
+LTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQTFAQLLAFRAIGGVGSTLF
+TVSAMAFLARKAPPSMRGRVSGAYASAFLIGNIVGPIVGSALAVFGYRAPFLIYGTSLVI
+AAALVFFMLKDTRLADRAARDARPAMPVKEALENPSYRAALVSFFANGWATFGVRNSVMP
+LFAASAFAGSGLLGWQVDGALMAGLALSVFALGNVVAVTFSSRLSDMHGRKPLILTGLLV
+MAVTTGVLGWMQSPLLFLLACLVSGAGTGVLNAPQQAAIADVVGQGRRSGAVMSSAQMSA
+DLGAIIGPLLAGLVVDAAGYGWAFVLTGGVILLGALAWWRAPETNLPIVPGGPRTGSLPL
+VRPEDARVTPREDG
+>GCF_020097155.1_01939
+MPTTPSAARAPLPREIKVLVAAAFVIAIGFGIIAPLLPQYAERFASDFANPATAVAAVVS
+AFGLTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMYLIAFAQDYTQLLVFRGLGGVGS
+TLFTVSAMAFLASKSPPSMRGRVSGAYASAFLIGNIVGPIVGSVLSVFGYRVPFLIYGTS
+LVIAAAIVFFMLKDTRLHDRAAADSRPVMRLREALDHPSYRAALVSMFANGWATFGVRNA
+VTPLFAASAFTGTALLGWTVTQENQALMAGLALSVFAAGNVAAVTFSSRLSDVRGRKPLI
+LLGLAVMAVCTGVIGWMTSPLLFLVACLLAGAGTGTLNAPQQAAVSDLVGQGRKAGPVMS
+VAQMAADLGAISGPMLVGLVVDGAGYGWAFAVTGAVLAVGFLAWLRAPETNLPIVPGGPR
+TGSLPKIAPEDVAPPHHREA
+>GCF_023573625.1_00849
+MAVMPSSSARSSRVPLPREIKVLVAAAFIIAIGFGIIAPLLPQYASSFNASATAVAAVVS
+AFGLTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQTFEQLLLFRALGGVGS
+TLFTVSAMAFLAAKSPPTMRGRVSGAYASAFLIGNIVGPIVGSALAVFGFRAPFLIYGTS
+LVIAAGMVFVLLRDTRRADRGTGDPRPTMPLKEAFGLPSYRAALASFFANGWATFGVRNS
+VMPLFAATAFAGTGLLGWQVDGAFMAGLALSVFALGNVVAVTFSSRLSDVHGRKPLILTG
+LLTMAATTGVIGWMSSPALFLLACLLAGAGTGTLNAPQQAAIADVVGQGRRSGAVMSAAQ
+MSADLGAISGPLLAGLVVDTAGYGWAFVLTGGVILLGALAWWRAPETNLPIVPGGPRTGS
+LPLVRPEDARVTPREDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000776.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000776.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a0623e6e30e2dae77b5acdf51285ed6cd9fd611
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000776.fa
@@ -0,0 +1,43 @@
+>GCF_002008305.4_00903
+MNEMTLDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWIL
+WVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRARF
+LTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAALV
+LALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLAA
+AAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASAL
+AVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVAV
+VVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPADA
+QAHRGGAAG
+>GCF_003691675.1_00622
+MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV
+LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK
+FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSEDGAIGARLGEALDFAGGLVVHISAGVAAL
+VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGGVDELGLIWVDTLA
+AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA
+LAVNLKYRLGFDDSLDVVGVHLTSGILGTVLIGFFALPGEGRAGLFYGGDAGLLVAQTVA
+VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESAYDVGFGGVPVPAEAR
+>GCF_005280335.1_02039
+MNEMTLDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWIL
+WVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRARF
+LTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAALV
+LALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLAA
+AAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASAL
+AVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVAV
+VVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPADA
+QAHRGGAAG
+>GCF_020097155.1_01937
+MTETTPLDAGAVWTVTAAALVLLMTPGLALFYGGMTRAKSALNMMMMSFVSMGLIGVAWI
+LWAYGMTSGDGLAGIVGSPLNDLGAVQSMADGDLISVGFSATFAIIAVALISGAVADRAK
+FSTWCVFVPVWVTLVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL
+VLAMMMGKRQGFGVDAAHRPHNVPFTMLGAALLWFGWFGFNSGAASDVEQLGLTWVTTLV
+AAAAGMLGWVLVEWLRRGRPTSIGTASGIVSGLVAITPACAFVSPLGAVVIGLVAGAACA
+LAVNLKYRWGFDDSLDVVGVHLTAGILGTLLIGLFALPETGHAGLFHGGDGSLLLAQTVA
+VVVAVVFTAVVTAVIAFVLRATLGLRVSVEEEERGVDLTLHDETAYDVGFGGVPVPTDAQ
+ARSTAAAE
+>GCF_023573625.1_00851
+MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV
+LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK
+FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL
+VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGSVDELGLIWVATLA
+AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA
+LAVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPDEGRAGLFYGGDAGLLVAQTVA
+VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESAYDVGFGGVPVPAEAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000778.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000778.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3386259b22987bb35a33a8d0bb57a6015c45f97a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000778.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00905
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAAEAPAEDAEKSE
+>GCF_003691675.1_00624
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAEEAAEAPAEDAEKSE
+>GCF_005280335.1_02037
+MAVKIRLKRFGKIRAPYYRIVVADSRTRRDGRAIEEIGKYHPTEEPSYIEVDSERAQYWL
+SVGAQPTEQVAALLKITGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKAEE
+PKAKESAEAETPAEEAPEAPAEDAEKSE
+>GCF_020097155.1_01935
+MAVKIRLKRFGKIRAPYYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKITGDWQKFKGEAGAEGTLKTKGEKEAFVAPAKESVILPEEPKQEE
+APAESAEAEAPVEEAADAEAPAEDAEKAE
+>GCF_023573625.1_00853
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAEEAAEAPAEDAEKSE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000780.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000780.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6805fa177b273dd85dd04546ed8b1e22e38c6bac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000780.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00907
+MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT
+RARWNKQILVVGFEESPDRNVAETLRGAQLFAVPAAPEESDEWYEEDLVDLEVRVDGERV
+GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDPEAGVLVLTPPPGLLELATGE
+DEGAADGPTDADAED
+>GCF_003691675.1_00626
+MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT
+RARWNKQILVVGFAESPDRNVAETLRGAQLFAVPAVPEESDEWYEEDLVDLEVRVEGERV
+GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDSEAGVLVLTPPPGLLELATGE
+DEGAVDGPADADAED
+>GCF_005280335.1_02035
+MSPAPQDGLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGATLTVRDGGPSLPAELTVT
+RARWNKQILVVGFEQSPDRNTAETLRGAQLFAAPAAPEESDEWYEDDLVDLEVRVDGRRV
+GVVTALTTGAVQDLLHVALDGVDEEALVPFVEEIVPEIDPEAGVLVLTPPPGLLELASGE
+AEQDDDAAASDAEADADAGREG
+>GCF_020097155.1_01933
+MSPAPQPAETEGQVRVARIGKPHGIRGEVTVQLFTDDPEARFAADSRLEVRQGPPGAPAA
+LTVTRARWNKAILVVGFAEVPDRNAAEALRGAQLYAAPLEKVEDDAWYEDDLLDLEVHVD
+GARVGVVTGLLTGTVQDLLQVRLDATGDDALVPFVEEIVPEVDQEAGVVVVAPPPGLLEL
+ASETTAGEG
+>GCF_023573625.1_00855
+MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT
+RARWNKQILVVGFAESPDRNVAETLRGAQLFAVPAAPEESDEWYEEDLVDLEVRVEGERV
+GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDSEAGVLVLTPPPGLLELATGE
+DEDAADGPADADAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000782.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000782.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76fe54cd95cd1b2b0f0a7467d16ee9ec7d240046
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000782.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00909
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGHGVRETFRV
+RKVSFGIGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK
+>GCF_003691675.1_00628
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGYGVRETFRV
+RKVSFGIGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRADAK
+>GCF_005280335.1_02033
+MHILDSLDSNSLRSDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRNGYGVRETFRV
+RKVSFGVGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK
+>GCF_020097155.1_01931
+MHILDSFDKASLREDIPAFGPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGHGVRETFRV
+RKVSFGVGVERVFPVHSPVIDKIEVLTKGDVRRAKLYYMRDRHGKAARIREKRADAK
+>GCF_023573625.1_00857
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGYGVRETFRV
+RKVSFGIGVERVFPVHSPIIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000784.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000784.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9231df38e1afb199eb0671bb70b07428f6bc828
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000784.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_00911
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
+>GCF_003691675.1_00630
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
+>GCF_005280335.1_02031
+MSRPDHRLVPPAAGHAHDSGAAPADDAARPAGPTGALLGHAVPSGAGSQALPAEPGRGPL
+RAVLAVVVLTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPEPYPVRRGDVV
+VFDDTKGWLADGGHVIKRVVGLPGDTVSFTPGEAALRVNGVPVAEPYLAPGDAPAQDAFE
+ATVPAGRLWVLGDHRSASADSRAHRDGPGGGFVSLDDVVGRARFVVWPLDRIGGAGAAPE
+AFEAVPDARGAGS
+>GCF_020097155.1_01929
+MAEAPVTPAAAGTADPAAAPAAEHPGHPLRAAAVTVAVTLALLLAVQLLLVRMFAIPSAS
+MEPTLRPGDRVAVDLLVPGPLELRRGDVVVFRDARGWLAGAEAVHADPLHAAVAALGLGT
+QEGHLVKRVVGLPGDRVRWSPEDARLEVNGVPVDEPYVAGPAAQEAFDVVVPDGGLWVLG
+DHRSASQDSRQHQHGPGGGMVSVDDVVGRVEGVVWPLDRAGAVGPGPLAKLP
+>GCF_023573625.1_00859
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000785.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000785.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0aec259a3a5ad2639051fa064395ad9f5ff854b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000785.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00912
+MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW
+LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR
+AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA
+ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA
+PAQAPPTLFD
+>GCF_003691675.1_00631
+MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW
+LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR
+AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA
+ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA
+PAQAPPTLFD
+>GCF_005280335.1_02030
+MTGSERAPRAGARTAVRAGLDVEAGLAAPFLAAGGTDRVLVAGMDEVGRGALAGPVVVGV
+CAAWLPAEGEIPAVRDSKALTDRRRRALVPEIRAWAAAVALGEANPAEIDALGISAALGL
+AGRRAWAAVCAAAGQEPVALVLDGRDDWLTRSDPDAGPAPAPRPVPPVPTMLVKAEDRCA
+TVAAASIAAKVARDDTMIALHADHPAYGWAGNKGYGAAAHRAAILDHGAGEHHRRSWSLG
+LPAAPADEPPTLFD
+>GCF_020097155.1_01928
+MSPRPPVVRAGLDVEASLAEAAIGPGASALVAGMDEVGRGALAGPVTVGVCAARVPALGV
+VPAVRDSKALTDRRRRALASEIEAWAAGVVLGEASPAEIDRLGITRALALAGCRAWAGLL
+AALGEEPVALILDGSDDWLRHARGGGMDDVVTGPVPPAPHMMVKAEDRCATVAAASIAAK
+VGRDDAMIALSAAHPAYGWAGNKGYGAAAHRSALVELGVTEHHRRSWNLGVPGTGAEPDV
+LF
+>GCF_023573625.1_00860
+MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW
+LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR
+AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA
+ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA
+PAQAPPTLFD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000787.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000787.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bcc96f35b67a2c0dab83d675026613a29e32bf25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000787.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00914
+MTGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP
+>GCF_003691675.1_00633
+MTGTAERIGAQPPGDRRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP
+>GCF_005280335.1_02028
+MTGTAEKVGADSPGGGRGSRAHTALGRFGEDAAARWLADRGYVIADRNWRGEAGELDLVA
+HHAGWWVGVEVKTRSGLAFGDPLESIDRRKLLRLHRLTAAWVRAHGEGRRAERWRVDAVA
+VLVPRTGGIRFDLLQDVRP
+>GCF_020097155.1_01926
+MVPLDTTTTTPAARRGSTAHTALGRYGEDAAARWLAERGYQIVARNWRGEDGELDLVARH
+GPWWVGVEVKTRSGLAYGDPLEAIGRRKLLRLHRLTAAWVREAAAREGRPLRSQQWRVDA
+VAVLVPRTGGVHFDLVQDVRP
+>GCF_023573625.1_00862
+MTGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000788.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000788.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b957dc8716a8005cd1dec76e001054af276a5ecc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000788.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00915
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
+>GCF_003691675.1_00634
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPARAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTAQGFDGDIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAARVAAAADRQARRWATAAERGLAPSGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
+>GCF_005280335.1_02027
+MSGIGRTRSISLSGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGAGHDLAIVLAAYAADGRVRGVEGPVFLAELGLDGALHRSPE
+TVAMVMASVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVILAFGGEPEGEAPQRRP
+VRPADDDGAPGLGPGAPDLSEVAGQAEARFALEVAAAGAHHLLLRGAPGAGKTMLAERLP
+GILPPLDRRTALECAALRSLRGADALARRGVGQGSAGTRAAGDLDRTPPFEAPHHSASMA
+ALVGGGANLARPGAVSLAHGGVLFLDEAPEFERRALESLRQPLESGEVLLHRARGTVAYP
+ARFQLVLAANPCPCGKGGGNGVECRCSVTERRRYGQRLSGPLLDRVDLQVTVRPVQARQL
+AGAPAAETSAQVAARVAEAARRQAERWARAAEEGLVAPGLRRNAHAPAGVLRHGPYAVPR
+AARRAADEAVDHGLLSARGHARVLRLAWTLADLRGAETPAPEDTDVALTLRHQEEDET
+>GCF_020097155.1_01925
+MSGIGRTRSISLTGLRGTVVDVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGAAHDLAIVLAAYAADGRVQGVDGPVFLAELGLDGTLHRAPE
+TVAMVMAAVDAGHDRVVVAADAVAEAELVPGARVRGFAHLHEAILAFGGRPDASVARPSG
+PSGTAGRGPAAGQEGPSGPVPDLAEVAGQAEARFALEVAAAGGHHLLLSGPPGAGKTMLA
+ERLPGILPPLDDRTALETAALRSLRGLEPSARGLRRTPPFEAPHHSASMAALVGGGTGLG
+RPGAVSLAHGGVLFLDEAPEFERRALDALRQPLESGEMIVHRAHGSVAYPARFQLVLAAN
+PCPCGFGSGTGAHCRCTSLQRRKYAARLSGPLLDRVDVQVSVRPVRADQLAAAPEAEPSR
+AVAARVAAAVAAQDARWAAAAREGSLPPGVCRNAHVPAALLRSGRFAVPPEARATADRAV
+DRGELSARGHGRVLRLAWTLADLRGASCPEAQDVEIALQLRIRSEEDR
+>GCF_023573625.1_00863
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000789.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000789.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85717418cb0d2c72289ea5511cef48317b008c25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000789.fa
@@ -0,0 +1,44 @@
+>GCF_002008305.4_00916
+MTTHVTPAADHVAGPRRPDAARLARAALTRLVEPGDALAVQTVTALGPERALALLTGRET
+IQPAERDLLADLAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA
+WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC
+VISGGAYGIDGAAHRAALQAPAAPEDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM
+AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG
+VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQGPARSGDTGGRTSARAAPEPAA
+RPTDGLTMEEALVHEALPLRQAVPADRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR
+RG
+>GCF_003691675.1_00635
+MTTYVTPAADHVAGPRRPDAARLARAALTRLLEPGDALAVQTVTALGPERALALLTGRET
+IQPAERDLLADRAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA
+WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC
+VISGGAYGIDGAAHRAALQALAAPGDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM
+AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG
+VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQAPARSGGAGGRASTRAAPEPAT
+RPTDGLTMEEALVHEALPLRQAVPADRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR
+RG
+>GCF_005280335.1_02026
+MTADTAHDHPVAAAQGPDTQRPDAHRPDTQRPDAQRPDTQRPDAARIARAALTRLVEPGD
+ALAVHAVAALGPERALVLLTGREAIQPAERDLLAEHAGAPDTLARRWSAGLDRWAPRAAR
+LDPVRDLVALHRLGGGLLVPEDEAWPAALDDLGEAAPLGLWFRGPGTLPPASRALAVVGS
+REATAYGRAVTTRLAAHAVQQGVCVVSGGAYGIDGAAHRAALAAPVGPEDPDAHDGPGGA
+SDRVPPTVAVLAGGLDRFYPAGHEDLLREVMAAGLLVSEMPPGASPTRYRFLQRNRVIAA
+LAGAVLVVEARWRSGAQNTAGHAFGLGREVGAVPGPVTSPSSAGCHRLLQETPARLVTSE
+TEALALLDGGAPAPRPGGTGGGNTAPPGDAPAPPPGGTGEGTRRPPRPPPPPRPCGSRTG
+>GCF_020097155.1_01924
+MTTAGETAQNARPDGPRVARAALTRLVEPGDDLALATVAALGPERALTLLTGAARIEAAE
+RDLLADRLGQDAFARRWSAGLARWAPRSARLDPVRDLVALHRLGGGLLIPEDPAWPAGLD
+DLGDAAPVGLWFRGRGTLPPLPRALAVVGSREATAYGRQVTRDVVACASAAGVCIVSGGA
+YGIDGAAHEAALETAAAAGRRSGPGSHDDAAPGVPPTVAVLAGGLDRFYPAGHERLLRAV
+MEEGLLLSEMPPGATPTRYRFLHRNRLIAALSGAVVVVEARWRSGAQNTAGHAHGLGREV
+GAVPGPVTSPSSAGCHRLLQEGPTRLIADPAQALTLLEPPRPGEPPAASPATTTRGEASR
+SPGRPTDGLTVEELLVHEALPLRRAVPVDNLTSSAGLALPTVLAVLTRLEGRRLAERRGD
+LWRRAPE
+>GCF_023573625.1_00864
+MTTHVTPAADHVAGPRRPDAARLARAALTRLVEPGDALAVQTVTALGPERALALLTGRET
+IQPAERDLLADLAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA
+WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC
+VISGGAYGIDGAAHRAALQALAAPGDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM
+AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG
+VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQGPARSGGAGGPSSTRAAPEPAA
+RPTDGLTMEEALVHEALPLRQAVPVDRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR
+RG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000790.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000790.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85c872ab04ff3a4f00d1204473ea9a1aa98bc2e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000790.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00917
+MAPSSSVRPAPAPRAPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLHSLIDYVAGTA
+ATAGTPPVDDDAPARHGPSAPDVLPELDIEDLRGWLAAMSGSGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQERVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WERLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA
+>GCF_003691675.1_00636
+MAPSSSARPAPAPRAPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLRALIDHVAGTA
+GTSGSPAADDDAPARHVPSAPDVLAELDIEDLRGWLAAMSGAGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQDRVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WQRLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA
+>GCF_005280335.1_02024
+MASSSSSARPAAARAFAPSPRDAAWLEAFEEHLRHERNRSPQTVRAYATDLRDLVAHVAS
+GTWGGHPGTATSEAAVEADAVAPDVFAEVDVEDLRGWLAAMTDAGLARTTLARRVAAVRT
+FTGWLRREGLREDDPALRLRSPRPAATLPHVLQEQQAERLLAGAQARVAEAAVGDDPAAH
+ALALRDAALLELLYATGARVAELSALDVDDLEPGRAVARLTGKGDRQRTVPYGAPAARAL
+DAWLRLGRPRLARDGSGPAVFLGVRGGRLGVRQVRAVVDRALEGLGDTAARGPHALRHTA
+ATHLLDGGADLRSVQEVLGHSSLRTTQVYTHVSIDRLREGYRQAHPRA
+>GCF_020097155.1_01923
+MHPPHAHHAPGAPLPPASARDEAWLEAFAEHLLHERGRRPRTVRAYLADLRHLAAHVTDD
+GADAFAEVDLEDLRRWLARMRDQGLSRATVARRVAAARTFLGWLHRSGLRPDDPTLRLRA
+PAPDSRLPQVLQAEQAQRLLQAAEERVHEARRADDLHGAALAARDVALFELLYATGARVA
+EVAALDVDDLDLDRRTARLTGKGDRQRTVPFGAPAAAAVERWLRVARPVLATEHSGVALL
+LGARGGRADVRVLRGAVDRALERLGDTAARGPHALRHTAATHLLDGGADLRSVQELLGHS
+SLQTTQRYTHVSVDRLRDGYRRAHPRA
+>GCF_023573625.1_00865
+MTPSSSARPAPVPRDPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLHSLIDHVAGTA
+GTSDTPAVDDDAPARHASSAPDVLAELDIEDLRGWLADMSGSGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQERVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WQRLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000791.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000791.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8526bf3b33519835c74b709ffb4e88dd56f321df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000791.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00918
+MTSTHTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
+>GCF_003691675.1_00637
+MTSTHTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
+>GCF_005280335.1_02023
+MTSTTTRGVVHILSAPTALCPHVEWALSSVLGPETPVEWQGQPVAPGQHRTELRWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNTMVSEDRIRY
+AYEAGAGEPAVLLHELSLALGEAWDEELEPFRLAAADANVRWLHRVG
+>GCF_020097155.1_01922
+MPDITTNGVVHLLSAPTAVCPHVEWTLTSVLGPGDPVDWRDQPAEAGTVCAELHWSAAQG
+SGARLASALRRWPGLRFEITETPSAGVDGSRWSHTPELGVFHATTDVSGNIMVSEERIRY
+AYEAGGGDPTVLVHELSLALGEAWDDELEPFRRAAAGAPVRWLHRAG
+>GCF_023573625.1_00866
+MTSTQTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000792.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000792.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43832429dfe92a33ef69d3a072cd60709542906d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000792.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00919
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLVRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKARGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADITPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>GCF_003691675.1_00638
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLIRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKARGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADIAPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGEHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>GCF_005280335.1_02022
+MTRTAVITGLGATTPIGGDVPTFWSNALKGVSGARTMEHEWVEELGLPVTFAAELAVPTA
+DVLSKVEQKRQDPGTQMATVAAREAWRDAGLEGVELDGDRLAVAFGTGIGGVWTLLDGWD
+ILRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLIRS
+GQADVVICGASEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+VESEEHARARGARVYAELAGTGVTSDSHHITAPEPEGLGATRAMRAALKAADLTPEDVCH
+VNAHATSTPKGDAPEYLAMKAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLENQDPEIPLNVVTGSPAQLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>GCF_020097155.1_01921
+MTRTALITGLGATTPIGGDVPTFWANAQKGVSGAATMQHEWVEQYDLPVTFAAELAVPTS
+EVLSKVELKRQDPSTQMATVAAREAWADAGLADADVDPERLAVAMGTGIGGVWTILDAWD
+ALRERGPRRVMPMTVPMLMPNGAAGALSLEFGARAGARTVVAACAAGTEALDTALTLIRT
+GQADVVLCGATEAAVHPMPMAAFAAMQALSKRNDDPQSASRPYDVDRDGFVLGEGAGVMV
+VESEEHAAARGARVYARLAGTGVTSDSHHITAPEPEGLGATRAMRRALADAGLRPEDVGH
+VNAHATSTPKGDAPEYLAMKAVFGTGLDDVLVSATKSQTGHLLGASGAIESILSVLAVHH
+GVAPVTINLENQDPEIPLNVVTGTPAALPADRRVVVKNSFGFGGHNAVAVFTGV
+>GCF_023573625.1_00867
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLVRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKTRGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADITPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000793.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000793.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74b905d8acd1f3f8ca2590d7bb29bf610cdaa0bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000793.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00920
+MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA
+>GCF_003691675.1_00639
+MASKEEILAGLAEIVNEETGLDAAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA
+>GCF_005280335.1_02021
+MASKEEILAGLAEIVNEETGLDTADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDNAQA
+>GCF_020097155.1_01920
+MASKEEILAGLAEIVNEETGLETADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDQAQA
+>GCF_023573625.1_00868
+MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000794.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000794.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67c392bc90f69483ca26f04b160eb883bc9e88ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000794.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00921
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLIGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSQLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP
+>GCF_003691675.1_00640
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSQLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP
+>GCF_005280335.1_02020
+MTVTLKQHERPAASRIVSVGAYRPKNLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATAGE
+TVPAMAVAAGREALERAGLTGADLDAVIVSTVTFPHATPPRPPSWPTSSAPPPAPAFDVS
+AACAGYCYGVAQADALVRAGTAKHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWETISFTHSQLELRDVVEQARTSGDASAITGSEEMVWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLVAFIPHQANMRIIDEFAKQLKLPESVTVARD
+IADAGNTSAASIPLAMHRLLEEDPSLSGGLALQIGFGAGLVYGAQVVRLP
+>GCF_020097155.1_01919
+MTVTLKQHERPAGSRIVSVGAYRPATLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATPEE
+TVVTMAVGAGREALQRAGLEASDLGAVVVATVTFPYPTPSAAAAVADALGATPAPAYDIS
+AACAGYCYGVAQADALVRAGSAQHVLVVGVERLSDFIDPTDRSISFLLGDGAGAVVVSAS
+DEAGIAPSVWGSDGSRWSTISPTRSLLDLRAEVEHARETGDASAIIGAEEMLWPTLRQDG
+PSVFRWAVWSMAEKAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IAEAGNTSAASIPLAMHRLLQEHPELSGGLALQIGFGAGLVYGAQVVRLP
+>GCF_023573625.1_00869
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLIGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSRLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000795.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000795.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b46f928159ed2fed484cf737bf712e9dce4e3357
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000795.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00922
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLAPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLATHVAGLSPSDPRLPLLSNRDGETVESGTDVLARIV
+DQVTRPVRWDLCMATMAARQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
+>GCF_003691675.1_00641
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLTPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLAAHVAGLSPSDPRLPLLSNRDGEAVESGTDVLARIV
+DQVTRPVRWDLCMATMATRQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
+>GCF_005280335.1_02019
+MLAIVCPGQGSQTPGFLSPWLELDGTRALLESLSDAAGVDLVRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPASTLVAGHSVGEITAAAVTGVLSPADALALVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIEAADLAPANVNGAGQIVAAGTAEALAALGESAPAR
+ARVIPLKVAGAFHTEHMRPAVEELAAHVAGLSPADPRLTLLSNRDGQAVDAGAEVLSRIV
+DQVTRPVRWDLCMEAMAEREVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHTA
+>GCF_020097155.1_01918
+MLAIVCPGQGSQTPGFLAPWRELEGVPSLLDRLSAAAGVDLTAHGTVSDEETIKDTAVAQ
+PLIVAAGLVAADVLGLDALAPDRVLAAGHSVGEITAAAVAGVLSPEDALALVRVRATGMA
+EAAAATPTGMAAVVGGDQDEVLAAVEAAGLTPANVNGGGQIVAAGTQDALDALAAQPPAR
+ARVIPLKVAGAFHTEHMRPAVDALAAHVTGLSPADPRLTLLSNREGAAVASGTEVLERIV
+NQVTRPVRWDLCMEAMAERGVTGIMEVLPGGTLAGLAKRGLKGVPSLAVKAPDDLDAARA
+FIAEHTA
+>GCF_023573625.1_00870
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLAPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLAAHVAGLSPSDPRLPLLSNRDGEAVESGTDVLARIV
+DQVTRPVRWDLCMATMATRQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000796.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000796.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ed4bb506785ce4d4d858a67d9d97b7c64e89ef8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000796.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00923
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALAPWFAPGPVIVGPVVDSLVSAHVSARHTLAGLSAAAAHPRASRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD
+>GCF_003691675.1_00642
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALAPWFAPGPVIVGPVVDSLVSVHVSARHTLAGLSAAAAHPRASRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGAGSD
+>GCF_005280335.1_02018
+MPEPRSAASRPVSTEGRARLRSHLGALNTAVLQRLDATLPWYRGLTPDERSALGLVAQRA
+LQGFISWFDRPKTTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPIREHVLHYSREVAFALADVYARAAEMRGAMDSRLEAVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHRVMVMAGLAPGQDQPAFIPGLRRAAAKLDCDLLVGVQAERLVLVIGSVTDAQ
+VVGEALTPWFAPGPVILGPVVDSLVEAHVSARHTLAGLGAAPAHPRAIRPTPAEDLLPER
+ALLGDPTACEALVEGVYAPLADAGTALLDTVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAVTLGRLAGSRPGVAEASA
+>GCF_020097155.1_01917
+MPAPRPSAPRRVSADGLARLRAHLGTFNTATLRRLDETLPWYRELTPDERSALGLIAQRA
+LQGFITSFERPQTTTVDVLRDVFGQSPTELTRAISLHRALQLIRTIVDVVETGVPDAVSE
+ADQPVVAEHVLHYSREIAFAIADVYARAAELRGAMDSRLEAVLLDAVLRGQEPDEIQHRA
+TAFGWRGGDGVMVMAGSARDGATAAFLPGLRRDAARLQCELLVGVQSRRLVLVVGSVSDP
+DAVAEALLPWFADGPVIVGPVVDSLLEAHVSAHHALAGLGAAAAHPRAGRPARSDDLLPE
+RALAGDATACAALVDGVYAALADAGPSLLETVDVYTACGHSLEGTARELYVHANTVRYRL
+RRAAEVTGWDPQRPRDAYVLQTAVALGRLSEGAPRL
+>GCF_023573625.1_00871
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLHRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALARWFAPGPVIVGPVVDSLISAHVSARHTLAGLSAAAAHPRACRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000798.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000798.fa
new file mode 100644
index 0000000000000000000000000000000000000000..772859f69f37f2d67a38e9286204a69f7042a8e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000798.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00925
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEDALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG
+>GCF_003691675.1_00644
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEGALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG
+>GCF_005280335.1_02016
+MEAGSTPTSTDSALLAELALAQGDLVQEWGYDDDVDFTFRDGLEDALGEELLTEEDQEPA
+DAVLYWWRAEDGDVTDLADALVDAQRSLDSGPVWLMTPRKGRAGHVNPADVQEAAGTAGL
+HATTGAGVSEDWAAQRLVQKRGG
+>GCF_020097155.1_01915
+METPSDGTSTHQELLDAYGLTAGELVQEWGYDDYIDFDFRDALEDALGEELLTEEDQEPA
+DAVLFWWRTDDGDVSDLTDALVDAQRSLDAGPVWLMTPRNGRPGHVSPTDVAEAAATAGL
+HVTTGAGGSADWAAVRLEKRGG
+>GCF_023573625.1_00873
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEDALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000799.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000799.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a61fd8f847e4235dc8bf3e31af2d5468141fe6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000799.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00926
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR
+>GCF_003691675.1_00645
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDEVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DAETGRPRRVSVLLDADGVEAARVVAAPGQARTRGEHEAATRDLLVDR
+>GCF_005280335.1_02015
+MAEEPGAVPALRDDRGQDWPWPPTRGPEDAAAPRATWLVLLPGAFTPVCTGELGWLGELA
+TDLAADDVAVRVIACDAAPVLRRVREELGLPEDLVLLSDFWPHGAACAALDAFDAASGRA
+RRVSVLLDADGVEVSRVTAAPGRPRSRTEHEAATRALLGDR
+>GCF_020097155.1_01914
+MAEPALRDIHGTPWPWPPVVSGERAAWLVFLPGAFTPVCAGELAWLGPLAVELAAEDVGL
+RVVSCDAAPVLREVADRTGLPAECVLLSDFWPHGAAAARFGLLDETTGRPRRVSVLVDES
+GTELVRVRPGEPGGPRTAQAHRRAAEGALGRRR
+>GCF_023573625.1_00874
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000801.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000801.fa
new file mode 100644
index 0000000000000000000000000000000000000000..013807375037829d9f6a3ed3b03c3186e2f107a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000801.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00929
+MTGAAYLVAAAVVAGLVTFCLRAVPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD
+AAALAPGEPVDGTRVAHALFAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA
+>GCF_003691675.1_00648
+MTGAAYLVAAAVVAGLVTFCLRALPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD
+AAALAPGEPVDGTRVAHALIAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA
+>GCF_005280335.1_02011
+MTDAAYLVAVAVVAGAVTFALRALPFALLRPLRESVLAARLAVWMPAGVLTILAVVMLLD
+AAALAPGAPVDPRRVAHALIAAVVTVAVHLLGGRRTLLSIAAGTLAYVLLVNLA
+>GCF_020097155.1_01910
+MIDGVVHPGYIVAAALVAGGVTFLLRALPFVLLRPLRESRLVARLAVWMPAGILTILAVV
+MVLDSAALAPGDPVDWPRVGCTLAAGAVTVLVHLLGGRRTLLSIGAGTLAYVLLVNLAL
+>GCF_023573625.1_00877
+MTGAAYLVAAAVVAGLVTFCLRALPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD
+AAALAPGEPVDGARVAHALIAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000802.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000802.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52858d255cbd4a2a511630d1ba46e67e991e9499
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000802.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00930
+MGLLRDLLTRRSARDRSSDPPATLGRHLDNAAAIVAAARRADVPLAVAAALAELESGGRN
+VFGHDAGGVHSAPRGTDVLVTRERYEELVARVAQGETSNGVGPAQITWPPYFAQAAERGL
+HLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLSDGVTAYGRRLAAASRAWA
+ERLGEPAPPPVRPG
+>GCF_003691675.1_00649
+MGLLRDLLTRRSARDRSSDPTATLGRHLDNAAAIVAAARRADVPLAVAAALAELESGGRN
+VFGHDAGGVHSAPRGTDVLVTRERYEELVARVAQGEKSNGVGPAQITWPPYFAQAAERGL
+HLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLSDGVTAYGRRLAAATRAWA
+ERLGESAPPPVRPG
+>GCF_005280335.1_02010
+MATTPSVGRMSWFPRRRAASAPRALAARLENADAIAAAARRADVPLPVAAALAQLESGGR
+NVFGHDAGGVHAAPRGTDVPVTRELFEELEARVAAGETSNGVGPAQITWPPYFAQARRRG
+LRLWEPEDNMAFGLEILRGHLGGDLTEEGIARAGTLYNAGTLQGGVTDYGRRLARASRDW
+ARRLGEPAPPSSSPGRGAGRDGDRGRARSGAPGRTHVIEPGDTLWAIARANGTDVATLRR
+LNPDLVPEALAVGAPVRLP
+>GCF_020097155.1_01908
+MDPVTVLSASLAHPEAIVAAAGRARVPVSVAAALAELESGGRNVFGNDVGGVFSSPGAPD
+VEVTPERVAELRRRVADGERSNGVGPAQITWPPLFDRADAEGLDLADPEDNMTLGLSLLR
+DSARGDFSVAGLERAGTLYNAGTLAGGVTDYGRRLAAAAAAWERRLTARG
+>GCF_023573625.1_00878
+MGLLRDLLTRRSARDRPSDPTATLGRHLDNAATIVAAARRADVPLPVAAALAELESGGRN
+VFGHDAGGVHSAPRGTDVPVTRERYEELVARVAQGETSNGVGPAQITWPPYFAQAAERGF
+RLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLTHGVTAYGRRLAAATRVWA
+ERLGELAPPPVRPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000803.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000803.fa
new file mode 100644
index 0000000000000000000000000000000000000000..335c9b8c45976d87468da7db3993fc414cc4bbb2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000803.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00931
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART
+LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA
+TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG
+>GCF_003691675.1_00650
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART
+LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA
+TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG
+>GCF_005280335.1_02009
+MLFLQDGQWSILGLFQDELAGKATARTLDALLQSVTCLRMGGRDVLDGADTPRPGVEWAG
+YDREFEEADVAESRDVEPHGRIWILPATDGATVGLKLPGHRRYHDAVAQFADVDAARAAV
+AAIDELLGVGPRG
+>GCF_020097155.1_01907
+MPATPHGFWKLPAPSDAGPRHLAVITGGEAEQTMLFLQDAAGWHVLALFQDELAGRTTAR
+TLDRLLQSVTYLRMGGADLMDGADTERPGVEWAGYDREFEEQDAADETAADPAARLWILP
+ATDGASVGLKLPGHPRYADAVAQFVDAGTARAAVDAVDALIGARRPGAARPAAD
+>GCF_023573625.1_00880
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART
+LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA
+TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000804.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000804.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba853a09515550a445d82ba6557066ece743d09b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000804.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00932
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP
+LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
+>GCF_003691675.1_00651
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP
+LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
+>GCF_005280335.1_02008
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHLNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRSGVERVMGFSTDEQYRRFMNQVP
+LFEKMLADDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
+>GCF_020097155.1_01904
+MELLQPDAPRENLREFIDNLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYEERLSR
+EEYEIEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHLNPRTARTVA
+LSKPTERELGQWYFQRYIQHFPTAGEIVLFDRSWYNRSGVERVMGFSTDHQYDLFMRQVP
+VFEKMLVEDGVHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIKSNDKKRARLNAMRYFLSRFEYEGKDHDVVGVPDPLIVQRGRD
+AVGD
+>GCF_023573625.1_00881
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP
+LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000810.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000810.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5cb80aa08d214aa8760602f1403476e16b146cd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000810.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00938
+MSEVTAPPAVQARLLELQELDTALDQARAAVHRLQADPEHARLRARAQEFEEALPGLQDA
+ARTADRAGAEATEKAAATRARRDRTRERLETGQGGPKELQAMQHEDDTLTALLDDHEAAA
+LEAMEATDAAESRLSKGHAALERARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF
+PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI
+LIRD
+>GCF_003691675.1_00657
+MSEVTAPPAVQARLLELQELDTALDQARAAVRRLKADPEHARLRARALELEEALPGLEDA
+ARTADRAGAEATEKAAATRARRDRTRERLEAGQGGSKELQAMQHEDDTLTALLDDHEAAA
+LEAMETADAAESRLAKGHAALEQARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF
+PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI
+LIRD
+>GCF_005280335.1_02001
+MSEVTAPPAVQARLLELQELDTALDQARTQIRRLKADPELARLRARAQELEDALPEVEDA
+ARTADRAGAEASEKAAATRARRDRTRERLEAGQGGSKELQAMQHEDGTLTALLDEHEGAA
+LEAMEAADEAESRLAAARQALEQARAEVDARAAEVRREGQVVTQRGRDLTQRRTALAAVF
+PAPLLALYEKARERNGGIGAARLVGRRSQASGTELSPADVARIEALPPAAVARCPESGAI
+LVRG
+>GCF_020097155.1_01898
+MNRVTAPAAEQARLLELQQLDLGIGRAKTRLAQLRADAALADLQKAVAAAEEAAAEQEAH
+ERETDAAAAQASERATTTRARRDRTRAHLDAGDGGSKELTALQHELEGLESLLAEHEGAA
+LAAMEAADEAEEALARARAAVDEARAAVAARADEVRAEGRRVTEEGRELAALRAGLAGRL
+PADLLARYEEARAANAGIGATRLEGRRTGAGTELSPADLDAVLATPADEVAVDPETGILI
+IRA
+>GCF_023573625.1_00887
+MSEVTAPPAVQARLLELQELDTALDQARAAVRRLKADPEHARLRARAQEFEEALPGLQDA
+ARTADRAGAEATEKAAATRARRDRTRERLETGQGGSKELQAMQHEDDTLTALLDDHEAAA
+LEAMEAADAAESRLAQGHAALERARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF
+PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI
+LIRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000812.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000812.fa
new file mode 100644
index 0000000000000000000000000000000000000000..128bed29038ccb6607391f7dbbc442c041c14d95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000812.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00940
+MLILLPPSEGKTAPRSGAPLDLDALALADDAAVTGARADLLTRLAAVSAAPDALAALGVG
+ASLTGEVEANTRLASAPAAPGHRVFTGVLFDALDHASLSAAAKRRARASVLVFSALFGAT
+ALADRIPAFRLPVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA
+PAERTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLERVADVVARAGDG
+HGWEVELARPSGAKPGALRVILPEG
+>GCF_003691675.1_00659
+MLILLPPSEGKTAPRSGAPLDLDSLALADDAAVTGARADLLTRLAAVSAAPDALTTLGVG
+ASLAGEVEANTRLAVAPAAPGHRVFTGVLFDALDHASLSAAAKRRARLSVLVFSALFGAT
+ALADRIPAFRLPVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA
+PAEQTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLDRVADVVARAGDG
+PGWEVELARPSGGKPGALRVILPEG
+>GCF_005280335.1_01999
+MLILLPPSEGKTAPRSGAPLRLEDLALAEHDAVTAARRDLLARLAEASAAPDALETLGVG
+ASLAGEVAANTSLATAPAAPGHRVFTGVLFDALDHASLSPGAKRRARDAVLVFSALFGAT
+SLADRIPAHRLSVGARLPGLPGLAAHWRPVLAPALDAVAQADGGPIVDCRSGGYAAMWKA
+PAERTATVDVFQLRGGEPTVVSHFAKHTRGLVARALLEAGARATGALDRAAEVVAAAGAG
+DVEGRRWDVELVAPSGAKPGSLRVVLPEA
+>GCF_020097155.1_01896
+MLILLPPSEGKTGPRSGRPLDLSSLTLADDDAVTAARAELLPRLAEASARPDALDILGVG
+ASLADEVAANTRLATAPSAPARKVYTGVLFEALDLTSLSPAAKRRAASDVLVFSALFGAT
+TPGDRIPAYRLPVGARLPGMPGLAAWWRPRLAPALDGYAEARGGVVVDCRSGGYAAQWKA
+PAERSLAVDVFQLRAGRRTVVSHFAKHTRGLVARALLEAGSRAAGTPATAADVVARAGDG
+GVPGQRWEVELVPPTGRKAGSLQVILPEE
+>GCF_023573625.1_00889
+MLILLPPSEGKTAPRSGAPLDLESLALADDAAVTGARADLLTRLAAVSAAPDALTALGVG
+ASLAGEVEANTCLASAPAAPGHRVFTGVLFDALDHVSLSSAAKRRARASVLVFSALFGAT
+ALADRIPAFRLSVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA
+PAERTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLERVADVVARAGDG
+HGWEVELARPSGAKPGALRVILPEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000813.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000813.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a61cec7035d033097269c7cb956b062cde15663
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000813.fa
@@ -0,0 +1,14 @@
+>GCF_002008305.4_00941
+MTAMNVFGVVYPFVLLVIAAAVWLGIRSSGRERTHASAVEQRLRERTFTGQDRVTLEWPR
+DRRRPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF
+>GCF_003691675.1_00660
+MTAMNVFGVVYPFVLLVIAAAVWLGVRSSGRERTHASALEHRLRERTFTGQDRVTLEWPR
+DRRHPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF
+>GCF_005280335.1_01997
+MTLEWPRDRRRPTPAKVVAIAESYGYRLLEKRERDHVIELDFERIRDDEGF
+>GCF_020097155.1_01895
+MQTIPVMGWVFPVVLLVIAAAFWLGVRSSGGARGDSDLERRLRERTFTGAPRARLEWPRD
+RRRPTLAQLVRIGASHGYRLVSRTEAEHVYILDFQRVEDDDL
+>GCF_023573625.1_00890
+MTAMNVFGVVYPFVLLVIAAAVWLGIRSSGRERTHASAVEQRLRERTFTGQDRVTLEWPR
+DRRRPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000815.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000815.fa
new file mode 100644
index 0000000000000000000000000000000000000000..302286f0865712e5ec6f6aa89288330e1b8d8052
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000815.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00943
+MASIRPVTVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQEAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREEPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHDADDHEDHEHGPDGDHGDDEA
+>GCF_003691675.1_00662
+MASIRPITVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQDAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREDPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHDADDHEDHEHGPDGDHGDDEA
+>GCF_005280335.1_01995
+MASIRPITVYGEPVLHTRAAEVEVIDDEIRRLVEDMYVTQDAARGVGLAAPQVGVGLRVF
+TWTYPHSGDAPSVGHVINPVLTVLDKASQEATDPDEHTEGCLSVPGHGYPLQRAPRVRLA
+GQRVDGEMFEFVAEGWFARVMQHEYDHLNGTLYVNRLEGRWQRRWKRAQRAERMNVPGVT
+WLPGTDEDPFGHDELDEAEAIEQHGPDADHGRADGA
+>GCF_020097155.1_01892
+MPSIRPITVYGEPVLHTRAAEVEVIDDSIRELVEDMYVTQDVANGVGLAAPQVGVGLRVF
+TWTFQDTGDAPNLGHVINPVLTMLSKPSTEEPDRHEDTEGCLSVPGHGFPLKRSAHVRMT
+GQRMDGSTVDIEATGWFARILQHEYDHLNGTLYVNRLEGKWARRWKRAQRAERLNVPGVT
+WLPGTDPDPFGHDVDVDEDAPAHEHHDHDHEGHDHAQEAR
+>GCF_023573625.1_00893
+MASIRPITVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQEAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREDPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHEEIEDHEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000817.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000817.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7f256c70d88c9a52b82c81a03cb629db4fb64b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000817.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00956
+MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSAAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAEVVSGAQA
+>GCF_003691675.1_00669
+MSETSTPAPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNTLDEGIDLVIRPSAAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAEVVSGAQA
+>GCF_005280335.1_01931
+MSETSTPAPENAPLVWIDCEMTGLHPHVDELVEVAVLITDAELNILDEGIDLVIRPSEAA
+LAQMDPFVRDMHTTSGLLPELEHGLTLENATARVMEYLTARVPAGKALLAGNTVGQDKLF
+LSAYMPAVVEHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY
+RAAVMAPSPGPTSEEAQAIARVVAEAQA
+>GCF_020097155.1_01883
+MSETSTPAPESAPLVWIDCEMTGLDPDVDVLVEVAVLITDSELNVLDEGLDLVIRPTPEA
+LAQMDPFVRDMHTSSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNSVGQDKLF
+LARYMPAVIDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY
+REAVMVPAPGPTSEEARAIAEVVSGAQA
+>GCF_023573625.1_00902
+MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSEAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAQVVSGAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000819.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000819.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a844ab653c76061aa5a210ecb678e43b43ea946
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000819.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00959
+MTSHPRSPAPSRPSGRWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGLLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAALAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHIVALVWLMTTVVKDILDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGARDRLLLPPAGLGLQPLGESAGR
+>GCF_003691675.1_00672
+MTSHPRSPAPSRPSGRWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGLLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAALAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHIVALVWLMTTVVKDILDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGAPDRLLLPPAGRGLQPLGGSADR
+>GCF_005280335.1_01929
+MRRAGLAPTPAPPGLPERETAPPEPAVAVRQGTWAAVLIMVGSWGVGWLPMTPDSVFSGS
+TLLNPLRVNLPGVLASTLLLASGSLLLVRAWLVLGRSLRGRWEGHGRLVSRAAWQWSAPL
+MLALPIFSRDVFSYLQQGRLFALGLDPYTQGVSALPGWFMQGADSIWAESPSPYGPLFLL
+CAEAIWRVTGGQIELSVTAFRLLALAGLALCLWAVPRLAEAAGRCGAWAAWVCVANPLFL
+LYMIAGVHNDALMSGLMLAGIVLMVRVPRRRLHALWGIVLIALSVAIKPLTALVLPFVGL
+LLPTGWDRFRRADPGLRRRDRLGPWITTAAIALAVLTILGAGSRLWFGWVPAMLTSGDAA
+FPYAPVGVLGLLLGAAADGLAGLPARAVAGGFYTLMTLAALGFGAWLALRRRAPEPVSAA
+AAVLFVAVVTAPIVQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTALAVLLLTGVGVV
+DQISVAQWLPVAAVRALTAVVVLAGIAWIVVRDPATAPLFPGRRRPPREVVEPREAVGPR
+EPGAPPGPPTAAPDAEFPPDALAADPDRRRRPAPDRRPARPGETVTSQPRRPADTRTGSA
+AAPPSPAALRPGPRWIGILVGLTAVAAVVGLLTKQWCRVNGWAAPGVHVHMCYSDFAQLF
+PTRGLSDGYFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPDSGDLHERTVMYFDVNALGV
+VLCWVVLVIATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAHRPT
+LAGLLIGLGTALKLYPLFFFGAILVLALRTGRWRGLITSLAAGVAAWLAVNVPFMLTAFD
+QWSRFYTFSGDRAVSFSSTWLSLAWTGWSGETFSTLQNGMFALFCAGIAWLGLSARHRPR
+MAQLCFLIVASFLLWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWMESA
+RITSGGAFADGAWWITAWYASGIVAHIVALVWLMVTVVKDILDPSRDPVRRTALAQGAPT
+IAPGVAEDPHAGVYAGAPDRLVLPPAGRGLQPAEGATSGS
+>GCF_020097155.1_01880
+MSSHPRAADAAPRPAAGLRPAGRPSPRWIGVLIAVTAAAAVVGLLTKQWCRLNGWATPGV
+HVHMCYSDFAQLFPTRGLSDGYFPFYTPLPEEQWMEYPALLAVVAGASSWLVPSTGTLAE
+RTVTYFDVNAAGVVLCWMAVVVATAFTARGRSKDALLVAVAPGIILTSMLNWDLWAVMLA
+ALALWAWSEDRPVLSGLLLGLGAAMKLYPLFFFGALLVLALRTGRWRGFLGALAAGAAAW
+LAVNVPFMLTAFDQWSRFYTFSGDREVSFSSMWLAFTWTGLSGSAFSVISNGLFALCCVG
+VAYLGLSSRHRPRLAQLCLLIVAAFLLLGKVYSPQFVMWLIPLVVLATPRRKQFWIWQAA
+EFFHWAGVWMESARITSGGEFGGTWVTVWYASGIVLHMATLIWICVTVIRDIRDPERDPV
+RRSALEQGVEPLAPGVAEDPNAGVFTGAADRFLLPPAGHGLQPTR
+>GCF_023573625.1_00905
+MTSHPRSPAPTRPSARWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWFVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGMLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAAVAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHVVALVWLMTTVVKDVLDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGARDRLLLPPAGRGLQPLGESAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000821.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000821.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3944ef74422c0ffc316463f56d13195b3000bca5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000821.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_00962
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDRETAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGERSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDDASGGRAGAVGDGFSAGLPDGFQGGDAPASPGPDESDAGAPGREPAAA
+GVA
+>GCF_003691675.1_00675
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDREAAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGERSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDASGGRAGAVGDGFNVGLPDGFQGGDAPASPGPGEPDAEAPDREPAAAG
+VA
+>GCF_005280335.1_01926
+MQDIITVRGFVATDPVTRTTASGATVAGFRLATTERRFDREAGAWVDAHTNWYSVSAFGQ
+LGSNTAQSVRKGNPVIVTGRLRVRDWSTEERSGTTVDVVADAVGLDLAFGSAAFQRSQRA
+ASARPEGADEQDGQGQAGAVASAGPAEADGTAAGTGDGYVTELPPALRGGDAPATPPPPS
+SEEGDEADEADDDAHGVRALCGGVSAA
+>GCF_020097155.1_01877
+MQDTVTIRGFVATDPTTRHTASGAAVVGFRLASTERRFDRDAGMWVDAHTNWYSVSAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSTEDRSGTSVDVVADAVGLDLAYGASAFMRNGRR
+ADAVERADAPVDADAGASLDAAPADGFGLALPPAFTGGDAPASSAEDAHEAAGALAVA
+>GCF_023573625.1_00908
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDRETAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGDRSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDASGGRAGAVGDGFSAGLPDGFQGGDAPASPGPDESDAGAPEREPAAAG
+VA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000822.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000822.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87bd6aaa3df26c9e259688ce5f4eb6912aee5273
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000822.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00963
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL
+MGEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV
+GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD
+RLGPEAARPHRMTHRKLTRD
+>GCF_003691675.1_00676
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL
+MEEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV
+GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD
+RLGPEAARPHRMTHRKLTRD
+>GCF_005280335.1_01925
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPEYTVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMASPDADFDAL
+MEEMGELQTAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLAAYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLHAYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIEGLSFSLPRNGIVGVIGPNGV
+GKSTLFKTIVGLEPLDGGELKIGETVKISYVDQSRANIDPEKSLWEVVSDGLDYIKVGQV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVE
+RLGPEAARPHRVTHRKLTRD
+>GCF_020097155.1_01876
+MSRFPPPPTSLERMAEFIYTMVKARKKVGDKLILDDVTMSFFPGAKIGMVGPNGAGKSTI
+LKIMAGLDEPSNGEARLSPGYSVGILLQEPKLDEDKTVLENVQQGVGEIYGKIQRYNAIS
+EEMADPDADFDALMEEMGQLQTEIDAADAWDLDSQLDQAMDALRCPPPEAQVSHLSGGEK
+RRVALCALLLSKPDLLLLDEPTNHLDAESVLWLEQHLSSYPGAVVAVTHDRYFLDHVAGW
+ICEVDRGRLYPYEGNYSTYLETKRQRLEIQGKKDAKLAKRLAEELDWVRSNAKGRQAKSK
+ARLARYEEMAAEAEKTRKLDFEEIQIPPGPRLGNVVIEATNLQKGFDGRTLIDGLSFSLP
+RNGIVGVIGPNGVGKTTLFKTIVGLEPLDGGDLKIGETVKISYVDQNRTNIDPEKSLWEV
+VSDGLDYIKVGNVEMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLL
+LDEPTNDLDVETLTSLENALLEFPGCAVVVSHDRWFLDRTATHMLAYEGTEENPANWYWY
+EGNFESYEANKVERLGPEAARPHRVTHRKLTRD
+>GCF_023573625.1_00909
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL
+MEEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLADELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV
+GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD
+RLGPEAARPHRMTHRKLTRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000824.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000824.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b62f4028dd0d53cb0516db538b76b42e7300d94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000824.fa
@@ -0,0 +1,37 @@
+>GCF_002008305.4_00966
+MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFTAITLRPEVTLQDEAD
+RERAEALHAEAHRLCFIANSLSAPVAVEPVRPEALPTGAPTLPDHSARLGAPLAVLRPRV
+AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPAGATPGTPAAPGQAASFYD
+AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG
+HPRLRMRHAPYRIDPAARNAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA
+>GCF_003691675.1_00679
+MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFTAITLRPEVTLQDEAD
+RERAEALHAEAHRLCFIANSLSAPVAVEPVRPEALPTGTSTLPDHSARLGAPLAVLRPRV
+AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPTGATPGTPAVPGQATSFYD
+AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG
+HPRLRMRHAPYRIDPAARDAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA
+>GCF_005280335.1_01921
+MKHTFALRTEWTGNRGTGTSGVRDYDRSVVIQDAAVGEIHASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGLVVTGMACAAEGVLEVDGDGAGRFAAVTLRPEVALQDEAD
+RERADALHAEAHRLCFIANSLSAPVSVEPAVAGSGAAASGGPALPDHSSRLGAPLAVLRP
+RVAKRPSQVTGLAERPTEVEPVMKAGAPAPVDQMQARDAAAGRAASPATPAPAAETAAPG
+QAASFYEAVGGRETFDRLTAEFYARVREDELLSPMYPQDDFEGAQRRLLMFLEQYWGGPR
+TYSEERGHPRLRMRHAPYRIDPAARDAWLTHMRAAVDTLGLSPLHEAELWDYLERAAHSL
+QNSA
+>GCF_020097155.1_01869
+MKHTFSLRAEWTGDRGTGTTGVRDFDRSVVIQESEVGEIHASAARPFRGDAAKWNPETLL
+LGALAECHVLSYLHAAATGGLVVTGMTCAAEGTLEVDSDGAGRFASITLRPEVALRDEAD
+RARADELHAEAHRMCFIANSISAPITVEAGPGSSPTRGDGAALPDHSARLGAPLAVLRPR
+VANRPTRVTGLADRPTEAEPVVRADAPSGAEQARARDEATARGERPPSATPIATPAPGAT
+PAASPATAAPGQATSFYEAVGGHPTFEKLVHVFYQGVREDPLLAPMYPHQDWDGAEERLR
+MFLEQYWGGPRTYSERRGHPRLRMRHMPFTVDPAARDAWLRHMRAAVDAVELSPLHEAEL
+WDYLERAAHSLQNSA
+>GCF_023573625.1_00912
+MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFIAITLRPEVTLQDEAD
+RERAEALHAEAHRLCFIANSLSAPVTVEPVRPEALPTGTPTLPDHSARLGAPLAVLRPRV
+AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPAGATPGTPAAPGQATSFYD
+AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG
+HPRLRMRHASYRIDPAARDAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000825.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000825.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a24b61d54ac312ee63671c65353551286ec1b0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000825.fa
@@ -0,0 +1,80 @@
+>GCF_002008305.4_00967
+MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN
+EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTGAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MVGVRAYIAKHAWQNTELPDLMTELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLIRTERFELDVAGEVTEVV
+EAAARRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLSALVDGTRTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAVWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADAYFEGVEAMWDSRSHEMAETAATLGYPTAQVTPEIADRATALSERL
+ADTRAGLSRVLAEGRDETIRALAAREHATAHVHQVHAGA
+>GCF_003691675.1_00680
+MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAGQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEDSRRTLGVVAN
+EENLQGVDAAVWEFTPTPRISSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTSQVSRETADRATALSERL
+ADTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA
+>GCF_005280335.1_01920
+MSSSARLNITREEAAQRAAALTVDAYEVSLDLTRGPERFRTASTVTFAASEDAVGTHTWI
+DFVASQAPEVTLNGERVAVEDYDGARLPIGPLAAQNTLVVEGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVEN
+EDQLSGVDAAVWEFVPTPRISSYITALVAGPYAAVHSELTSADGRTIPLGVYCRASLVEH
+LDADNVFELTRQGFEFFEAQYGHPYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEAMVERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTRYTGSWT
+TFSSMEKNWAYRQDQLSSTHPIKAQIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAKHAWSNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGV
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAAGRRRPALILPNDDDLAYAKLRLDHASWEAASTRLKDVDSSLARTLLWGAAWDAVRDG
+EASAAWFADLILANIGHEQDSSVVQTLLRQLATSLGQYLPEEQSTAARAAVADRLWGLVA
+GAEDGSDSQLQFVKAFALHARTAAQLDRLAGVVDGTHTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAAAEREDATATGALAAIQARAAVPTAEAKQAAWDRVMAGELSNTEQRQALIGF
+ARAHEAALLAPFADAYFEGVEAMWDSRSHEMAETAAVLGYPAAQVSDETAQRATALSEKT
+AGTRAGLSRVLAEGRDETVRALAAREHAAAHVHEVSASA
+>GCF_020097155.1_01868
+MTTAAAMNITREEAAARAAALTVESYQVALDLTRGAERFGSTTTVTFSAADEAVGTQTWI
+DFMATQAPEVTLNGQAVDVADFDGARLPIGPLAAENTLVVDGLADYTTTGEGLHRFVDPV
+DDEVYLYSQFEVPDSRRMFAVFEQPDLKATFAFTVTAPAHWAVVSNQPEAAHRTLGVVET
+PEAPEGVDAAVWEFTPTPRISSYITALVAGPYKSVHSELTSADGRTVPLGVYCRGSLFEH
+LDADEVFDLTRRGFEFFEAQYGHPYPFDKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VTDAVRERRAITILHELAHMWFGDLVTMKWWNDLWLNESFAEFMSTLAAAENTRYEGAWT
+TFSSMEKNWAYRQDQLSSTHPITAEIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIEKNAWSNTELPDLMTELEAASGRDLSEWTRLWLETSGVNTLAVQVDADYAGT
+ITSLRLHQSAPDGSPAAPGDDVLRPHRIAVGFYDLDEATGRLTRTERFELDAAGEVTEVA
+EAAGRRRPALILPNDDDLAYAKIRLDDASWETAGARLADVDSSLARTLLWGAAWDTVRDG
+EASAAWFVDLILTNIGREQDSTVIQTLLRQLATAISQYLPEERSAQVRADAANRLWMLVE
+QAEPGSDAQLQFVKAFALHAREEGQLTALADVWDRSSELPGLDLTTDLRWELLTALVAAG
+RAGETEIAAAETEDPTATGALAAALARAAVPTAEAKQTAWDQVVAGTLSNTTQRQVLLGF
+QRAHDPALLAPFTDAFFGSIQDVWGSRSHEMAETVAVLGFPSSQVCQEVVDRATALSDEV
+RGTNAGLARTLAESRDEMARALKARAAA
+>GCF_023573625.1_00913
+MTTVAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN
+EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAS
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTAQVTREIADRATALSERL
+AGTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000827.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000827.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a475ee1fcb221ce14ce354eb6aa2eedfe7723eb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000827.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00974
+MMHGSRPALRRAASALAGRRPLSLRGATVLVTGGASGIGRLIALGAARRGAGRVVVWDLD
+LQGAEAVAAEIRSQGADAQAERVDVTDAAAVEAAAARAGEVDVAVNNAGVVTGVRLEDAT
+EEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAV
+GFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPRHVAQEVLDAVE
+AGRTRLLLPRAVGLIAPLRALPAPVFDRAMDVLGVNATMDGFTGRRSRLFAGRETAR
+>GCF_003691675.1_00688
+MHGSRPALRRAASALAGRRPLPLHGATVLVTGGASGIGRLIALGAAHRGAGRVVVWDLDL
+QGVEAVAAEIRSQGADARAERVDVTDAAAVEAAAAGAGEVDVAVNNAGVVTGAPLEDATE
+EGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAVG
+FAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPHHVAQEVLDAVEA
+GRTRLLLPRAVGLIAPLRALPAPVFDRAMDVLGVNATMDGFTGRRSRLFAGRETAR
+>GCF_005280335.1_01916
+MPRSRTPRPALRALAGALPRRRRLPLRGTAVLITGGASGIGRLMALGAARRGAARVVVWD
+LDLSAAEAVAAEARALGAEAVAERVDVTDAAAVEAAAARAGAVDVAVNNAGVVTGARLED
+ATEEGIRRTFEVNALAPYWLTRAVLPGMKARDRGAVVVIASAAGLVGVARQTDYSATKHA
+AVGFAESLSAELRKDGSAVTALAVCPFYIDTGMFDGVRSRIPWLLPVLRQEEVAEQVLDA
+VEAGRTRLPLPRAVGLLAPLRALPTPVFDRAMDVMGVNDTMDGFTGRRPAVDVPAPDPRV
+FAPDGAAR
+>GCF_020097155.1_01863
+MTPILNRLRGRRPLPLAGRAVLITGAGSGIGRLMALEAARRGAAVVHVWDRDDAAARTVA
+AEVAALGARGEAACVDVTDTAAVEAAAARAEAVDVLVNNAGVVTGTPLLETTEEGIRRTF
+EVNALAGYWTTRALLPGMLERGRGAVVTVASAAGLVGVARQTDYSASKHAAVGFAESLRA
+ELRRADAPVTSLVVCPFYISTGMFAGVRTKVPALLPILEPEAVAAQVVDAVEAGRERLVL
+PPAVQLIAPLRALPVPAFDRVMDVLGVNRAMDGFTGRR
+>GCF_023573625.1_00917
+MMHGSRPALRRAASALAGRRPLSLRGATVLVTGGASGIGRLIALGAARRGAGRVVVWDLD
+LQGAEAVAAEIRSQGADAQAERVDVTDAAAVEAAAARAGEVDVAVNNAGVVTGVRLEDAT
+EEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAV
+GFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPRHVAQEVLDAVE
+AGRTRLLLPRAVGLIAPLRALPAPVFDLAMDVLGVNATMDGFTGRRSRLFAGRETAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000830.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000830.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07f84bcbae4f8670b683c00a68276457a6101cb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000830.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00978
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLQIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA
+>GCF_003691675.1_00692
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA
+>GCF_005280335.1_01912
+MTQFPAGLPTGTPSMPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGSQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIQAQEINRMRVWMEQTLASLTN
+RTPEEVSRDIDRDKFLSAEQALEYGLVDEVLASRKITRPAG
+>GCF_020097155.1_01859
+MTQFPAGLPVGTPSQAAPSARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGSQVDDAS
+ADDIMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHANEINRMRVWMEQTLASLSN
+RTPEDVSRDIDRDKFLSAEGAKEYGLVDEVLAPRKITRTGA
+>GCF_023573625.1_00921
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000831.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000831.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5852ded3ea96fd98609d566cdd1f61d9312f7760
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000831.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00979
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA
+>GCF_003691675.1_00693
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA
+>GCF_005280335.1_01911
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAADSDEMV
+LPTPQEIFDHLEGYVIGQEVAKRSLAVAVYNHYKRVRGPQGRGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGEVSYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPNNALLKQYQKLFLMDGAELEFEPE
+ALDAVVELAEARGTGARGLRSIMEDVLKPVMFELPSRTDVGTVVISGEAVRGEAEPVLIP
+AEVERRRRGRSA
+>GCF_020097155.1_01858
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAETDELE
+LPTPREIFEHLERYVIGQEAAKRSLAVAVYNHYKRVRGPQGRGGDLAERLEERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARMLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DHDVKRAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGSGEVSYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHDQLVRVLTEPKNALLKQYQKMFLMDGVELEFEPE
+ALDAVVELAQARGTGARGLRSIMEDVLKPVMFELPSRTDVGTVVISGDVVTGQAEPLLIP
+AEVERKRRRRTA
+>GCF_023573625.1_00922
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000832.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000832.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd019530698c1463fc4755ff66314aee73aa62bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000832.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00980
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD
+>GCF_003691675.1_00694
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD
+>GCF_005280335.1_01910
+MSENTQPVVDFYFDPTCPFAWITSRWILEVEKVRDIQVKFHQMSLYMLNEGRDLPEDYRR
+STDRGLIPGRGTQHVGAEHPERLAEWYTALGTRIHNEGQKDYEAALTGAAVDLGLDPAPI
+LAATETDAEDERLREKQRAAEELVGNDVGTPVVSFNGTAFFGPVLTRIPRGEEAGRIFDG
+AVALAEYPYFYEIKRARTTDPQFD
+>GCF_020097155.1_01857
+MSENTAPVVDFYFDPTCPFAWITSRWILEVEKVRDLSVTFHQMSLYMLNEGRELPEDYRR
+HTDRGLMPGRATLHVGEHHPELLSDWYTAVGTRIHNEGNQDYEAVVTGAAAELGLDAAPI
+LEATRTDAADDDLRAKQRAAEELVGNDVGTPVVSFDGTAFFGPVMTRIPRGEEAGEIFDA
+AVRLAQFPYFYEIKRARTTDPQFD
+>GCF_023573625.1_00923
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000833.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000833.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1f605ea3bbdea0baa20c1dacf84088415a85c1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000833.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00981
+MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARS
+>GCF_003691675.1_00695
+MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARS
+>GCF_005280335.1_01908
+MRRASAPRTDTAGATGTGARRMAAALAGMGVLHFARPKPFDGLIPPALPGPARAWTVGSG
+VAELAVAGMLAAPRTRRAGGRAAQALFLGVWPGNAWMAWRWRGRSWPWRALALGRLPLQV
+PMIRAAGRIARG
+>GCF_020097155.1_01856
+MKPTPDPAPAGRRASDGSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPHTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARR
+>GCF_023573625.1_00924
+MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000834.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000834.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce1289e66e17fb63989700c5a60a886b56274526
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000834.fa
@@ -0,0 +1,80 @@
+>GCF_002008305.4_00982
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLTRLAATVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVASLSFAASAGDAEVLPTVAQVLGGIRKAKSEAKVKQRTEVRSA
+VVTGPADWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPVDDD
+>GCF_003691675.1_00696
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLTRLAATVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVAALSFAASAGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA
+VVTGPTEWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPVEDD
+>GCF_005280335.1_01907
+MAENTQGTDTPIDASTASTPAAGAVAVPDKPGLEGLEEKLTARWAQEGTYAFDPRTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMTGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPTKPYIEGYTPPAQPAKNQRDWDVVSRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWSMTYRTIDDVSRAVSQRAFLRNVAAGDAYLSEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYPFTAADGTQVFIETTRPELLASCSALVAHPEDERYQPLFGTMVRSPLFDVEVEV
+KAHELAKPDKGSGIAMVCTFGDLTDVTWWRELQLPTRTLIGRDGRFAAETPEWISSEAGR
+AFYAESIAGKTVFSAKEAVVTALTEAGLMDGEPKKVQHAVNFYEKGDKPLEIVTSRQWYI
+RNGGRDADRREQLIARGRELDWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYRL
+DAEGEPVYDEPIVPEDAALPVDPVAETAPGFTEDQRDQPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEEFFANVFPFDLRPQGHDIIRTWLFSTVVRADALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILEEFGSDAVRYWASSARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATRDAVVRTPDDAARVTNALDASLLARLATTVEQATAAFDAYDYARALNVTE
+SFFWQFTDDYVELIKDRAYGGHGEAEQASVVAALATTLDSLLRLLAPFQPFATEEVWSWW
+RTGSVHRAPWPGLESEAAGLRAAAEGGDPQVLAVVAQVLGRVRKAKSEAKVKQRTQVRTA
+TVRAAAAQLDALRGGLADLKGAGNVADVTLTEADGELEVTDIELAPAEEA
+>GCF_020097155.1_01854
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDDAFFSSVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLARLAVSVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVASLSFAASSGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA
+VVTGPAEWLEKLRGGLADLKAAGNIADLSLTQGEAGEAAPLTVSDVQLAPVEDD
+>GCF_023573625.1_00925
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLARLAATVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVAALSFAASGGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA
+VVTGPADWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPAEDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000835.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000835.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae408cb20d50fa37d5234011e1d8414492437fab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000835.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00983
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
+>GCF_003691675.1_00697
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGVGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
+>GCF_005280335.1_01906
+MDVSHTTENQSPRAAVVTGATTGIGRATALELARRGWRVYAVGRRAERLDALAAQAREEA
+VPGEVVPAPLDVTDEAAVAGLVARVDTDGGIDTLVNIAGGARGTDFVGAGNREDWEWMYR
+ANVLGTLAMCQAFLPGLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTAALRLE
+EAEHNVRVIEVLPGMVHTEEFSLMRLGGDAAAAEKVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVIRPVAQAAQHKVIRR
+>GCF_020097155.1_01853
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAPLDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRTHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
+>GCF_023573625.1_00926
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000836.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000836.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23b959324b8127a907e849bd5380b3729914a59e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000836.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00984
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE
+APRGAAGGR
+>GCF_003691675.1_00698
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVSRVRAAGRRAVVAAHLLAPGHFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>GCF_005280335.1_01905
+MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAGDDVEPRLVAVLAER
+VAQAVPAGEAATSEVILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPPVPD
+AVSRVRATGRRAVAAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>GCF_020097155.1_01852
+MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAEDDVEPRLVTVLAER
+VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPRVPD
+AVARVRATGRRAVVAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>GCF_023573625.1_00927
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE
+APRGAAGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000837.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000837.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd6e36266a530076ad4ff2d48a80d70505cc71c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000837.fa
@@ -0,0 +1,48 @@
+>GCF_002008305.4_00985
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAHEG
+FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEISNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERVVRRYDEQREPGETFARWAHRVDEEALR
+>GCF_003691675.1_00699
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTTPLNHNEEFKQQDDGLNVRERIEQVYAREG
+FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEVSNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERLVRRYDEQREPGETFARWAHRVDEEALR
+>GCF_005280335.1_01904
+MVLDVEGDRVDAVVAGLKELGLDPEPSVFRRSTIACTGLEFCKLAIVDTKDTATAAIAQL
+EERLADLADRLPERLSLHVNGCPNSCARIQTADIGLKGQLLPDDDGGQTPGFQIHLGGGL
+ASVDRAEAGLGRSVRGLKVRADGLVDYVERLVRRYDEQREPGETFARWAHRVDEEALR
+>GCF_020097155.1_01851
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAREG
+FDSIPSDDLHGRFRWWGLYTQRKQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEVSNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERLVRRYDEQREPGETFARWAHRVDEEALR
+>GCF_023573625.1_00928
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAHEG
+FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEISNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERVVRRYDEQREPGETFARWAHRVDEEALR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000838.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000838.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84e00b4b093ce820b971ac7c3222172c09e4e94d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000838.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00986
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLDTGYHFTETLATRDEVARRLAVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
+>GCF_003691675.1_00700
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSLDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
+>GCF_005280335.1_01903
+MSTVPPTRPTEELERLQALAESGAAELGWDAPAAAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWTGTAKTECGIH
+V
+>GCF_020097155.1_01850
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
+>GCF_023573625.1_00929
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLDTGYHFTETLATRDEVARRLAVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHSMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000839.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000839.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2bdeaefb8b7c98422cf54dc4bdcc285e562b46c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000839.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00987
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
+>GCF_003691675.1_00701
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIVREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAENEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
+>GCF_005280335.1_01902
+MTLTHAPDPGTVSPAGPDVLDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPPIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
+>GCF_020097155.1_01849
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
+>GCF_023573625.1_00930
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000840.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000840.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68391a3164240b11883c78adae9128cc6f1216d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000840.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00988
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
+>GCF_003691675.1_00702
+MSTALLDRRAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPVRTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
+>GCF_005280335.1_01901
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARSGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYSEEVFTAIADDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVLRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPQDGATLAAGMVRGGDEA
+>GCF_020097155.1_01848
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPQVIVAVNKIDLVDYSEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPQDGATLAAGMVRGGDEA
+>GCF_023573625.1_00931
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000842.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000842.fa
new file mode 100644
index 0000000000000000000000000000000000000000..858ed8c40982816661fbf6a7ccd7898d8ee87381
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000842.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00990
+MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQAFAWLAGARGEPITGPGDVVGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLLLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHEGRAESDLAVVLCAVLAILAVGVLVELTAFGPAERRMLRRRG
+LLEGSTR
+>GCF_003691675.1_00704
+MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQAFAWLAGARGEPITGPGDVVGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLVLGQVGVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHEGRAASDLAVVLCAVLTILAVGVLVELAAFGPVERRMLRRRG
+LLEGSTR
+>GCF_005280335.1_01899
+MRTDTPTLDAPGRAPGAAADDELRELDSGLDALQAVDSARRTGLAGWDWSRVLLPVAAVV
+LLVAIWQVAAWLAGARGEPITGPGDVLGAFGALWAQGLVQQAVATSVGRAVVGFALAVVA
+GVGLGLLLAQVGVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVILTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGAPMGVGLGTLLHQGRTESDLAVVLCAVLAILAVGVLVELTAFGPVERRMLRRQG
+LLEGSTR
+>GCF_020097155.1_01846
+MRTDTPTLDAPGRAPGAAADDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQVAAWLAAARGEPITGPGDVLRAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLLLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHQGRAESDLAVVLCAVLAILAVGVLVELTAFGPVERRMLRRQG
+LLEGSTR
+>GCF_023573625.1_00933
+MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQAFAWLAGARGEPITGPGDVLGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLVLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHEGRAASDLAVVLCAVLTILAVGVLVELAAFGPVERRMLRRRG
+LLEGSTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000845.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000845.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb634fe3af148e170915acfb314f229b6cccfa0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000845.fa
@@ -0,0 +1,53 @@
+>GCF_002008305.4_00995
+MRGDAPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST
+ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL
+EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH
+TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQVLLEAAQAADVPFRFEGVEFGVLE
+RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE
+GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP
+GMLAALYRAFGDDVEDLAVTQSSSARAIPAGELARMAVDAGWPEDDVYATESVPDALEWA
+VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL
+DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR
+>GCF_003691675.1_00709
+MRGDVPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST
+ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL
+EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH
+TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQVLLEAARAADVPFRFEGVEFGVLE
+RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE
+GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP
+GMLAALYRAFGDDVEDLAVTQSSSARAIPAGELARMAVDAGWPEDDVYATESVPDALEWA
+VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL
+DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR
+>GCF_005280335.1_01894
+MSGAPAPQTVEQVYADLLARAPENAMEPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTS
+TARMIEAVLRSYGLRTGRYTSPHLQSVTERISIDGAPVSDETFVRVWGEILPIVQAVDAE
+LEAEGRPRLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGITDATNVADGAVSVVTPISLD
+HTDLLGETEAEIAEEKAGIVKPGGALVSAVQERDAAQVLLEAARAADVPFRFEGVEFGVL
+ERSLAVGGQQVSVRGLAAEYRDLFLPLHGEHQAQNLAVAVAALEMFLGGGDRPLDEELLR
+EGLAQVASPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLALVVGILREKDA
+PAMLEALFRAFGDDVEDLALTQSSSPRAIPAGDLARMAVDAGWPEADVFAAESVPDALEW
+AVGRAEALETSADELASGTGGGVLVLGSVTLAAEVRALVGEPRHAGPVTVAARGLDPADL
+PRRRRPGRGGRGRPGPRDPRAARGPRRRRLPPPHRGGPMSTPQPGTGRTPEEDERFGDES
+WRPERETRAQRAWRPGTRRRRRSVRALFTSTVLMLEAVVIFFLGMMLFGMNRDQPGAVWF
+IAGYTLLAAVAVLTCALVRRPVGIAIGWAIQAVLVLSGFWEYSMFVVGALFALTWAYAVI
+KGGGMDVENAERDRLQAEWEAEHGQ
+>GCF_020097155.1_01841
+MSAPAEGRVPGTVEEVYADLLARAPEHRMEPRLDPVRRVLALLGDPQHAAPVIHLTGTNG
+KTSTARMIEAVLRAYGLRTGRYTSPHLERVTERISVDGEPVADEDFVRVWGEILPMVHTV
+DAELEAAGEPRLTYFEAVTVLGFAVFADAPVEVVVLEVGLGGITDATNVADGAVSVVTPI
+SLDHTDLLGDTEAEIAEEKAGIIKPGGFLVSAAQDADAAQVLLEAARAADVPFRFEGVEF
+GVLERRLAVGGQQVDVRGLADEYRELFLPLHGAHQAENLAVAVAALEAFLGGGQRPLDVE
+LLREGLAQVTSPGRLEVLRTAPTVVVDAAHNPDGVAVTARAVQEVFSFTRLALVVGVLQE
+KDARTMLEVLHREFGDLISDVALTQSASPRAIPAGDLAALAVDAGWPEDDLFITESVPDA
+LEWAVGRAEAVETSADALASGTAGGVLVLGSITLAAEVRSLLGAPAHAGPVTVAARGMDP
+ADLLAAVGLEDDDADAVDPEVLELLDDREEHTR
+>GCF_023573625.1_00938
+MRGDVPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST
+ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL
+EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH
+TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQALLEAARAADVPFRFEGVEFGVLE
+RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE
+GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP
+AMLAALYRAFGDDVEDLAVTQSSSARAIPAGELVRMAVDAGWPEDDVYATESVPDALEWA
+VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL
+DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000847.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000847.fa
new file mode 100644
index 0000000000000000000000000000000000000000..222a397957d1828de54892b2d834bb9ed4521072
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000847.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00998
+MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIIIIVERTLLT
+ADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFARW
+YWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTLPA
+PAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
+>GCF_003691675.1_00712
+MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIIIIVERTLLT
+ADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFARW
+YWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTLPA
+PAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
+>GCF_005280335.1_01892
+MPSTPTADRVRPAQPAETPASDGTLSWYARPAGMAWTLLVTSLVALTATIVIIVERSILA
+ADPGHRTSCDLNPWVSCGRVMQSWQAMTFGFPNTYIGIVAFSVLITVAVSLFAGARFARW
+YWLLMNVGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNIQTGTLPA
+SPGAARLARELAWPVILILYVLVFATILLELGFGVIGLD
+>GCF_020097155.1_01838
+MDVTETAENPPAPRAHHAAHALPEDRSLSWYARPLGTAWMLLITSIVAVTATIIIIVERS
+ILAENPNYRTSCDINPWLSCGTVMQSWQAHTFGFPNTFVGIVAFPVLITVAVSLFAGARF
+ARWYWVLMNVGILAGFAFAAWLWYSAVYSIGTLCLYCMIVWAMVILQLVLVTSRNLQTGA
+LPSSPGLARLAQDFAWPVIVLLYALVFASILLQLGLGVIGIR
+>GCF_023573625.1_00941
+MSMPTTPPTDDVRLSPADDVPAEEARLTWYARPAGTAALLLITSLVALTATIVIIVERAL
+LTADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFA
+RWYWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTL
+PAPAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000849.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000849.fa
new file mode 100644
index 0000000000000000000000000000000000000000..617336ab63f93504b9868156a7f3d0e683ded5b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000849.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01000
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA
+>GCF_003691675.1_00714
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA
+>GCF_005280335.1_01890
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDKVTAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA
+>GCF_020097155.1_01818
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAEEGGSVELPALMLVDGDKVKAGADAADVKVTA
+EVVSHSRGKKIVIVKYKNKTGYKKRQGHRSELSTVKITGIA
+>GCF_023573625.1_00943
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000850.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000850.fa
new file mode 100644
index 0000000000000000000000000000000000000000..892b7b1e75ca2685e277bc548793b2c82fe26c34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000850.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01001
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
+>GCF_003691675.1_00715
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
+>GCF_005280335.1_01889
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
+>GCF_020097155.1_01817
+MAHKKAGSSSKNGRDSNPQYLGVKRFGGQDVNAGEILIRQRGTKFHPGRNVGRGKDDTLF
+ALSAGTVSFGQRRGRKVVDIVAAGE
+>GCF_023573625.1_00944
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000852.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000852.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c90c28beb63e109b78e21128ec87d9a795e4b0e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000852.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01003
+MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID
+RLVDVLAAERQKGTQVVLVSSGAIAAGFPHLGLSRRPKDTATQQASAAVGQSKLMAHYTT
+SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALARLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLCKADLLVLLSDVDALYTGHPSNPDARRIPEVTSDDDLSGVDVRVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGEDVGTWFSATGRRRSARAAWLGLT
+AEVRGRLIIDDGAVAGAIDRGRSLLAAGITGCTGAFTPGDVVEIVDAHGRVRARGLVQYS
+SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR
+>GCF_003691675.1_00717
+MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID
+RLVDVLAAERQKGTQVVLVSSGAIAAGFPHLGLGRRPKDTATQQASAAVGQSKLMAHYTT
+SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALSRLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLCKADLLVLLSDVDALYTGHPSHPDARRIPEVTSDDDLAGVDVRVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGEDVGTWFSATGRRRSARAAWLGLT
+AEVRGRLIIDDGAVAGAIDRGRSLLAAGITGCTGAFTPGDVVEIVDAHGRVRARGLVQYS
+SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR
+>GCF_005280335.1_01887
+MSARRTVVTRYPTPATRGAEDPRANPVTTRDTMAAARRVVIKIGSSSLTTATGLDVAAID
+RLVDVIAELRGRGTQVVLVSSGAIAAGFPHLGLDRRPKDTATQQAAAAVGQGRLLAHYTH
+SFGRHETEVAQVLLTAEELMRRTQYTNAHRALARLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLVKADLLVLLSDVDALYTGHPSLPDSRRIPVVATDADLEGVDVHVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAPNAGSAFAGEDVGTWFEATGRRRSARAAWLGLT
+AEVRGQLVIDDGAVAGAIDRGRSLLAAGIIGLSGRFTPGDVVEILDATGRVLARGLVQYS
+SSQLPRMLGRSTSDLKEDLGAGYDGVVVHADDWVRLAPPRR
+>GCF_020097155.1_01815
+MARRPSTVHRHATPSSRGAEDPKANPVHTRADIGAARRVVIKVGSSSLTTGTGLNTDAID
+ALVELVARLRGRGTQVVLVSSGAIAAGFPALGLSRRPKDTATQQAAAAVGQNRLVAYYSQ
+SFARFDTTVAQVLLTAEELMRRGQYINAHRALARLLTLDVLPIVNENDAVATREIRFGDN
+DRLAALTANLVKADLLVLLSDVDALYTGHPSRPGSRRIDTVTAETDLGGVDVRTPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAALASAALDGEDVGTWFSAAGRRRTARAAWLGLT
+AQVRGRLTIDDGAVAGAIDRGRSLLAAGITAAEGDFTAGDVVEIADAQGTVLARGLAAYS
+SSQLPRMLGRQTAQLKEEIGAGYDGVVVHADDWVRLAPTHSAFR
+>GCF_023573625.1_00946
+MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID
+RLVDVLAAERQKGTQVVLVSSGAVAAGFPHLGLGRRPKDTATQQASAAVGQSKLMAHYTT
+SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALSRLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLCKADLLVLLSDVDALYTGHPSNPDARRIPEVTSDDDLAGVDVRVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGQDVGTWFSATGRRRSARAAWLGLT
+AEVRGRLVIDDGAVAGAIDRGRSLLAAGITGCTGDFTPGDVVEIVDTHGRVRARGLVQYS
+SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000853.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000853.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9be80998aa039bc395718cdf0c6a23ebedafcd83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000853.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01004
+MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAVAGRARKDAVLRHMAE
+ALRANTAAILTANREDRSRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV
+VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA
+VLIQVLREALVDQGFDANIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYVDASAPKQMAVDIALNSKTHRTSVCNAAETLLLHRDAEETGREVL
+RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLGQ
+AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQIRR
+>GCF_003691675.1_00718
+MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAVAGRARKDAVLRHMAE
+ALRANTAAIITANREDRSRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV
+VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA
+VLIQVLREALVDQGFDANIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYVDASAPKQMAVDIALNSKTHRTSVCNAAETLLLHRDAEETGREVL
+RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLGQ
+AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQIRR
+>GCF_005280335.1_01886
+MENQESTAPQDQSAGQEAEAPSQEVVDAIRQRAEWARLAVPELATAGRTRKDAVLRHMAE
+SLRSNAAAIITANQEDRARGAEAGTSAALLDRLKLDEPRVEALALGLEALAALPDPVGAV
+VRGGTLPNGVRMTQTRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAQSTNA
+VLIQVLREALADQGFDPNVVQGIDDLGRPGVAALMATRGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYLDASAPKDMAVEIALNAKTHRTSVCNAAETLLIHREAEETGREVL
+RALMRGGVLLHVDEAAKAWLPGPTDRGDHARDAVDATEEDWGTEYLDMDMAVRIVDSLDQ
+AIEHIGRWSTGHTEAIVTNDLAAAEQFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQVRR
+>GCF_020097155.1_01814
+MTTEHTETEPAERVQQTPTPEQGASADGRPGADVVAEVRSRSARARAAAPELARAGRERK
+DALLRSMADAVRAAAASILAANAEDLARGEENGTSAAMLDRLRLDEPRLESLAVALEDLA
+SLPDPVGAVVRGGDLPNGIHMQQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNAVLLRG
+GSAAEHTNAVLIQVLREALRDQGFESDLVQGIDDLGRPGVAALMSTRGAVDVLIPRGGRE
+LIQRVVAEARVPVIETGEGNVHLFIDASAPADMAVDIALNAKTHRTSVCNAAETLLLHKD
+AERAGREVLRALTRAGVLLHVDEASRARLPSPADRGQDAREPQAASDEDWGREYLDMEMA
+VRTVDSIDEAMEHVRRWSTGHTEAIVTNDLANADRWVSEVDAAAVIVNASTRFTDGGQLG
+LGAEVGISTQRMHARGPMGLEELTTTKWVLRGAGQVRR
+>GCF_023573625.1_00947
+MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAIAGRARKDAVLRHMAE
+ALRANTAAILTANREDRGRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV
+VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA
+VLIQVLREALVDQGFDPNIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYVDASAPKQMAVDIALNAKTHRTSVCNAAETLLLHRDAEETGREVL
+RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLDQ
+AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQIRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000854.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000854.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d756d669a4b5b476eebc13a50fb54759b29a1e84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000854.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01005
+MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ
+HHGTGRGSHTSGH
+>GCF_003691675.1_00719
+MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ
+HHGTGRGSHTSGH
+>GCF_005280335.1_01885
+MLNTSLVLAAAEGPHVVNELPIPTVWYGIIVFALLMAALLATMSMRSRALRLPEPTTAVQ
+HHGTGHGSHTPGH
+>GCF_020097155.1_01813
+MLNSALVLAAAEEGHHVVNELPIPPVWFGIIVFLLLMAGLLAILSMRSVGLRHAEPTTAV
+QHHGTHGTGSHSAGH
+>GCF_023573625.1_00948
+MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ
+HHGTGRSSHTSGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000856.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000856.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33f92713b47f9ce5af5a882adaf248b9bfa934d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000856.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01007
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAATQDDGASASHAS
+>GCF_003691675.1_00721
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAATQDDGASASHAS
+>GCF_005280335.1_01883
+MTVPQTTLDALTVAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKEEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLA
+EEHTRPDAAGEGAADDAAPHAS
+>GCF_020097155.1_01810
+MTVPQTTLDALQVAAAAAAEKVATHIVAVDVAERLGLTDAFLIASGASERQVNAIVDGIE
+EDLLVKEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDSPAIDLGLP
+EEATRPDDALDAAAQD
+>GCF_023573625.1_00950
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAAAQDDDASASHAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000859.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000859.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53b5a755d458b9c0a7add8d4431b57d9ee1bc522
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000859.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_01017
+MYPTPMTFDVARAGRALAQVSARTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALLK
+YGVGLVPEDEFGGAGVRRIFSAEKSRRIKAMENEGGPAYEDDI
+>GCF_003691675.1_00731
+MYPTPITFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALLK
+YGVGLVPEDEFGGTGVRRIFTAEKSRRIEAMENEGGPAYEDDI
+>GCF_005280335.1_01870
+MYPTPMTFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALRK
+YGVGLVPEDEFGGTGVRRIFTAEKSRRLEAMENEGGPAYEDDI
+>GCF_020097155.1_00705
+MESQHISNGDMTRAARILVKVSAQYIAREANVTKEELRDFEKGRHDLSEKKQERVRAALE
+ELGAEFLPDGPNGGYGIRLKFGRSRIYSLERCEGEGGPRLTTESDRRTQAHVPFSEPDSN
+LPFHLEDRTTASLRILVPLRLGRLWPSHLASVPGMEARAR
+>GCF_023573625.1_00961
+MYPTPMTFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALRK
+YGVGLVPEDEFGGAGVRRIFTAEKSRRLEVLENEGGPAYEDDI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000860.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000860.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c183ce6c5bfe2b149fbe78fa9736e87eaafb749d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000860.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01018
+MTATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQDQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPGE
+TRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFEQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTKALQSA
+>GCF_003691675.1_00732
+MTATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPGE
+TRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFAQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRAAGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTNALQSA
+>GCF_005280335.1_01869
+MSSTPDLEQSRHLATALPGPRSQALAERQKAAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTAPISGQ
+TRTALFNSGAEAVENAVKVARSYTGKQAVAAFDHAYHGRTTLTMALTAKNMPYKHHFGPF
+APEVYRVPGSYPLRDGLSGAEAARRAIGALETQIGAENLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCRANDVLFIADEVQSGVARTGSWFACEAEGVEPDLMTTAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVAAAAALAVFEAIEDEDLLAKATRIEEVIREHFAAHADD
+RIAEVRGRGAMMAIELVEPGTGEPDAALTAAVAAAVRATGVILLTCGTYGNVIRFLPPLT
+IGEDLLKEGLSEVTKALQSA
+>GCF_020097155.1_01761
+MTSPVTAPEQSRHIATELPGPKSRELAARQAGAVPAGVATTMPVFASRAGGGIIEDVDGN
+RLIDLGSGIAVTSVGASHPKVVEAVQEQVADFTHTCFMITPYEGYVAVAEKLGEKAPISG
+ETRTALFNSGSEAVENAVKVARAYTRKQAVVAFDHAYHGRTTLTMSLTAKSMPYKHSFGP
+FAPEVYRVAGSYPLRDGLNGAAAAKKAISAMEKQIGADNLAAVIMEPLQGEGGFIVPAEG
+FLQAIVEWCTANDVLFIADEVQSGFARTGAWSASELEGIEPDLMCTAKGIAGGMPLSAVT
+GRAEVMDAVHPGGLGGTYGGNPVATAASLAVFEAIEEDGLLQEAQMIERVIREHFEQNAD
+ERIAEVRGRGGMMAIEFVDPASGEPDAALTGKLAAAVRAAGVVLLTCGTYGNVVRFLPPL
+TIGEELLREGLAEVTTALQSA
+>GCF_023573625.1_00962
+MTATPDLEQTRHLVTELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTCPIPGE
+TRTALFNSGAEAVENAVKVARAYTGRQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIRDHFEQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTKALQSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000861.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000861.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0614f8b925927f4c9c8e52bda5843c410fbcfa12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000861.fa
@@ -0,0 +1,33 @@
+>GCF_002008305.4_01019
+MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRLELTTA
+GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALTEANSGRVAQALVAAGAGVAVVTEDP
+AFGLTPVRVIAQGRTLTVRLHAAWRGDHFAAETLEAIARRLQAFVRDRYAEPGDDAPGRG
+RSA
+>GCF_003691675.1_00733
+MDEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRFELTTA
+GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP
+AFGLTPVRVIAQGRTLAVRLHAAWREDHFAAETLQALARRLQAFVRDRYAEPGDDAPR
+>GCF_005280335.1_01868
+MEERLLRAFVTVAEAGTVSAAAQRLDLVQSALSRQLQRLQRELRLPLFARVGSRLELTTA
+GEAFLPVARRVLAAHRQAEQAARTLASGSLAEVAIAAPGTTLIDVVLPFVATLDEDDPRP
+RVAETQLDDSLQDAVARHDLVVMPMAPGPTVQALHLIDLPVWAYVAPGHPWADRADVALE
+ELVDVRVVAPSRSFMARRVLDGAVAVAGLTAPELSEANSGRVAQALVATGAGVAVVTEDP
+AFGLVPLRVLLDGRALSVGLHAAWRADHFAAATLARIAASLQDFVRTRYPQPGPADDIPV
+TTRASPLSAAPSQ
+>GCF_020097155.1_01760
+MDSIAAGGRALDLDHLLDPALLRTFVAVVDEGTVTAAARELGLGQSALTRHLQRLQRDLG
+LALFAPEGARLRITPAGQAWLPVARSLLAAHAHARQAARILAAGRLTELSLGAPGTTLID
+VVIPFLTVLGEGDPAVRVTETQLDDSLQDSVARLDLVVLPSTPPDDVAALPLQSMPVWAC
+VAPGHPWADRDELDAAELAGARLVLPSRSFKARRVFDAALEVAGAAPRQVVEANSGRVAQ
+ALAANGTAVAVVTEDPAFGLRPLPIRAGGRRLEVHLHAVWRRDHFAAEEIAGVAAQLRVF
+VRRRYDVAEAQDDADGSLSRAVSVD
+>GCF_023573625.1_00963
+MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVGGRLELTTA
+GEAFLPVAREVLVAHRRAEQAARTLASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP
+AFGLTPVRVIAQGRALAVRLHAAWREDHFATATLEKIARRLQAFVRDRYAEPGDDAPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000862.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000862.fa
new file mode 100644
index 0000000000000000000000000000000000000000..880811e3b44151bf5a2e22b202297a05d56e4370
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000862.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01020
+MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSATASATPSPSPSPSSAR
+FTPSPATTATPTPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEPAPS
+EEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGGDLDPEPQTV
+GWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRDVFWNLGDVRAGAVVVVTYDDGTQAAFE
+ADSDAVSVEKEALTQDPANRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFNNWVVQATRV
+A
+>GCF_003691675.1_00734
+MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSATASATPSPSPSPSSAR
+FTPSPAPTATPIPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEPAPS
+EEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGGDLDPEPQTV
+GWYGPPQWGTTPGERSRYAGVLAGHVVYYGVRDVFWNLGDVRAGAVVVVTYDDGTQAAFE
+ADADAVSVEKEALTQDPAHRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFNNWVVQATRV
+A
+>GCF_005280335.1_01867
+MTGPAAPWESIDAAPVHVEVHQDGERIVGASVEHTQMNEAGELDPDPQTVGWYGAPQWGT
+DPGERSPYAGILAGHVVYYGVKDVFWNLDAVRAGDVVVLTYDDGSQAVFEADADAVSVEK
+EALTQDPANRWAWEPGGDDARLTLITCDLVPGTGMAGNAFNNWVVQATRVA
+>GCF_020097155.1_01763
+MSTTVKRAVWALLLLICLGVGAFALRGMFAFGDVPISAAPTVSARASTASSTPSAATGSP
+SSTSASASAGPSVPAATSASSAAASTTTPASPTSSTTTPASPTSSTTPASTEAAAPAVGA
+ASSTATASSSATPTGTDSRMTKPAASWERITAAPVHIDVYADGEQVVGAPVELVQTRDDG
+ELNPDPQMAGWYGPPQWTTTPGERSAHPGVIAGHVIHSGLKDVFWNLQTLKAGSIVVITY
+DDGTQAEFRTDFDVRSMDKDDLTQSPDYAWAWELPEAGNKVTLITCDLVDGSGMTGWSTN
+NWVTQATRIG
+>GCF_023573625.1_00964
+MNTTVRRALWVVLLLLCLSLVFLALRGVLAVGAVPISAAPTLSATASVSPSSAATTREAA
+VPVETQELAGTPTPSEEPTPTEEPAPSEEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQD
+GEQIVGAGIDLTQLDEGGDLDPEPQTVGWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRD
+VFWNLGDVRAGAVVVVTYDDGTQAAFEADADAVSVEKEALTQDPSHRWAWEPGGDDAKVT
+LITCDLVPGTGMAGNAFNNWVVQATRVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000863.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000863.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec2a434fa8c56328040e2b58054f26fc0d972bf4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000863.fa
@@ -0,0 +1,33 @@
+>GCF_002008305.4_01021
+MSRADIAPARVRPRRWSVAVGGALLSITLATGGCSVAEEPGQTGGTEAGNTYLEGVLASP
+SQTSADPLAADIQFAGLLLRNHRDAIQQSDQVLGKDGVDQEIRATAERMKSEHEERAGRL
+ESMLEGWGVPSDDVRGAGAESTPSAQPESTEDAEPTQIVGDELRAGLLSDREKNVLAAAE
+PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLGEM
+GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRSFRATQKPVLPSSSS
+PSSSSASGSASASGRDAEDQRGRDAASASPSPSPADTAQATPRPSSGASPSPSASR
+>GCF_003691675.1_00735
+MSRADIAPARVRPRRWSVAVGGALLSITLATGGCSVAEEPGQTGGTEAGNTYLEGVLASP
+SQTSADPLAADIQFAGLLLRNHRDAIQQSDEVLGKDGVDQEIRATAERMKSEHEERARRL
+ESMLEGWGVPSDDVRGAGAESTPSAQPESTEDAEPTQIVGDELRAGLLSDREKNVLAAAE
+PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLGEM
+GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRNFRATQKPVLPSSSS
+PSSSSASGPASASGRDAEDQRGRDAASASPSPSPADTAQATPRPSSGASPSSSASR
+>GCF_005280335.1_01866
+MPVTGDELRAGLLSEREKNVLAAADAEDAGRIYLLQMHRVYQGALTISATEAESGTDEEA
+KALAASVVADHQEDMQRMVEVLADMGAIGADASHTALPSGYTGPIKIEGTGADGGPVPSD
+FVPEPVQRVQSFRATQRPVLPTSSSPGDAEDRRGRDSATASPSPTPADTARPSPSPSSAA
+SPSPSATTGSPSGTNR
+>GCF_020097155.1_01762
+MNRATDATAPVCPVRWSAAAGGLLGLSLVLAGCGTSAQPVPAGSGSNTYLEGVLATPSAT
+KADPLAADQRFVASLLQNQYQVVQEADHVLSRPDMDGEVRDMAQQHKDVANQRIGDLSSR
+LQAWGLEVPAAPEPLVDDTKPSGRPTGDPSEIQASKGQQAAADIRAGLLTASDQSALVTA
+DDDAAGRIYLLQVHRLLQGGVSLAGTESDEGTDEETKKIASDLIDADRPRMQRILEKLGE
+NGVVAAVPSPTAPNSGYQGPISLPSQAGGDGANVDYTPSALYEMWSTLPPPATSSSADGS
+STGPSPSAQPTPTPADTASPRPTPGASAQPGAASSTASTTGAASTRNG
+>GCF_023573625.1_00965
+MSRADIAPARVHPRRWSVAVGGALLSITLATGGCSVVEEPGQTGDTEAGNTYLEGVLASP
+SQTSADPLAADIQFAGLLLRNHRDAIQQSDQVLGKDGVDQEIRATAERMKSEHEERAGRL
+ESMLEGWGVPSDDVRGAGAEATPSAQPESTEDAEPAEIVGDELRAGLLSDREKNVLAAAE
+PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLAEM
+GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRNFRATQKPVLPSSSS
+PSSSSASGSASASGRDAEDQRGRDTASASPSPSPADTAQATPRPSSGASPSPSASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000866.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000866.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d10d77b55247b1a9d7b87d57b5b4487a9b81bcd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000866.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01024
+MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS
+WSGFRPDKIAELAESAAASVA
+>GCF_003691675.1_00739
+MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS
+WSGFRPDKIAELAESAAASVA
+>GCF_005280335.1_01861
+MTVTVYTKPACVQCNATYRALDKKGIAYEIVDMSQDPAALERVRGLGFMQAPVVVTETDS
+WSGFRPDKIAELAEAAAASVA
+>GCF_020097155.1_01751
+MTVTVYTKPACVQCNATYRALDKKGIAYETVDMSQDPEALDRVRALGFMQAPVVITDTDS
+WSGFRPDKIAELAESAATQVA
+>GCF_023573625.1_00968
+MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS
+WSGFRPDKIAELAESAAASVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000867.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15ca45899869572182388c32c0b1c5f8c3d967aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000867.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01025
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGMWT
+>GCF_003691675.1_00740
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGLWT
+>GCF_005280335.1_01860
+MTVAADPGHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVQKLELPEDRVARLPLITREPT
+LGATAPYVLLTPTYGGGDGPGAVPKQVIKFLNVPGNRTWIRGVIASGNTNFHEAYCLAGY
+IIARKCQVPLMYKFELMGTPEDVDSVRGGLEGLWT
+>GCF_020097155.1_01750
+MTTATAGPNHMRDAEAQGLVPTDARLIYFSSASGYTHRFVEKLGLPLGQAARLPLLTREP
+TLGATAPYVLLTPTYGGGGDTGGEVPKQVIKFLNVPGNRALIRGVIASGNTNFSGAYAAA
+GYIISRKCQVPLMYKFELMGTPEDVVAVREGLERLEEGQHA
+>GCF_023573625.1_00969
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGLWT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000869.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000869.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97b0780ac18375f61fa17644d4e74306dc6bc95b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000869.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01027
+MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTPEIDEAFRWSRENRNLQAKARLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL
+SGHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDEDWDF
+>GCF_003691675.1_00742
+MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTPEIDEAFRWSRENRNLQAKAGLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL
+SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDEDWDF
+>GCF_005280335.1_01858
+MTEVTDTVKTNHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAITPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTKEIDEAFRWSRENENLQRKASLIVERYDGEDPYKRKIASTLLESFLFYSGFYWPMYL
+SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRNIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLSEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDADWDF
+>GCF_020097155.1_01745
+MTEPHHGPSVHDHLVEAINWNRIQDEKDNEVWQRLVNNFWLPEKVPLSNDVQSWNQLTDD
+ERLLSMRVFTGLTLLDTIQGTVGAVSLIPDAITPHEEAVYTNIAFMESVHAKSYSSIFST
+LASTKEIDEAFRWSRENPNLQRKAQLILERYDGEDPYKKKIASTLLESFLFYSGFYWPMY
+LSSHARLTNTADLIRLIIRDEAVHGYYIGYKYQRNIETLPEERREELKAFTFELMFELYE
+NEVEYTHSLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTDVNPAILSALSPNSD
+ENHDFFSGSGSSYVIGKAEATEDEDWDF
+>GCF_023573625.1_00971
+MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTPEIDEAFRWSRENPNLQAKARLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL
+SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDEDWDF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000870.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000870.fa
new file mode 100644
index 0000000000000000000000000000000000000000..522ba948ddfb2f984e6a8e6e76cccf19fb15b465
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000870.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01031
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLNGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>GCF_003691675.1_00746
+MTDITSTPATSVAGDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLDGVVLPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHAEQTLTLRSWPAEGGL
+>GCF_005280335.1_01851
+MTDISSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQEHNALDGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVVGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>GCF_020097155.1_01741
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQAHNALHGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+PWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>GCF_023573625.1_00975
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000871.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000871.fa
new file mode 100644
index 0000000000000000000000000000000000000000..397f3ccb6e06acfed517272295700d4042dedb52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000871.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01032
+MSVAPRLRWAVQERTLGAVEDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFAAAAAAARAHGFAPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGI
+EVVAEQLAVLGARTSG
+>GCF_003691675.1_00747
+MSAAPRLRWAVQERTLGAVEDLDWAMDELAVFRAAAAEGRALDGLIRVYVPEPTVAFGQR
+DARLPGFEAAAAAARAHGFEPVVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAGLE
+VVDEQLAVLTAGTAG
+>GCF_005280335.1_01850
+MSAAPRLRWAVQERTLGATDDLDWAMDELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFEAAAAAARTHGFEPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMGVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGL
+KVVDEHLAVLAAGTSG
+>GCF_020097155.1_01740
+MSAAPRLRWAVQERTLGAADDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFEAAAAAARAHGFEPAVRRAGGRAAAYHHGCLVVDHLSQQEDATLTQQARFAEF
+ADLFVRAFARMGVPASVGEIPGEYCPGEFSVQGPAPAYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLGMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGL
+EVVDEQLAVLGAGTSG
+>GCF_023573625.1_00976
+MSAAPRLRWAVQERTLGAVEDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFAAAAAAARAHGFAPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGI
+EVVAEQLAVLGARTSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000873.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000873.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8a4ee9bcdbd9a967a6c677aaeeebe85fdd26573
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000873.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01036
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPALLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLLSLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
+>GCF_003691675.1_00749
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLLPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
+>GCF_005280335.1_01848
+MARIDHLVTSGTFSLDGETFDVDNNVWLVGGAEQCIVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGGATGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
+>GCF_020097155.1_01738
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
+>GCF_023573625.1_00978
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDAVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000876.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000876.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c320c1614a1a594387d71be9c8b8046000dc584b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000876.fa
@@ -0,0 +1,28 @@
+>GCF_002008305.4_01043
+MSLTAPGRALRRHRFAQAGTLSVALALALTACGGQSEPAESSTTSPSSAKPAVETSAPAS
+TSETAGVSSSPTATESGSGEYVPASADGPARSVPKPEMPADMKEETKEGAEAAIRYFWDV
+HYYAEQTGDTELLDSLYSEYCEFCQFSSNDLQMIYKDGGWYTGTEVQIDSILTHRSETGY
+VSTLLVTTGTGTGYTKGGVVPENGDVEAASKQPWIAEVSFNPESSHWIVDEMSYEGSIGS
+N
+>GCF_003691675.1_00756
+MSLTAPGRALRRHRFAQAGTLSVALALTLTACGGQSEPAESSTTSPSSAKPAVETSAPAS
+TSATAGVSSSPTATESGSGEYVPASADGPARNVPKPEMPAAMKEETKEGAEAAIRYFWEA
+IYYTDQTGETADFDSTYSEYCELCQAVSDSTAQHYKEGGWSTGEHTSIKSLTLTPSEFGY
+TATLVRDASAVDVFDSQGVRDDSASGAETHDETWLADVVYEPSKGHWVIDEMQNQQDAQ
+>GCF_005280335.1_00543
+MSFTAPRRVLRRHRLTQVGALGAGLALLLTACGGGSEPAESSSPAPTGSSSSPAEATTAS
+PSAESSPTTSPSGSVGSTAAAGSSGSGGAYVPASAEGPARNVPKPEMPAVTKEETQEGAE
+AAVEYFWEAAYYLQQTGDSEYQESVSSPTCKFCDLQRTSMEGHYRDGGWMKVEAVNIASM
+VTRPSANGYMSTLLLDMPKEEAFASQGGKAESIGTQPALEESPWIAETSFSEEAGHWVIE
+AMIAGGS
+>GCF_020097155.1_01734
+MTLPAPRRTLRRRRLARTGALSGALLLALTACAGGGADSGASSASTTTTAPAASSTSAAA
+SSSTGGASASESDATTSGAAGEYVPASSKGPAQNVPKPVMPAAVKENTPEGAEAAVKYWW
+EAVNYLQQTNDPEPLKSISMEECNLCSAHIKTIKRIYGDGGWATGENFAVNSVSMEKKKD
+FTLATVAISTDDSATFNADGVKVDQAPADAGTDAPWGVLLKFDSNKGQWVVREAEYDFQE
+G
+>GCF_023573625.1_00984
+MSLTAPGRALRRHRFAQAGTLSVALALALTACGGQSEPAESSTTSPSSAKPAVETSAPAS
+TSETAGVSSSPTATESGSGEYVPASADGPARNVPKPEMPAAMKEETKEGAEAAIRYFWEA
+IYYTDQTGETADFDSTYSEYCELCQAVSDSTAQHYKEGGWSTGEHTSIKSLTLTPSEFGY
+TATLVRDASAVEVFDSQGVRDDSASGVETHDETWLADVVYEPSKGHWVIDEMQNHQDAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000878.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000878.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d648df4cdb73858cdf2d217a1cd986b25ce66271
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000878.fa
@@ -0,0 +1,109 @@
+>GCF_002008305.4_01045
+MSQAAAAGRTAAPFAHLHVASAFSAHHGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDGDAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPSTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALHRWKAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVAFAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRERTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYHAVVERFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDATLLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSLD
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEIDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQLALDLPDTELTALAPLFPDPGPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGDRAVSVQAVRAWDLHRPETLPDPDY
+LDATRQQWRDWLAADRRAAAARRSSRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR
+>GCF_003691675.1_00758
+MSRAAAAGRTVAPFAHLHVASAFSAHYGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDEDAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPPTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALHRWKAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVASAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRARTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYHAVVERFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDAALLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDDATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSPE
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEVDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQMALDLPDTELTALAPLFPDPAPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGGRAVSVQAVRAWDLHRPQTLPDPDY
+LDATRQQWRDWLAADRRAAAARRSGRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR
+>GCF_005280335.1_01844
+MGLRRRARRRRGSSRVPTAANRDNPPTPELFVLVGPDADVGRHLARRRSAAGLAALRRWK
+EALPAGSLHADVVTHLSTPGRRLDAGHAVKALRTARRAGVPAVLTNAVRYAGPDGAATAD
+VLDAVRALSSLDAVHDLQPNGQGWLKPTAAMHRVAHEVASAADERAAPLLEATRRLAEAC
+VLDPEADLGWGVPRVPEAAVIGIEGPPERVLRERTYAGLAARYPRLHAGGRLTSAAEARD
+LEARAEHELGIITRLGFSSYFLTVAAVVDLIEGMGVRVAARGSGASSLVNHALRISNVDP
+VANGLIMERFLSDARSTLPDIDIDVESARRHEIYRAVFERFGAERTTLMSMQNAYRARGA
+VRDAGLALGMPEPEVDGIAKQLWRFSASSFREALERMPELGGLSRRIESGRAEGSRQLDL
+LVDLTERLDRLPRHISMHPCGVILGDAALLHRTPVQPSGMGLPMSQFDKHDMDPMGFLKL
+DILGVRMQSAIAYTLAEVERTTGERVDLEQVPLDDPATYAMIRTTHTLGCFQIESPGQRE
+LVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPARYPHPDLRPVLAETHGV
+TVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHRVEEAFRAGALARGYSLDVIDEVWA
+TLAAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPEAFMAAILEHDPGMYPARLMVAEARRM
+GIPVLPVDVNASSRHVRVEWVPWHPELDGPPAEDAGAGGGEPGDVVARPHAEGGAEADLA
+EGAGRGPGRWGIRLPLTGLSGLSEAETERLDAGRPYRSLADVRDRARPTARNLERLAQLG
+ALDCLLPAGGASRTDLVHHLELQHSATRGSGPGRAAARSRSARPRQVDGQLALDLPDTEL
+AALTPLFPDPSVAARVRTELELTALDVTAHLMDSHAPYLDALGVTRAADLLGLRTQSRVL
+VAGVRVATQTPPMRSGKRVVFLSVDDGTGCVDASFFTEAQHASGEMLFSARLLLIEGTVR
+RTGPRAVSVQAVRAWDLHRPESLPDPDYLDATRRQWREWLAADRRAAAARRRGQEDAGAP
+RLPDIPHHGTGGWPVKVALGGAGAPSPSSDARAPAGRGVSAGAGPGAAGQGAAARVGAGG
+VPADRRPIPVPHPDTWELLPTPER
+>GCF_020097155.1_01731
+MSAFPHLHVASAFSAHHGVSWPADLAAAAAAADMDLLACTDRDGLYGTVKHVGACLARRI
+TPIVGVDLAVRWDEDEPAGRVVVLARGGCHGTGYRALCRLVSAAHARTAGGAAGGAPWVL
+VAEVAAAAAGPIPTGANPGNPPTPELFVLVGPDSDVGRHLARRRTAAGLAALRRWRAALP
+AGATRAEVVSHLSAPGRRLDTGHAVKMLRTARTARVAPILTNAVRYAAPDGAATADVLDA
+VRALSALDAVHDLQPNGQGWLKPTAAMEALAAEIAHAADEHPAALLESTRALAEACALDP
+ETDLGWGRPRVPEASVVGTVGDPRQVLRERTRAGLAARYPHLHTGAGLPGTTQAARDLQD
+RAEQELGIIDRLGFAGYFLTVAAVVELIEGMGVRVAARGSGASSLVNHALRISHVDPMAN
+GLIMERFLSDARSTLPDIDIDVESARRHEIYRAVVDRFGAERTTLMSMQNAYRARGAVRD
+AGLVLGMEEDEVDGIAKQLWRFSASSFRDALDRMPELSSLAARIDAGRAAGRHQLDLLVD
+LTERLDRLPRHISMHPCGVILSDAALLDRTPVQPSGMGLPMSQFDKHDMDPMGFLKLDIL
+GVRMQSAIAYTLQEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQIESPGQRELIG
+KLEPREFNDLTVDISLFRPGPMQSDMVRPFLEHRHGWAPAHYPHPHLEPVLAETHGVTVF
+HEQVLRTLDVMTGCGLARADELRRLVGGPEEHRVETFFRTAALENGYSLDVVDEVWHTLH
+AFGSFGFCKAHGAAFAVPTYHSAWLKTHHPEAFMAAVLEHDPGMYPARLMVAEARRMGIP
+VLPVDVNASTRHVHVEWVPSHPEVDGADPTTDPATGAPGRWGIRLPLTSLSGLSAAEVDR
+LDAGRPYATLADVRDRARPTARSLERLAQLGALDSLLPAGGASRTDLVHHLELQHSATRS
+TDPGRTARRSRTARPRQVDGQLALDVPDTELTALTPLFPEPSRDAAVRTELDLTALDVTA
+HLMDSHAPYLDALGVTRAEDLLSLRSQSRVLVAGVRVATQTPPMRSGKRVVFVSVDDGTG
+CVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGARAVSVQGVRAWDLHRPERLPDPDYL
+DATREQWRAWLAADRRAAAARRRGETPVGAVPDIPHHSTGGWPVKVRADVAVGRERAAVE
+RPAPAPSSRPIPVPHPETWELLPTPES
+>GCF_023573625.1_00986
+MSQAAAAGRTAAPFAHLHVASAFSAHYGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDENAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPPTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALRRWEAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVAFAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRERTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYRAVVDRFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDATLLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSLE
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEIDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQLALDLPDTELTALAPLFPDPGPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGDRAVSVQAVRAWDLHRPETLPDPDY
+LDATRQQWRDWLAADRRAAAARRSGRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000879.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000879.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7fbce1e4285afbca0253f45380741dc6b2b31c74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000879.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_01046
+MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVESVD
+ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS
+SLMQKIVKSGQTFRRRVVDEETARAEMAEEPYKLELLGKKDAADTAGEGASVEVGAGEIT
+IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI
+RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREANAVSFRFRDGTQDNGVPVEEAIER
+IVKAVREREVTP
+>GCF_003691675.1_00759
+MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVESVD
+ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS
+SLMQKIVKSGQTFRRRVVDEETARAEMADEPYKLELLGKKDAADTAGEGASVEVGAGEIT
+IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI
+RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREAGAVSFRFRDGTQDNGVPVEEAIER
+IVKAVREREVTP
+>GCF_005280335.1_01842
+MSEPNNILLTVDGQMREVAHGITGLELFRDQSTTVVMRVDGVLWDLSREIPGGASVESVD
+ITEQDGLDVLRHSTAHVMAQAVQQLRPDAKLGIGPYITDGFYFDFDVAEPFTPEDLRTLE
+KMMQKIINSGQAFRRRVVTEDEARAEMADEPYKLELLGKKNDAATAGEGASVEVGAGEIT
+IYDNVDRKSGDAVWCDLCRGPHLPQTKLISNAFALTRSAAAYWLGNQDNKQLQRIYGTAW
+PTKADLKAYQERLAEAERRDHRRLGSELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYETSGHLDWYADGMFPPMQIDEQRDPETGEVTRQGQNYY
+LKPMNCPMHNLVFRSRGRSYRELPLRLFEFGAVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKDELTTTLNFVLDLLKDYGLDDFYLELSTRDPEKSVGSDEIWEEATRTLDEVARA
+SGLDLVPDPGGAAFYGPKISVQAKDAIGRTWQMSTIQLDFNLPERFDLEYQAPDGSRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFADYLGDVVKRLRAEGI
+RARLDDSSDRFPKKIRTASKEKVPFVLIAGGEDAEAGAVSFRFRDGSQDNGVPVDEAIER
+IVRAVREREATP
+>GCF_020097155.1_01730
+MSESNPILLTVDGEMREVTHAITGAELFKDQPTTVVMRVDGQLWDLSRELHGGEAVESVD
+ITEQDGLNVLRHSTAHVMAQAVQELRPDAKLGIGPFITDGFYFDFDVAEPFTPEDLKQLE
+KMMQRIVKSGQTFRRRVVTEDEARAEMADEPYKLELLGKKDDAEAAGEGATVEVGAGEIT
+IYDNVDRKSGDAVWCDLCRGPHLPTTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+PTKEDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+KRHAAAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMQIDEVRDPETGQITKQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKDELTTTLNFVLDLLKDYGLDDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLELVPDPAGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGSRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLADVVATLKAEGI
+RVRLDESSDRFPKKIRTASKEKVPFVLIAGGEDAEAGAVSFRYRDGSQDNGVPVDEAVAR
+IVKAVREREVTP
+>GCF_023573625.1_00987
+MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVEAVD
+ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS
+SLMQKIVKSGQTFRRRVVDEETARAEMADEPYKLELLGKKDAADTAGEGASVEVGAGEIT
+IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI
+RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREANAVSFRFRDGTQDNGVPVEEAIER
+IVKAVREREVTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000881.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000881.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2e814ce805010ac379ef3bb41eefebd55471566
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000881.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01048
+MLDRHARDLTTRLFTPVAHTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT
+AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG
+ACLALGMLVSYVRAKAEALGWSAHVGIAERAERLVAALVVAGLTGLGLPPVVLAVTLGLL
+AAASLVTVGQRMAAVRRQARDDA
+>GCF_003691675.1_00761
+MLDRHARGVTTRLFTPVARTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT
+AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG
+ACLALGMLVSYVRAKAEALGWDAHVGIAERAERLVATLVVAGLTGLGLPPVVLAVTLGLL
+AAASLVTVGQRMVAVRRQARDDA
+>GCF_005280335.1_01840
+MLDRHARGATTRVFTPVARALLRAGVSPDAVTVVGTLGVSLGALVLFPLGELFWGTLFIT
+AFVFSDLVDGIMAREAGTTGRWGAFLDSTLDRVQDAAVFLGLSLWGFGVGGEPAVGTLAA
+VCLALGMLVSYVRAKAEALGLTANVGIAERAERLVAALVLAGLTGLGLPPAFLAATLGLL
+AAASLVTVGQRVAAVRSQTRRAA
+>GCF_020097155.1_01728
+MLDRRARGTTTALFTPLARRLLRAGVTPDAVTVAGTVGVSAAALLLYPAGHLFWGTIVIT
+LFVFSDVLDGVMAREAGTTGPWGSFLDSTLDRVQDAAIFLALSWWGFGVGAHPAVGVLAG
+VCLALGMLVSYARAKAESLGFTAAGGIAERAERLIVTLVFAGLTGLGLPSAVLTAVLGLL
+ALASLITVAQRVAGVRRQSRTA
+>GCF_023573625.1_00989
+MLDRHARGVTTRLFTPVARTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT
+AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG
+ACLALGMLVSYVRAKAEALGWDAHVGIAERAERLVATLVVAGLTGLGLPPVVLAVTLGLL
+AAASLVTVGQRMAVVRRQARDDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000884.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9bb0cdf3cf845b75bb6fc49b2ec5b766e1326a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000884.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01051
+MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
+>GCF_003691675.1_00764
+MTDTAAKFSEYAHPEKLVSTQWVADHVDDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEVAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRTDAGLREGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
+>GCF_005280335.1_01835
+MTETATEFSQYAHPEKLVSTQWVADHVGEEGVVVLESNEDALLYATGHIPGAQRIDWHTE
+LNDPVTRDFIGPEAFAEMAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDVRLMN
+GGRDKWIAEGRETTREVPTVARGEYPVVPRDDTTERAAREDVLQAVGTTPLIDVRSRPEY
+TGETTHMDGYPQEGTLRGGHIPTAASVPWAQAANEDGTFKSREELEAVYRDGAGLKDGDD
+VIAYCRIGERSSHTWFVLKHLLGHENVRNYDGSWTEWGNSVRLPIVVGEEPGAAPAR
+>GCF_020097155.1_01725
+MTETPAEFAEYAHPEKLVSTQWVADHIDDEGVVVLESNEDTLLYSTGHIPGAVKIDWHTE
+LNDPVSRDFVGPEAFAELVASKGIGPDTTVVFYGDKSNWWAAYALWVFTLYGHRDVRLMN
+GGRDKWIAEGRPTTREVPEVTPAPSYPVSQRDDATDRAAREDVLAAIGSTPLVDVRSPKE
+YTGETTHMDGYPQEGTLRGGHIPTAASVPWAKAANEDGTFKSRAELEEIYKEGAGLGESD
+SVIAYCRIGERSSHTWFVLKQLLGYENVRNYDGSWTEWGNGVRLPIALGDEPGEAPAR
+>GCF_023573625.1_00992
+MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTDRAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000886.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000886.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da2b45e0adcd77d134e8b0a7929498e93b9944f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000886.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_01057
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPVSAATGLQAVRAAAFGGGSHAAPAVAPDGLS
+SRPASAEGGDRVTA
+>GCF_003691675.1_00776
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPVSAATGLQAVRAAAFGGGSHAAPAVAPDGSS
+SRPASAEGGDRVTA
+>GCF_005280335.1_01829
+MTQPRLAHQTPLGRMYARSLTGLPEVPSITTVIGMERTDLDGWIGWMAAQSVTQDPRLAE
+SVGSAARLKQVARQSADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTLAETRAKLIE
+HGEGAYADRFDEWWDLYDVRPLAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTG
+RDGRVKALDPKVVMQLTAGLKAEESLVDAEAGTWEEWRHGQAEMLLGVALGETEVAVHQA
+NPGVLPRHWHKFWALRQVWKHAQAADDAGPALRVIGPPPPSVPLHRG
+>GCF_020097155.1_01719
+MYARSLSGLPEVPSITTVIGMERTDLDGWVGWMAANAVAQDPRLGESLGSPARLRQVAKQ
+SADAAARYRDAAAERGDRVHDYAEQVALRALGRPHTMAASREELQRHGEGAYADRFDEWW
+DLYDVQPVAAEITVWNHSVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDAEAGTWEPWAHGGAEMLLGVALGETEVAVHQANNAALPRHWHKFWA
+LRQVWKHALAVDDAGPALRVIGPPPVSVPGAAGGLSAARAAAFGAPPAVAHDPGTSAPAD
+RLQP
+>GCF_023573625.1_01004
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPASAATGLQAVRAAAFGGGSHAAPDVAPDGSS
+SRPASAAEGGDRVTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000887.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000887.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dbc59ebb42ccd1cca8eb3e008f526df7372d9fbc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000887.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01058
+MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPGAPAAGTGAAR
+>GCF_003691675.1_00777
+MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPAVPAAGTGAAR
+>GCF_005280335.1_01828
+MSVLPVRTVPDPVLRTPARPVPAGMDVRALVADMVETMHAVGGVGLAAPQVGVGLRVFVF
+DVQGVAGHVVNPVLETGEETVREPGEGCLSVPGLRYHPARAAEAVVRGVNVDGHPVEHRG
+TGLVARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRTARRVGAERAAAVGSVF
+AAPAAPPTPARAPRGGTR
+>GCF_020097155.1_01718
+MTVLTLRTVPDPVLRTPAAPVAAGQDVRALVEDMVETMHAVGGVGLAAPQVGVGLRVFVF
+DCAGASGHVLNPVLETFGSPVREPGEGCLSVPGLRYHPARAERAVVRGVDVDGNPVEHRG
+EGLLARCLQHETDHLDGILYVDRLDGDDRREARRRLRADAPDPEAERIRARRDALAGSVF
+GARPSVSPSAARTTPRRGAQ
+>GCF_023573625.1_01005
+MTVLPVRTVPDPVLRTAASPVPAGADVRALVADMIATMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPTRAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPAVPAAGTGAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000890.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000890.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68b584df94c3e91f6dd89c23107a9765c2bcd8f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000890.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01061
+MTARPPRLHPSILSADFARLADDLARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT
+AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN
+RETIERAAEAGADVFVAGSAVFGAEDPDAALAGLRTAAARACH
+>GCF_003691675.1_00780
+MTARPPRLHPSILSADFARLADDLARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT
+AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN
+RETIERAAEAGADVFVAGSAVFGAADPDAALVGLRTAAARACH
+>GCF_005280335.1_01825
+MSPRAPRLHPSILSADFAHLAEELGRIRGADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDIHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGARAGMALKPAT
+PVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGAAAPLALQVDGGVN
+AETIERAAEAGADVFVAGSAVFGAEDPDAAVDGLRRAAARACC
+>GCF_020097155.1_01715
+MSAHPCIHPSILSADFARLADELARIPGSDAVHVDVMDGHFVPNLTLGLPVVEAIRAATD
+LPLDIHLMIEDADRWAPAYADAGAESVTFHAEAARAPIVLARSLRAAGAQAGLAVRPATP
+IEPYLDLLPELDMLLIMTVEPGFGGQSFLDVTLPKIRRARQALDGAPVPVRLQVDGGVNR
+ETILRAAEAGADVFVAGSAVFGADDPGAAIAGLRDLAAGVAPACHTR
+>GCF_023573625.1_01008
+MTARALRLHPSILSADFARLADELARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT
+AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN
+RETIERAAEAGADVFVAGSAVFGAEDPDAALAGLRTAAARACH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000891.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000891.fa
new file mode 100644
index 0000000000000000000000000000000000000000..759b820d50a54976e0d4e91f19e0196ca8f6fc35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000891.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01062
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWARWRQARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR
+>GCF_003691675.1_00781
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWARWRRARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR
+>GCF_005280335.1_01824
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARKVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWVRWNEARRGRSEHATAITPEWAGLGGRAFL
+VLGMLIGTLALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLVWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLVGFFVWLRAKDRDKPAVETLLPDGPEEHAAR
+>GCF_020097155.1_01714
+MQWLVDVFNWTIPVAGGGLLMREVVGNVFGLASALGGMARKVWAWPVGILGNLLLLTVFL
+ASLFNDAPHATLLGQAGRQVMFIAVSVYGWKRWRDAQRGRADHAPAITPEWAGWGNRAFL
+AVALVLGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSSGYYASAVMYAFYGVFTLTGFFVWMRARDRDKPAVETLLPDGPAPEEAAR
+>GCF_023573625.1_01009
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWVRWRQARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000892.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..466c652976e9a694167341a3c570b1731a044e3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000892.fa
@@ -0,0 +1,43 @@
+>GCF_002008305.4_01063
+MNAAETPSADPMDLAVGAALRGVRGANPLVGAVLTDAAGRILAVGHHRGRGTAHAEVDAL
+TRWRAARAADPALATLDPAGLTLHVTLEPCDHTGSTGPCSQAVLDAGIGALRYAVADPTG
+HDGGGAARLAAHGVHVTGPTGEAAALTLTARWREVRDAGRPWVTGHLAQSLDGHAAAADG
+TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAAGAELAHQPVPVVQGHR
+PVPDGAALRTHPVLLHVPDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA
+GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGPRWHPDPAEGGPARALGVDVWTHLSPV
+PAPRLPTAPAPTRFQED
+>GCF_003691675.1_00782
+MSAAETPSADPMDLAVRAALRGVRGANPLVGAVLTDEAGRVLAVGHHRGRGTAHAEVDAL
+TRWRAARATDPALAALDPAGLTLHVTLEPCNHTGSTGPCSQAVLDAGVGALRYAVADPTG
+HDGGGAARLAAHGVRVTGPTGEVAALALTARWREARDAGRPWVTGHLAQSLDGHAAAADG
+TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAAGAELAHQPVPVVQGHR
+PVPDGAALRAHPVLLHVPDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA
+GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGPRWHPDPAEGGPARALGDDVWTHLSPV
+PAPRLPTAPAPTRFQED
+>GCF_005280335.1_01823
+MSGAPDPMALAVGAALRGVRGANPLVGAVLTDDAGRVLAAGHHRGRGTAHAEVDALARWE
+AARAADPALAALDPAGLTLHVTLEPCDHTGSTGPCSGAILASGVGAVRYAVADPTGVDGG
+GAARLAAHGVRVSGPTGEPAALALTERWRRARDAGRPWITGHLAQSLDGHAAAADGTSRW
+ITGAASRAHAHRVRARVDAIVVGTGTVLADDPRLTVRDAAGAETGPQPVPVVQGRTPIPA
+GAALRARPETLHVPAHEPEAVLAALAARPGPWPHGGARPGHVLIEGGPRVLGAWIRAGLV
+DELMVYTAPLLLGAGRPAVAGLDVGTLADGLRWHPDPAEDGPVRALGEDVWTHLAPVPAP
+APEGPDPQEDCMFTGIVTHLGTVLALEPDPAADTARLVLDAGGALEGLPAGGSLAVDGVC
+LTALDGPGAEPGVFRADLMGQTLRMTSLGGRTPGDRVNLERCLRPTDHLDGHVVQGHVDG
+VGEVLSVTPQGAWTTVRIGLPAALARYVPAQGAIALQGVSLTVSAVSEPGADAHWFEVGL
+IPATLEATTLGALRPGDRVNLETDVLARYAERLALLPAAPAASPSAAPAEEVRP
+>GCF_020097155.1_01713
+MSAPAARHDDAGRPAEPLDLAAAAALAGVRGANPLVGAVITGPDGAVLAVGHHRGRGTAH
+AEVDALNRWAAARAADPSLHVDPAACTIHVTLEPCDHTGSTGPCAGAILDAGLGAVRYAV
+ADATGTAGGGAARLTRAGLRVEGPTGHAASAALTARWRRVRDAGRPWITVHLAQSLDGRA
+AAADGTSRWITGPASRAHAHAVRARVDAVVCGTGTVAADDPRLTARDAAGEQLPVQPVPV
+VMGERDLPAGAALAARADLIHVRSHDPRAVLAALASRPGPWPHGGSRPGHVLIEGGPHVL
+GAWLAAGLVDEVFAYTAPVLLGDGLPGVAGLDVPTLAAGHRWAPDPAEDGPVRALGDDVL
+THLAPVTDPAD
+>GCF_023573625.1_01010
+MNAAETPSADPMDLAVRAALRGVRGANPLVGAVLTDEAGRVLAVGHHRGRGTAHAEVDAL
+TRWRAARATDPALAALDPAGLTLHVTLEPCDHTGSTGPCSQAVLDAGIGALRYAVADPTG
+HDGGGAARLAAHGVHVTGPTGEAAALTLTARWREVRDAGRPWVTGHLAQSLDGHAAAADG
+TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAVGAELAHQPVPVVQGHR
+PVPDGAVLRTHPVVLEVLDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA
+GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGLRWHPDPAEGGPVRALGVDVWTHLSPV
+PAPRLPTAPAPTRFQED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000893.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000893.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2674a96b95f3008bc8cdebf9a069321010dda2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000893.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01066
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TEQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
+>GCF_003691675.1_00785
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
+>GCF_005280335.1_01821
+MAVVAAQWHTEIMDGLIAGARAAAADLGLEPVLVRVPGTVELSVAAARLAEDFDAVVVLG
+VVVRGDTPHFDYVCQAVTQGVTEVSVRTGTPVGFGVLTVDTEQQARDRAGLPGSREDKGR
+ESLEAAVLTELALRDVQA
+>GCF_020097155.1_01710
+MSGAGAPTLALTTLTDADRAAAGSLRVAVVAAQWHTEIMDGLIAGSRAAAADLGIDVDLV
+RVPGTVELSVAAARLAATHDVVVVLGVVVRGGTPHFDYVCQSVTQGVTEVSVRTGVPVGF
+GVLTVDTVEQARDRAGLPGSQEDKGREALEAAVLTELALRAALG
+>GCF_023573625.1_01013
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000895.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000895.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2dda30e6725b64650787b9616871b47ae8ac5681
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000895.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01079
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
+>GCF_003691675.1_00798
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
+>GCF_005280335.1_01819
+MLRIAVPNKGALAEAAREILQEAGYRQRRDSRELVLVDPENQVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFRDAQVDGGAEEIMALGFGRSVFRLAAPVGAFSSEAELSGKRIATSYDG
+LLSAYLERTGLDAEVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMETFGESILDSE
+AVMIARVGARPEGLDVLLRRLKGVLVARRWVMIDYDVRRELLEQATAVTPGLESPTISPL
+RDESMVAVRSMVRKADANRAMDDLYALGARGILISAIHAIRL
+>GCF_020097155.1_01706
+MLRIAVPNKGALSESAREILIEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFRDARVGETAEEIMALGFGKSVFRLAAPVGSFTSAEELAGRRIATSYDG
+LLTEYLAESGLDARVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMETFGEPILDSE
+AIMIARVGARPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEQATAVTPGLESPTVSPL
+RDESMVAVRSMVRKADANRAMDDLYDLGARGILISAIHAIRL
+>GCF_023573625.1_01028
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000897.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000897.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf2b86ffbda46a0a8bcddc82b30a65663d1aead3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000897.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01081
+MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNEESLRATLETGWATYWSRSR
+GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD
+PEEAAR
+>GCF_003691675.1_00800
+MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRATLETGWATYWSRSR
+GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD
+PEEAAR
+>GCF_005280335.1_01816
+MSISSHHDLVASLAFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRLTLETGWATYWSRSR
+GELWRKGETSGHLQRVLAVHADCDADTLLLTVDQTGPACHTGTRSCFTDRLLAEPAAPAG
+DQAEGAGR
+>GCF_020097155.1_01704
+MSPSDVVADLPPLIFDERGLIPAIAQQHDSGEVLMMAWMNEESLRRTLEDGWATYWSRSR
+QEYWRKGETSGHLQRVLAVAADCDGDTLLLTVDQTGPACHTGTTSCFTDRRFAAPTAADE
+DPQTEDAEAVR
+>GCF_023573625.1_01030
+MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRATLETGWATYWSRSR
+GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD
+PEEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000899.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000899.fa
new file mode 100644
index 0000000000000000000000000000000000000000..521a663d99a59709890301d26b19bae7e61a027c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000899.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01083
+MRRRTVVLAALAAGALVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG
+ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV
+TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA
+QRRRVDQMDAWDELSRGNDPT
+>GCF_003691675.1_00802
+MRRRTVVLAALAAGGLVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG
+ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV
+TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA
+QRRRVDQMDAWDELSRGNDPT
+>GCF_005280335.1_01814
+MRRRTVVLAALAAGSLVLLAAGQTWVVGSGLTGGLSEEATTSGGAAAPGATAMALVVLAG
+ALALTTARRVGVVVVGALLVLAGIVIVTGAAGAALDPAGTAASAVAEATGTTAAAGSYAV
+TAWPWVAVTGGVLAALCGAVAALAGRGWVSVRRYEKAEATDAAEPAAPGRAAAPGRTEAE
+RRRTEQMDAWDELSRGNDPT
+>GCF_020097155.1_01702
+MRRRWIVLAALLAGVLVLAATGQTWVTASGLEGSPVPQATAGGGRVAPVATALALVVMAG
+ALALTTARRVGVVLVGVLMTLAGVVIASTAVTAALDPVAAAAGAVSELTGTTAPAAAYAV
+SAWPWVSAAGGVMAAVLGVATLVVGPRWAASRRFESPATADEPAAAAPPSRHVDRMDAWD
+ELSRGEDPT
+>GCF_023573625.1_01032
+MRRRTVVLAALAAGGLVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG
+ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV
+TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA
+QRRRVDQMDAWDELSRGNDPT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000900.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000900.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70a919b2c4b28f836a50dd386ebb2ab72b09ff6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000900.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01084
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGVALMAVGVVVGIVAGKAGAGRGQHGH
+>GCF_003691675.1_00803
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGLALMAVGVVVGIVAGKAGAGRGQHGH
+>GCF_005280335.1_01813
+MSHTANTEHTTRRAARNGAVEDVVVTEDGRVLNDPTHLELPDHGNTPGGWAMVALVLVGF
+VAGCIGLLADWMIVVWIGVALIVVGVLVGIVAGRGGSARSGHRAH
+>GCF_020097155.1_01701
+MSHTEATVNHTAQAGAHAAGHTTGHTASREVVVTEDGRVLNDPTHAKVPGHGNSPAAWAM
+AGLVVLGFLAGCIGLLNDALVIVWIGVAVIVVGVLVGIVGGKAAGRSDH
+>GCF_023573625.1_01033
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGLALMAVGVVVGIVAGKAGAGRGQHGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000902.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000902.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb487b76de7bff1ec87f4e7701bb4e90b5064e0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000902.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01086
+MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEEARQDPAFEA
+ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG
+ARTLKDAINEALRDWVASVDTTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR
+LPDAVAACVGGGSNAMGLFHGFLDDPGVELYGFEAGGEGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGQERIIIVNLSGRGDKDVATAAAWF
+GLGTATEEKDPLEEMTPGEEQ
+>GCF_003691675.1_00805
+MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEQARQDPAFEA
+ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG
+ARTLKDAINEALRDWVASVDNTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR
+LPDAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGEGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGEERIIIVNLSGRGDKDVATAAAWF
+GLGTAAEEKDPLEEMTPGEEQ
+>GCF_005280335.1_01811
+MSADRPSTEPTVEFEGPYQGQSGPYFGDYGGQWMPESLMAALQEVQRTYEEARQDPAFEG
+ELRTLFRDYVNRPSLLSDVPRFAADSPGVRIMLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG
+ARTLKDAINEALRDWVASVDTTHYLLGTVTGPHPFPAMVRYFHSVIGEEARQQVLAQTGR
+LPHAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGDGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLNDTGRAVYEPVTDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDTPEGEERIIVVNLSGRGDKDVATAAAWF
+GLGQADAEKDPLEELTPGEEQ
+>GCF_020097155.1_01699
+MTSTESVDVAGPFQDQPGPYFGRYGGQWMPESLMAALKEVADTYEAARQDPEFLAELEDL
+YANYVNRPSLLTEAPRFAAEVPGVRIFLKREDLNHTGSHKINNVIGQALLARRMGKTRLI
+AETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVIPVTIGARTLK
+DAINEALRDWVASVDTTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQTGRLPDAV
+AACVGGGSNAMGLFHGFLDDPEVELYGFEAGGDGVETGRHAASITLGRTGVLHGARTYLM
+QDEDGQTIDSHSISAGLDYPAVGPEHAFLNDTGRATYEPVTDTECMDALLRLTRTEGITP
+AIESAHALAGALRLARRWRDEGLVGEGTPEGEERIIIVNLSGRGDKDVATAAAWFGLGEA
+DEQKDPLEEMTPGEEQ
+>GCF_023573625.1_01035
+MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEQARQDPAFEA
+ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVIPVAIG
+ARTLKDAINEALRDWVASVDNTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR
+LPDAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGEGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGQERIIIVNLSGRGDKDVATAAAWF
+GLGTAAEEKDPLEEMTPGEEQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000903.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000903.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14a610ce264812154218d367c84b636aa6c0b694
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000903.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01087
+MTVNSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAADNGADVIELGLPYTDP
+VMDGPVIQAATQAALQAGFHVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGALARELAAGAVREG
+>GCF_003691675.1_00806
+MTVHSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQTALQAGFRVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGTLTRELAAGTVREG
+>GCF_005280335.1_01810
+MTVHSKTAAALDAARRAGRTGLVAYLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQASLRAGFRVADVFEIIRRVTQRVDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWLEASDRHGLDRVFLTAPSSTDERVRLAVESSRGFVYAVS
+VMGVTGARDAVSTAAETVVRRAEEAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALGEGGPQAVGALARELAAGAVREG
+>GCF_020097155.1_01698
+MSTPDQQHEATAEKPSTAGDAIERARAAGRTALIGYLPAGYPSIDESVEAAVQLGENGVD
+VIEIGLPYSDPVMDGPVIQAATSHALANGFHTRDVFEVVRRITERTEAAVVVMTYWNLVD
+RMGVDEFARRLAEAGGAGLVTPDLVPEEAGEWFEASEEHGLDRIFLTAPSSSDERVRLAV
+ESSRGFVYGVSVMGVTGARGKVSDAAERVVARAKAAGARNVCVGLGISSADHVREIGSYA
+DGAIVGTALVKALRDGGPEAVGALARELAAGTAKES
+>GCF_023573625.1_01036
+MTVHSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQTALQAGFRVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGTLTRELAAGTVREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000905.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000905.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a3d972b8c42ca1812ff1fc778634cfc56651b48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000905.fa
@@ -0,0 +1,135 @@
+>GCF_002008305.4_01089
+MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ
+HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV
+DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT
+EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL
+GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF
+PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM
+EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR
+VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL
+QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN
+PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR
+LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT
+SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV
+SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS
+PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL
+QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST
+GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS
+LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED
+LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK
+HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV
+SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD
+EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID
+HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA
+GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT
+SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA
+WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG
+DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG
+>GCF_003691675.1_00808
+MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ
+HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV
+DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT
+EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL
+GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF
+PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM
+EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR
+VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL
+QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN
+PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR
+LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT
+SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV
+SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS
+PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL
+QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST
+GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS
+LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED
+LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK
+HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV
+SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD
+EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID
+HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA
+GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT
+SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA
+WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG
+DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG
+>GCF_005280335.1_01807
+MQHPSKTPHADPFRAFAAQPEAAGLYDPEQEKDACGLAAVATLRGPATHKIVQDALTALR
+ALEHRGAVGADEGTGDGAGIITQVPDALLRATVSFELPAAGEYAVGTAFLPQDEAARTAA
+QEAIAEAAVVEGLDLLGWRPVPTDESVLGPGSRAVVPVFEQLFLAVSAGEDVEAPGQSLD
+ARAWRLRRRAQRSGVYFPSLSSRTLVYKGMLSTAQVEPFYPDLSDERYVTRLAVVHSRFS
+TNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGELRHPLLGEVPEEMFPIVSASGS
+DSASFDEVAELIHLAGRPLSHAIMMMVPEAWENHTTMDEDRRAFYQYHSMLMEPWDGPAA
+IAFTDGVQLGSVLDRNGLRPARYWETRDGLVVLASEVGVLDIDPATVVRKGRVKPGRMFL
+LDTEQGRIIEDEEVKAEIAASAPWKDWVADSLRRIEDLPEREPVRYHGDSVRLRQRLFGY
+TDEEVRTIIEPMARHGAEPLGAMGTDTPIAALSPRPRLLFDYFTQNFAQVTNPPLDSIRE
+EQVTSMRTCIGPQASLLAAGKVTTDAVEIPFPVLDNEQLARIAAVRAEDGTRRALKVKGL
+YLVAGGAEEMRSRLKEICEQVSAAVQRGVQYVVLSDRDANAQWAPIPSLLLTSAVHHHLL
+ASASRTRTSLLVEAGDVREVHHVAVLIGYGASAVNPYLSMETAEELVRTGTLTGVTEQEA
+TRNLIHGLGKGVQKIMSKMGISTVASYCGAQTFEALGLSRSFVDRYFTGTRSPMDGVGLD
+VIAAESAARHATAFPVDGSSASTVGPRGTSGLPVGGEYKWRREGPPHLFNPETVFRLQHA
+TRERRYDIFKDYTRRVDEQSADLMTLRGLLGLATKGRERVPVSEVESVESIVKRFSTGAM
+SYGSISQEAHETLAVAMNRLGARSNSGEGGEDPERLLDPERNSRVKQIASGRFGVTSLYL
+STATDLQIKMAQGAKPGEGGQLMGAKVYPWVARTRHSTPGVSLVSPPPHHDIYSIEDLAQ
+LIHDLKRANPQARVHVKLVSETGVGTVAAGVTKAKADVVLISGHDGGTGASPLNSLKHAG
+TPWELGLSEAQQTLRLNGLRDRVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVVSGC
+IMMRVCHLDTCPVGVATQNPELRARFTGRPEFVVTFFEYIAQEVRELLAELGLRSLDEAI
+GRQDLLHKDAAIGHFKTEGLDLSGVLSDAGVPEEAPRRRLTEQDHRLQDQADQRWLDQVA
+DAVVTETPVTVTDRLVNTDRSVGTLLGHRVTAARLDDELPRDTIRIELTGEAGQSLGAFL
+PAGVSITLSGDANDYVGKGLSGGTVALRPAPEAPFAAEENMIAGNVVGYGATSGRLFLNG
+RVGERFLVRNSGAVAVVEGIGDHGLEYMTGGTALVLGNTGRNLAAGMSGGVGFFLDLDPA
+QLNPLAVKDDELLLGRPEGADRALIRELLEEHRAATGSDLAARLLAELDGPAESAEALWE
+RFTTVLPRRYAAVQEIRTDSRDAGTDPDGDAAWARILEVTRG
+>GCF_020097155.1_01696
+MTVAPLSAPTPRSGRSDDPFVRYAAFPEPQGLYDPARETENCGLAVIATLRGTPGHDIVE
+HALTALRALEHRGAVGADEGTGDGAGLLTQLPDELFRAVLDVELPPVGEYAAGIAFLPPL
+EGERAEAKAAVEELAQAEGLDVLAWRVVPTDPSALGTGSRAAMPSFEQVFLALAEGEDGT
+EPGQSLDVRAWRLRRRTQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDPRFTTRL
+GIVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEELF
+PLISPIGSDSASFDEVAELLMLSGRPLTQAVMMMIPEAWENHATMDPARRAFYQYHSMLM
+EPWDGPAAVAFSDGTQVGAVLDRNGLRPARYWETRDGLVVLASEVGVVSIDPADVVRKGR
+VAPGRMFLVDTEQGRIVEDEEIKAEVAAAAPWEEWVSQNLLDLDALPEREHLRPSSESIQ
+QRQRIFGYTAEELRVLVGPMARDGAEPLGAMGTDTPIAVLSKRPRLLFDYFVQSFAQVTN
+PPLDAIREEQVTSMRTGIGPQGNVLSAERVHTRQVDVPFPVIDNDQLARIQHLRDGDGGR
+LALKVTGTYRVAGGAEELRTRLKEICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT
+SAVHHHLLASANRTRTSLVVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEI
+EGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFAGTTS
+PLDGVGLEVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL
+QHSTRERRYDVFKDYTRRVDGQAEELMTLRGLMRLRSEDRTPVPISEVEPVESIVRRFST
+GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS
+LYLTTATDLQIKMAQGAKPGEGGQLMGAKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED
+LAQLIHDLKRSNPAARVHVKLVSESGVGTVAAGVAKAKADVVLISGHDGGTGASPLNSLK
+HAGTPWELGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVVAALLGAEEFGFATAPLVV
+SGCIMMRVCHLDTCPVGVATQNPELRSRFTGKPEFVVNFFEFVAQEVRELLAELGFRTLD
+EAIGHRELLDVDAALHHWKTEGLDLSGILADPSVGRRAGAADAPMRRMVDQDHDLAAHID
+NRLIARLGDTLATGAPVVMDESVVNTDRSIGTMLGHHVTSTRLADELPADTITVRLTGEA
+GQSLGAFLPAGVTLRLDGDANDYVGKGLSGGRVVVRPDATAPFAAEDNTVAGNVIGYGAT
+SGELFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALVLGETGRNLAAGMSGGRA
+WILDLDRADLNPLAVREGDLLLSTPSAADRERIAALLRTHRAETGSAVAERLLADLDAGG
+DAAQGVWDRFTTILPRRYDLVLRTRAEAVAEGLDPDGEAVWDRLLEVTRG
+>GCF_023573625.1_01038
+MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ
+HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV
+DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT
+EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL
+GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF
+PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM
+EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR
+VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL
+QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN
+PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR
+LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT
+SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV
+SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS
+PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL
+QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST
+GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS
+LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED
+LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK
+HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV
+SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD
+EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID
+HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA
+GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT
+SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA
+WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG
+DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000906.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000906.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5e9cd059dd17e4ed680a07aeffd6d587e0f31be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000906.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01090
+MADPRGFLKNRERVDRPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRRRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
+>GCF_003691675.1_00809
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRRRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
+>GCF_005280335.1_01806
+MADPRGFLKHRERVARPSRPVPVRIMDFKDVHVRQDEAIVRTEASRCMDCGVPFCHAGCP
+LGNLIPEFNDLVYRDDWDEAGARLEATNNFPEFTGRICPAPCEASCVLGINQPAVSIKQV
+EQSIADHLFDAPSLTPHPPQRQNGLTVAVVGSGPAGLAAAQQLTRSGYTVVVYEKDEALG
+GLLRFGIPDFKLEKHLIDRRIAQMTEEGTRFRTGVRIGTDMSWEALQRRYDAVVLATGAP
+VGRELPLPGRGLDGIHLAMDYLVPVNRRVAGGEPEPISAQGRHVVILGGGDTGADCIGTA
+HRQGAASVTTLAIGRRPPEQRPEHQPWPTVPTLFEVASAHAEGGERTYLASTVEFLGDAE
+GRVRALKVAETEIRADGTRGPRAGTEHEIPADLVLLALGFTGADLDELVDRSAVSLERGL
+VVRDETYATQAPGVFACGDVSRGASLVVWAIAEGRAVAAEVDRFLTGDTMLPAPVRPSDH
+GFVLR
+>GCF_020097155.1_01695
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAVVRTQASRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRGRWEDAAARLHSTNNFPEVTGRICPAPCEDACTLGINQPAVTIKQT
+EVAIAEQIFDHDWLEPVVPTRINGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDDRPG
+GLLRYGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGRDLAWDALKARFDAVIVATGAP
+VGRELPVPGRGLDGIHLAMDYLVQSNHATAGDDVPGQITAEGRHVVVLGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVDRPVHQPWPTVPKVHQMTTADAEGGQREHLASTVEFLGDE
+NGRVRALRVAETEYRADGTRGPKAGTEREVKADLVLLALGFTGVEEEALTAQLAVRTERG
+LVARAGTYETDEPGVFVCGDAGRGASLVVWAIAEGRACAQAVDESLESWSRLPHPVDPTD
+RGLVLG
+>GCF_023573625.1_01039
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRGRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000907.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000907.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d48e8787b08fefa4020367fa4fceb36e09eab3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000907.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01091
+MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEESRP
+VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV
+LLVDDGKVRLRAVEVTDTDVLAEVEVPGTVSDNKGINLPGVAVNVPALSEKDERDLRWAL
+RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAVMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE
+VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD
+STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGDDAAGGSSAASP
+QTREPLGFWPARSPL
+>GCF_003691675.1_00810
+MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEERRP
+VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV
+LLVDDGKVRLRAVEVTDTDVLAEVEVPGMVSDNKGINLPGVAVNVPALSEKDERDLRWAL
+RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAIMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE
+VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD
+STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGGDAAGGSSAASP
+QTREPVGFWPARSPL
+>GCF_005280335.1_01805
+MRHAKIIATFGPATASDETTRSIIRAGADVVRLNMSHGDHEVHAASFERVRRLSVEERRP
+VAIFADLQGPKIRLGRFADGPHHLETGDRFTITTRDVEGTAELVGTTHAGLPGDVRPGDT
+LLVDDGKVRLRAVEVTDTDVVTEVEVGGDVSDSKGINLPGVAVDVPALSEKDEEDLRWAL
+RTGVDMVALSFVRDAADIERVHAIMDEEERRIPVIAKIEKPQAVDNLEAIVDAFDAVMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIENPRPTRAEASDCANAVL
+DGADAVMLSGETSVGRYPVETVQTMARIIESTETHGLEMIHPLGSRPRTRGGAITRAAVE
+VADQLDIPFLATFTESGDSARRLSRLRPRQPIYAFTHREHTHNILCLTWGVYPKMVSFQD
+STDKMTLQVEESLTSEGIAERGDLVVIAAGSPPGMVGSTNTLRVHRVGDDAGGGSSPARP
+VQKEPVGFWPARSPL
+>GCF_020097155.1_01694
+MRHAKIIATFGPATQTDETTRALIRAGADVVRLNMSHGDHEVHASSYERVRRLSVEEKRP
+VAIFADLQGPKIRLARFSDGPHELAVGDRFTITTREVTGSREIVGTTHKGLPGDVSVGDP
+LLVDDGKVRLRAVEVTDTDVVTEVVVPGKVSDNKGINLPGVAVNVPALSEKDEEDLRWAL
+ETGVDMVALSFVRDAADVTRVHEVMDEVGRRIPVIAKIEKPQAVDNLEAIVDAFDAIMVA
+RGDLGVELPLEDVPIVQKRAIELARRWAKPVIVATQVLESMIENPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVQTVETMARIIESTETHGLDMIHPLGSRPRTRGGAITRAAVE
+VAGQLDIPFLATFTESGDTARRLSRLRPSQPIYAFTHEEHTHNILCLTWGVYPKMVPFAD
+STDKMTMQVEESLTSEGIAEQGDLVVIAAGSPPGKVGSTNTLRVHRVGDGVAADSSPVAP
+EDREPVGFWAAHSPM
+>GCF_023573625.1_01040
+MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEERRP
+VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV
+LLVDDGKVRLRAVEVTDTDVLAEVEVPGMVSNNKGINLPGVAVNVPALSEKDERDLRWAL
+RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAVMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE
+VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD
+STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGDDAAGGSSAASP
+QTREPVGFWPARSPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000908.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000908.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dec1af471236a64c0b41440591d08b473f65aed0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000908.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01092
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG
+>GCF_003691675.1_00811
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG
+>GCF_005280335.1_01804
+MPMTTPAEGTGLRAVVAEDETLIRLDLVEVLTGAGYEVVAEAGDGAAAVAAVREQRPDIV
+VMDVQMPVMDGIAAASEIAQDRLAPVVMLTAFSQRDLVERARTAGAMAYVVKPFTEHDLV
+PAVELAVARFEELRSLESEVRDLGDRLETRKLVDRAKSVLQDRLRLSEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVR
+>GCF_020097155.1_01693
+MTIPAESADPTAGLRVVVAEDEALIRLDVVETLTHAGHTVVAEVGDGQAAVAAVREHRPD
+IVVMDVMMPVMDGIAAAGEIAAERLAPVVMLTAFSQRDLVERASQVGAMAYVVKPFTEKD
+LLPAMELAVARFDQLRGLEEEVRGLEDRLATRKLVDRAKSLLQAHMGLSEAESFRWIQKT
+SMDRRLTMREVAQTVVDQIGA
+>GCF_023573625.1_01041
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000909.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000909.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c63e5ae7eafcdd699a8f7eb51363c2f0db88205f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000909.fa
@@ -0,0 +1,77 @@
+>GCF_002008305.4_01094
+MLLTSLLLTLLSVVAAVPASRALGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA
+VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL
+LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR
+TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH
+AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS
+QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM
+PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY
+SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEASATFWGVPVLAAAAGVALGLLPGVLD
+TPVSYAAEAASGAEVHAHLALWHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF
+SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ
+PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE
+VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY
+LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR
+SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA
+DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV
+YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR
+>GCF_003691675.1_00813
+MLLTSLLLTLLSVVAAVPASRVLGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA
+VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL
+LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR
+TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH
+AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS
+QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM
+PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY
+SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEAPATFWGVPVLAAAAGVALGLLPGVLD
+TPVSYAAEAASGAEVHAHLALWHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF
+SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ
+PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE
+VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY
+LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR
+SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA
+DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV
+YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR
+>GCF_005280335.1_01801
+MDEARHGLVRLGALVDRASGSVAPRVHLLIPACVLGAFALAGVFTVDDLPAVVGTPSRWH
+DWALVVLVGAGVVATIRAKTRISAMVVVGVVGFGVTLWFFTLGAVDVALTQLLVEVLTVC
+VMVLLLRRLPGRFRDEEAPRRVQAVVAATIAGVAATVGVLAFTGRSEMSEIAHFYLTQTY
+AQAGGVNVVNVILVDFRALDTLGEMTVLGATGLTVAALLLNRRPAPPQRSAVDLRSPLAH
+VRENLVHIRVFGRVFGVLIIALSVLLLLRGHYEPGGGFIAALVAGAGYALLYLAADHDTD
+RRLQWPYLTLIGGGIALGALTGVAGYLTGKGFLGAAGVKILGYGLSTTLAFDLGVYLAVL
+GLIVAAFSLLGPERSETEAGAEPDPTSPIADPAAEQTTGQTTEPTTAPGTAPTPAAAREE
+TSR
+>GCF_020097155.1_01691
+MLLTSLLLTLLAVVLAAPLGRTLGRDAGWVLALPLLTSAGALVSARAGGGGETVVERRPW
+IPSLGAHLDLRLDGLAFVFALLVLVVGAGILAYSSRYLPRDRDEARAGSFYTLMTAFAAS
+MLLLVLADNLVVLFVAWEFTSFASFLLIARSGDHARRPAIRTLLVTVGGGLCLLAAVALT
+AARTGTASLSGALASDAWADPGFAAPVAALLAVAAFTKSAQFPFQSWLPDSMVAISPVSA
+YLHAAAMVKAGIYLLLVFSPVLAGTPVWSALLIGSGLTTALLGAVSAIRRHDLKGLLAYS
+TMSQLGLLVTAIGVGTPTALAAAVVHTVAHALFKSTLFMLIGVVDHEAGTRDLRDLAARH
+VRMPVTGAAIAVAAASMAGLPPLLGFVSKEGLLDAALGAQGPAWLPGLVTAGIALTSVFT
+VAYSGRLVLGALGVWGTAPAGAADMWSAGRGEDVHEAPAAFWAVPVLGVVVTLVLGLVPG
+VLDEAVAAAATAAAGAPVHAHLALWHGVTPALLVSAGVIAAGLALVAARRPVERVASHAG
+LPFSGLGVVDGILRGAVSLGAAVSRVSGGIAPRAHLLMPALVLGAFAVAGVVASPDLPAV
+VGQPSRWHDWALVALVGVGVAATLRARTRIAAMVVVGTVGFGVTLWFFTLGAVDVALTQL
+MVEVLTVCVMVLLLRRLPARFSAESTPHRAGAVAAAVIAGVASTLSVLAFTGRREISDIA
+QYYLDRTYPDAGGHNVVNVILVDFRALDTLGEMTVLGVTGLTVAALLMNRRPAPPQPSAV
+DVRSPLAAVHENLVYARTFGRALGPIILVLSVLLLLRGHYEPGGGFIAALVGGAGYALLH
+LSADTDDEPRLRWPYLALIGGGVTLGTVAGLAGYLTGKGFLGSASVKVLGYSLGTTLAFD
+MGVYLAVLGLIVAAFRLLGPDNATADDAAPAPTTGGESAREEAAR
+>GCF_023573625.1_01043
+MLLTSLLLTLLSVVAAVPASRVLGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA
+VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL
+LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR
+TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH
+AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS
+QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM
+PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY
+SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEAPATFWGVPVLAAAAGVALGLLPGVLD
+TPVSYAAEAASGAEVHAHLALLHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF
+SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ
+PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE
+VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY
+LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR
+SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA
+DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV
+YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000914.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000914.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0da0ef43eb6a5fd8d04a254c0691f61c7bea370b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000914.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01099
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+APDEV
+>GCF_003691675.1_00818
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+APDEV
+>GCF_005280335.1_01796
+MDLVLTVIGSVLVVAGALVFVTAGLGLIRFPDPYTRISATGTAGGVGMILIVVGGLVLAP
+SVANVVKVALIVVLQLGSAAVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+TPDAS
+>GCF_020097155.1_01686
+MDLVMTVAGSVLAVAGAVVFLGAAVGLIRFPDPYTRISATGTAGGVGMILIVTGGLLLMP
+SVANLVKVVLIVVLQLGTAAIATMALGRSAYLTGVPMNLAHYDELAEDTPGREHGEPAPR
+HPED
+>GCF_023573625.1_01048
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREGGRAAPR
+LPDMD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000915.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000915.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ba783b38fa6f92827496d023d612ae88f02180f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000915.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01100
+MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAVISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP
+>GCF_003691675.1_00819
+MSEHTATTPAASDRVYRPGVTPELSPAELAAACAEAGLTPELVAALGGAAISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP
+>GCF_005280335.1_01795
+MTDHAERADAAPAPTSDLVYRPGVTPELTDAQREAACAAAGLTPELVAALGGATVSPLAQ
+KMGIRFLELTPERAVATMPVAGNEQPAGLLHGGAHLVLAESLGSMAAKLHAGPERGVVGI
+EIGATHHRAARSGLVTGTATAIHLGGTLTTHEVVMTDEQGRRLSTARITNMVLRGRG
+>GCF_020097155.1_01685
+MTDTTTAPERAQALLAGLTFHAGIRPELTDEERAALATAAGMTPAVQEALGGPAVSHLAL
+KMGIRFLELSAERSVATMPVAGNEQPVGLLHGGAHLVLAESLGSLSAKVHAGPHRGAVGT
+EIGATHHRSVRSGLVTGTATAIHLGRTLTTHEIVMTDEEGRRLSTVRMTNMLLDPR
+>GCF_023573625.1_01049
+MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAAISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDHNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000916.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000916.fa
new file mode 100644
index 0000000000000000000000000000000000000000..309ea1dc5e44ae3772bcdb0711343d7116002fd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000916.fa
@@ -0,0 +1,85 @@
+>GCF_002008305.4_01101
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVKAKYG
+VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLETMRLEMPEREPVEELFDALQFHRIRERVFEVFGE
+RVGEDAPPPEVEAAPEFTEATTAEDVRAFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGT
+FGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEGGLAKAVHDLKRTLKALAAPT
+EGDGLGPDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPRESAQQRAQGS
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM
+ELTGIAVDVDALTGLREDFTDAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLN
+MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE
+LEKATALLKERMGRAAELSVPLDVHVGQGRSWHDAAH
+>GCF_003691675.1_00820
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVMAKYG
+VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGE
+RVGEDAPPPEAEAAPEFTEATTAEDVRSFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGT
+FGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEGGLAKAVHDLKRTLKALAAPT
+EGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM
+ELTGIAVDVDALTGLREDFTDAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLN
+MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE
+LEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH
+>GCF_005280335.1_01794
+MAADPTPEDPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTITLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVMAKYG
+VSPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLTQYGDLDGVLAHADEIKGKKGEALR
+AHLDDVRRNRRLNALVRDLDLPIGLEAMALEMPEREPVEELFDALQFNRIRERVFEVFSE
+RIGETAPAAQVEEAPEFTEAATAQDVADFLAAEAGNLLGVHVDVEGPALLPKRKVPVPGT
+FGTAVGVALVGEHAGLHVSLDADAPDPALLAALREALGEGGLSKAVHDLKRVLKAIAEPA
+EATALEAGTPLDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLAAPREPAEADAQGA
+FDLDGGAAAAERAARAADAVRAAWVVRRLSVLFTPQVLERGAQRLLQELEIPLARLLARI
+ELTGIAVDAQALETLRADFSEAAAAAQESAWASVAEETGGMKVNLGSPKQLQEVLFEHLD
+MPRTRKTKTGWSTDVDSLQDLLEQTRHPFLENLMRHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADRVAGEDAVLLSADYSQIEMR
+IMAHLSEDAGLIQAFREGEDLHSFVGSQVFGVAPDEVSSEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARRDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLAEHGMASRLLLQVHDELILEVPAAE
+LEQATALLQERMGRAAELAVPLDVHVGQGRSWHDAAH
+>GCF_020097155.1_01684
+MGENSTEARPRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTSMLLTMIRQQAP
+THVAVAFDLSGPTFRSAEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTKEDFEAD
+DIVATLSAQAEAQGWDVCVVSGDRDAFQLISERTQVLYPKKGVSDIPPMTAADVEAKYGV
+RPEQYPELAALVGESADNLPGVPGVGPGFAAKWLQKYGDLDGVLAHADEITGKKGEALRA
+HLDDVRRNRRLNALVRDLDLDVSLDAMELTMPEREVVEELFDALQFQRIRERVFEVFAER
+LGSAAPAAPVAEAPAAVLAATADDVHAFVSAHAGTLLGLHVEIDGPDLLPKRKVPVPGTF
+GTPVGLALAAEDAALYVDLTDADADPGLVAALGDLLAEDGAAKAVHDLKRTLKAIAVPTG
+PTALPADTSLHGVVDDVALSAYLIQPDRRDTDLATLSQAHLQEPLEAPESAAAGAQGAFD
+LDGAQEEAERTARAARAARSAWVVRRLSQAFTPQVLERGAQRLLQEMEIPLARLLARMEL
+AGIAVDGDALSALLADFTDRAEAAKESAWASVAEETGGMKVNLGSPKQLQEVLFEHLDMP
+KTRKTKTGWSTDVDSLQDLLEQTQHPFLENLMAHRDATKLRQTVEGLRETVAPDGRIHTT
+YSQTVAATGRLSSLHPNLQNIPVRTEAGRRIREAFVAAPVDGEPAELLSADYSQIEMRIM
+AHLSEDAGLIEAFNSGEDLHSFVGSQVFGVDPDDVTSEQRSKVKAMSYGLAYGLSSFGLS
+KQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARRDGFTSTIEGRRRYLPDLTSDNRQ
+LRDMAERAALNAPIQGSAADIIKRAMLDVQAGLVEQGLRSRLLLQVHDELILEVPASELD
+AATALLQERMGRAADLSVPLDVHVGHGGTWHAAAH
+>GCF_023573625.1_01050
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVKAKYG
+VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGE
+RVGEDAPPPEVEAAPEFTEATTAEDVRAFLAAEAGTLLGVHVDVEGPALLPRRKVPVPGT
+FGTPVGVALVGEHAGLHVSLDGDAPDPALVGAVREALGEGGLAKAVHDLKRTLKALAAPT
+EGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM
+ELTGIAVDVDALTGLREDFTVAADAAKESAWASVAEETGGMQVNLGSPKQLQDVLFERLN
+MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIRGVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE
+LEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000917.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000917.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f00449c895ce92c90c5508a1547e0fbd429dc45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000917.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01103
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN
+>GCF_003691675.1_00822
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN
+>GCF_005280335.1_01791
+MTTTSNAPQVAINDIGTAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVESNEWMEGFESERAAWEQQY
+ADAQSRWEQHKEQVRRSFEEEANAGADTGAGMGGSSYSSEAPASDGGTLASDEALAALRE
+KLTGN
+>GCF_020097155.1_01682
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKVKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRQGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQDVTVEVLDVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDQLFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDDEGNYKYPEGFDVETNEWMEGFESERASWEQQY
+ADAQTRWEAHKEQVRRSLEEEAQAPAGNASTASSYSSEAPASDGGTLASDEALAALREKL
+TGN
+>GCF_023573625.1_01052
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000918.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000918.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8bf869f04ab0de4ad6e8bc8471dc7adff1ea5ad6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000918.fa
@@ -0,0 +1,37 @@
+>GCF_002008305.4_01104
+MSEPLPRGVTPDVAHGGLPDDLTAGVDFAALDRWPLPPEPDRQAHDAADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGEA
+GELERTATPEDAARGARTVLLPLPRSLDELDRLSRIVAAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTPRPPEEADRDVPGVGSLHLVAHAGAFG
+GAAADPGSRLLLASLADDPRPPGRLVDLGCGNGLLSVGAARLWPHVTVLATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGTEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRPVLEDLVGPTRQTARDRTFTVTVSERR
+>GCF_003691675.1_00823
+MSEPLPRGVTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHDTADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGET
+GELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVPGVGRLHLVAHAGTFG
+GAAADPGSRLLLASLADDPRPPGRVVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRSVLEDLVGPTRQTARDRTFTVTVSERR
+>GCF_005280335.1_01790
+MDLGCGNGLLGVGAARLWPHVRVLATDQSAVAVASTLATARANGVADRLEAVRDDALAGR
+PDASEECILLNPPFHDGNAVDPAVAHRLVAEAARVLAPGGRLWCVWNSHLRHRPVLEAEV
+GPTRQVARDRTFTVTVSTRR
+>GCF_020097155.1_01681
+MDAIAQTPPRDPGPARLTATELVTPDAAGRGLPRDWTAEFPFERLGRWPLPESRERQAHD
+AADLLLVDTLAGWTADGRVPGPVAVLHDQHGAVSLPLLARGLNVRLGLDEASAARSVERN
+LDLFRDADGALPAGWGRLTVGGVDAATLADARTVLLLLPRALDALHLTAARIAVHAAPDV
+LVLGAGRDKHMTPSMNDVLARSFAAVVPGRGRSKSRVITAARPVDDATEPAPRRAQHRLG
+RLGAVTLVGGWATFGGAAADPGSLLLAGTLADRAPALPVPAPHRMRTDSGLGVDIPWATR
+AGAPDVVDAGSGNGMLSVVAARVWPEAAVLASDQSADAVASSAATAEANGLAERITAVQD
+DALGALPDASVRAVLLNPPFHDGTAVDPTVAHRMIEAAGRILAPGGELWCVWNSHLRHRP
+VLETAVGPTRQVARNRTFTVTVSTRR
+>GCF_023573625.1_01053
+MSEPLPRGVTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHDAADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGET
+GELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVPGVGRLHLVAHAGTFG
+GAAADPGSRLLLASLADDPRPPGRVVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRSVLEDLVGPTRQTARDRTFTVTVSERR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000920.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000920.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7714943e57810f448b55d042bac8393bb362f8ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000920.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01107
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
+>GCF_003691675.1_00826
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
+>GCF_005280335.1_01786
+MTESVPVADRPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVLTSDGELDRVALAHIVFSDPQARQRLNRIVHPRIRAAARRIVAAAGPDAVVV
+QDVPLLVETGQQDAFDLVIVVEAPLEERLRRMVEDRGMTPEDAQARIDAQATDDQRRAAA
+DVVIVNDADLERLASVANQVWDRFLAPDAAEPSAD
+>GCF_020097155.1_01678
+MTDAVTDVTLRPRLHVGLTGGIAAGKSAVAAELERCGALLVDSDALARLVLEPGTEGLAA
+VQDAFGDRVIAADGSLDRAALAQIVFADPAARQRLNGIVHPRVRRMAREIVAQAGPDAVV
+VQDVPLLVETGQADAFDLVIVVEAPAEERIRRMVEDRGMSREDALARMAAQATDEERAAV
+ADVVIVNDGDLDRLREITRRVWEGMAA
+>GCF_023573625.1_01056
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000921.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000921.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff366da9815b1853417878c8f65005849e4589f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000921.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_01108
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDRLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRAPATGEGAEAPAVDPASL
+PAKDLADLIEQMSQQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
+>GCF_003691675.1_00827
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRDATTGEGTEAPAVDPASL
+PAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
+>GCF_005280335.1_01785
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSVNEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGEEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREETEMYIFPASHYVAGDERMGRAVTAIEDELRERLQELESQDRLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPDGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLDAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIEETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDYGMGHRGLSSLDREEGQERAGGGPAVDAASL
+PAKDLADLIEQMSLQMHQAAADLQFELAARLRDEVGELKKELRQMRREQ
+>GCF_020097155.1_01677
+MSLAKQINRVVAPFEVVSPYQPSGDQPTAIAEIAERVQAGEKDVVLMGATGTGKSATTAW
+VIEQLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVVVVATVSCIYGLGTPEEYIAQMVTLRRGQEMDRDA
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEVESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAIATIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGQYELSQADGVVEQII
+RPTGLVDPTVVVKPTQGQIDDLLEQIRTRTEKDERVLVTTLTKRMAEDLTEYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVSILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADRVTDSMRRAIEETERRREVQIRYNAEHGIDPQPLRKKI
+ADITDALAREDADSADFLKGMGGVKAGFDYGMGHRGLGSLDHEPPAGEVPSGSPAVDPAA
+LPAKDLAQLIEQMSAQMHQAAADLQFELAARLRDEIGDLKKELRQMKREQ
+>GCF_023573625.1_01057
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRDATTGEGTEAPAVDPASL
+PAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000922.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000922.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15e6c14c9079dc64a1c58acf2c9f2c92ab87332d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000922.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01109
+MSAAPPVAAVIADIVGSRALPDRDRAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGPAWYRAREAVERAHER
+AVGAATAFRAADPSLTAAVDGLVLLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQAVARSGIDRLLELDAELAAAATEVAP
+>GCF_003691675.1_00828
+MSAAPPVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGTAWYRAREAVEHAHER
+AAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQTVARSGIGRLLELDAELAAAATEVAP
+>GCF_005280335.1_01783
+MTRAPQAAAVIADIVGSRRLPDREAAQEQILAAFAVAEKDVPPLRAAWATVGDEFQALHG
+VWPQAVRAVVRVSLALPPGLELRFGIGVGERRSLDDGAGDRIEDGTAWYRARAAVERAHA
+RADGAATAFVAADPSLTAAVDGVLLLRDHVLGRLKARERRLAAALLGGATQTQAARAERI
+TQSAVSQAVTRSGIDRLLELDAALAEAAAGRPGHAGAAGEGAGDEGDAG
+>GCF_020097155.1_01676
+MSLTDEGPVRGTAVIADIVGSRGLRDRAAAQEAILAAFAAAEEAVPARIPAWATVGDEFQ
+ALHADWAAAVRATLRVAVALPEGVELRFGLGDGVHREVTGAADDDGRPILDGSAWHRARE
+ALEAAEHRTRGLAGAYRGPDADLTAAVDGQLLVRDHVLRRLKARERRIAAALLAGRTQAE
+TATAERITQGAVSQAVARSGVRELLALDAALGALPGAGRGAKATAEEDRP
+>GCF_023573625.1_01058
+MSAAPPVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGTAWYRAREAVEHAHER
+AAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQTVARSGIGRLLELDAELAAAATEVAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000924.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000924.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8af7af133060414914d7144470cb11746621283d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000924.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01113
+MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP
+HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD
+QRGTGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ
+SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR
+DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT
+GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD
+FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA
+AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT
+TTAPDPVD
+>GCF_003691675.1_00832
+MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP
+HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD
+QRATGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ
+SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR
+DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT
+GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD
+FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA
+AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT
+TTASDPVN
+>GCF_005280335.1_01780
+MSAPAPRVPGDPRGFAPLEPARHRVGERTELYDGTVAVDHWFTVPVDHALTLAEAEAQDA
+AGTGVGPHGRGTLTVFAREIRAAGDADGARPWALYLQGGPGGAGPRPARGGGWIGALASE
+HRVLLLDQRGTGRSTAASVAALTAPGAFASDEALAEHLVHLRAPSIVRDAEMVRLALGAA
+PWTTLGQSFGGFCTLTYLSFHPEGLRRCLVTGGLAPLTGHADRVYQATYARMRDRAHEFF
+ARHTGDRAAWAEAVALIRAAEQAGEPVRLPDGGLLTVARAQALGMLLGGNTRVDRLHWIL
+AEAVDRSGPAPRLSETFLAAVAEQNDRHVNPLYTVLHESIYAQPAELAGGRAATDWSAAR
+VLAEHPDFDPDAADAPLPTGEHVMPASLELDPHLRPLRGAARLLAERTDWGPLYDVEALA
+RNIVPVAAAVYTDDVYVDRDLSLETAGRVRGLRVWETDAFHHDGLADDGPAIVRRLLEMT
+GEGAAPAAAEGAERSDSAPAASETTTAPGPVD
+>GCF_020097155.1_01673
+MTRTGTGDAAFVPGDPRGFAPVGPAAHREGERTVLFDGTVAVDHWFTVPVDHALTLAEAL
+AQDAAGTGLGPGGRGTLEVFAREVRHPEDPEGERPWLLYLQGGPGSGGPRPARLGGWQCE
+LAQHHRLLLLDQRGTARSTPVTAATLAGLPDDAARAAYLTHLRAPQIVQDAEMIRVALGA
+PPWTTLGQSFGGFCTLSYLSWRAEGLERCLVTGGLAPLTGHADRVYRATTARMHARWQEF
+LERHPQDAGHWAEAVALIRAAQDDGDPYVLPDGTALTVGRAQQLGMLLGGNTRVDGLHWV
+LAEAVDRSGGEPRLSPGFLAAVAAQTTRAVNPLYAVLHEAIYAQPAALTDGRGATAWSAQ
+RVLAEHPDSSPAADPAPVPTGEHVLPWSFETEPELRALAGVAALLAAKDDWGALYDLDAL
+AANEVPVAAAVYTDDVYVDRDLSLETAARVRGLQVWETDAFHHDGLADDGPGIVRRLRGM
+LGA
+>GCF_023573625.1_01063
+MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP
+HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD
+QRGTGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ
+SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR
+DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT
+GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD
+FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA
+AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT
+TTAPDPVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000925.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000925.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f08d5cfff4ba3684abf8a96e72a2c0f782da258a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000925.fa
@@ -0,0 +1,80 @@
+>GCF_002008305.4_01114
+MTSAATNPPSLTDRIDALPPAPDADDVFGAFAAWTEDRGISLYPAQEEAALELVQGRHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEEFVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND
+RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRHTVPEAARTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA
+DDWADALDAYFDDHEDIDDGPAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDG
+DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>GCF_003691675.1_00833
+MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND
+RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA
+DDWADALDAYFDDHEDIDDGPAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDG
+DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>GCF_005280335.1_01779
+MTSPATNPPSLTDRIDALPPTPDADDVFGAFAAWTEVRGISLYPAQEEAALELVQGRHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLIERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKSPPAGFVSWGPATFERLVAAEPEPLVSRMQITHSMLLNILDRPGDPVVAVRRLL
+RGTHETPARQAILMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALELLDPAEPDHALDVVSVIEATLDPPRQVLSAQVKKAKGEAVAAMKAEGMDYND
+RMRALDEVTHPQPLADLLEQQFEVYRASAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRQTVPEASRTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIEELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEELARLSGDLSA
+DDWADALDAYFGDHEDIDDGPAARGTELFRVAESPDVAPPVELAGSRWWAVRQVLKDPDG
+VHDHGVNAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>GCF_020097155.1_01672
+MTPSATNPPSLTDRLDALPASPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGRHVI
+LATPTGSGKSLVALGAHADALAHGKVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+SVNADAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQLPLLELPQAR
+FLLMSATLGDTSMLERDLAERTGREVAVVAHAERPIPLSFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAVGLASISVTTKEEKEAIAERIAGFRFSAGFGKTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQEGRLKVISGTDTLGVGINVPIRTVLLTALSKFDGEKTRILQS
+REFHQIAGRAGRAGFDTQGYVVVQAPEHVIENKAAERKAAAKFAGIKDEAERAKRMKQSV
+KGSKRKTPPQGFVSWGPATFDKLVASEPEPLVSRMRITHSMLLNILDRPGDPVLAVRRLL
+RATHETPARQAQLMRRALGIFRELLATGVVEVLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPAAPDHHLDVVSVIEATLDAPRQVLSAQVKKAKGEAVAAMKAEGMDYSD
+RMRALDEVTHPQPLAELLEQAFERYRQDAPWLAEFELSPKSVVRDMFERAMGFGDYVRFY
+GLARSEGVLLRYLTDAVKALRQTVPQEDRTEDLQVLLDWLDEMVKQTDSSLLEEWEDLMS
+GDIAELRRDLESLEPTPPPRLTDNAAVFRVMVRNAMFHRVRLFGDEQDARLAELSGDLSA
+NDWADALDAYFDEHEDIDDGPDARGQEFFRVATAPGARCPVELEGSRWWAVRQVLKDHDG
+DHDHGINAVVDLEASDEAGHPAIRVVSVGAPVPGWDL
+>GCF_023573625.1_01064
+MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND
+RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA
+DDWADALDAYFDDHEDIDDGPAARGPELFRVTAAPDVAAPLELAGPRWWAVRQVLKDPDG
+DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000926.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000926.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b05b9ca9c51190e1c04cd65f3692adab4adfeeb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000926.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_01115
+MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGAPANLRFEAVDASQW
+RPSGATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEEGAAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MAGQKPA
+>GCF_003691675.1_00834
+MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGTPANLRFEAVDASQW
+RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEEGSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MVGQKPA
+>GCF_005280335.1_01778
+MSQIAPESPHPDTDAVAGDVTGRQGGGFTWDPAQYESFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLKRAREQAARTGAPANLRFEAVDASQW
+RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEECSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MVGQKPA
+>GCF_020097155.1_01671
+MSTVPAVTGRETAGFTWDPAQYEGFAEHRARPFHDLVARVEAEAPRVVVDLGCGPGTLTR
+TLAERWPAAEVIGLDDSPAMLERAREGAADADLPNLRFDRVDASQWRPGPEVDVIVSNAM
+LQWIPTHRRLIRRWLGDLHPGAWFGAQLPRPYQQASHATIVALADEPVFSEALHGVETTR
+TVAPPEEYTRLFLEAGWTPSVWETEYQQVLTGPDPVLRWTSGAALRPSLQALAAWDAEEG
+AAEGAGLLELFVARYRQAMREAYPPVPGVSDADGGPLTVFPVRRMFLVGRKPGE
+>GCF_023573625.1_01065
+MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGTPANLRFEAVDASQW
+RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEEGSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MVGQKPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000927.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000927.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49f7f28adc1f671756fad6df4294d7f3cd7cf5b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000927.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01116
+MPETARNRLLHDLPAVTVRTCSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA
+ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR
+HGDTVGADGLRLEVVALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVSDRIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERSW
+>GCF_003691675.1_00835
+MPETARNRLLHDLPAVTVRACSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA
+ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR
+HGDIVGVDGLRLEVLALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVTERIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERGW
+>GCF_005280335.1_01777
+MPETARNRLLHDLPAVTVRTSSVSEMDNNVYLLTSKTTGAQVLIDAADDAEAIRDLIASA
+AGDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLH
+HGDIVGADGLRLEVVALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVSERIFDAFDDDVVVHPGHGASTTLGAERPHLPKWAERGW
+>GCF_020097155.1_01670
+MPATAEPRLLHDLPAVTVRAVSVSEMDNNAYVLTSKTTGAQVLIDAAAEPETLRDLLASA
+AADTPCELRLELIVTTHRHWDHVRALPALATVTGARTAAGEDDADAIAAETGVTPDVRLA
+HGSRTGAEGIELEVIALRGHTPGSVALAYRPEADEPAVLFTGDSLFPGGVGNTQGDAERF
+ASLIRDVEDRVFAAFDDDVVVHPGHGASTTLGAERPHLQEWRERGW
+>GCF_023573625.1_01066
+MPETARNRLLHDLPAVTVRACSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA
+ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR
+HGDIVGVDGLRLEVLALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVTERIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERGW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000928.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000928.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61b3a25f2050c42d9e5937d3fb77fb3021f3ef09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000928.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01119
+MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTR
+TMVFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQ
+VMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGK
+CSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA
+ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEP
+EMVAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKAD
+LMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEITEPLLRIECYDISHSQGTNV
+VGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE
+ADDQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEF
+PVVLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHF
+GSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES
+>GCF_003691675.1_00838
+MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTRAM
+VFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVM
+RGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGKCS
+APCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIAAL
+RRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEPEM
+VAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKADLM
+ETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEVTEPLLRIECYDISHSQGTNVVG
+SMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVEGD
+DQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLAELGLDDLPVVGLAKRLEEVWLPGDEFPV
+VLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHFGS
+VAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES
+>GCF_005280335.1_01774
+MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLGSYFQDPARLTTKTRTM
+VFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVM
+RGDRRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGKCS
+APCVGRISPAEHRELAQDFCDFMAGDAQRFIRELERAMQGAVEELRYEDAARLRDDIAAL
+RRVFERNAVVLPESTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVSEPEM
+VTHLLQQVYGDLAGEDRIPHEILVPAEPDDAAQLVEWLSGLRGARVNVRVPRRGTKADLM
+ETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEIAEPLLRIECYDISHSQGTNVVG
+SMVVMEDGLPKKKDYRRFNVTGEAARDDTASMKDVLSRRFARLAEERAEGAPLSGQLEGE
+EEGRDRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEFPV
+VLPRTSEALYLLQRIRDESHRFAIAGHRGRRAKAMTASALDGISGLGPAKRTALLNHFGS
+VAQIRAAGVERLTEVAGIGPTLAQTVHAALAPAEPTDTVEP
+>GCF_020097155.1_01667
+MADPRTYRPAPGEISTSPGVYRFRDPDGRVIYVGKAKNLRARLSSYFQDPARLATKTRTM
+VFTASAVEWTVVASELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNERFPRVQVM
+RGDKRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRAQAQDRPCLLGYIGKCS
+APCVGRISPDEHRALAQDFCDFMAGDADRFVRELEKAMAGAVEELRFEDAARLRDDIAAL
+RRVFERNAVVLAESTEADVFALHSDELETAVQVFHVRQGRIRGQRGWIMERVEDVGEDEA
+VAELLTQVYGDVPDTERIPHEVLVPVLPAGAEQVTEWLSGLRGARVQVRVPQRGPKADLM
+GTVRENAEMALKLHKTRRSGDLTTRSAALRELQDALEIDEPLLRIECYDISHSQGTNVVG
+SMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARMAEDRREGGVLTGQIDAE
+EAEGERRRFAYPPSLVVVDGGPPQVAAAAEVLAELGLDDLPVVGLAKRLEEVWLPGDEFP
+VVLPRTSEGLFLLQRIRDESHRFAIAGHRSRRTKAMTASALDDVPGLGPTRRRALLTHFG
+SVERMRQAGPAGLTEVAGIGPALAEAVHAALTASDGGDTVAP
+>GCF_023573625.1_01069
+MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTR
+TMVFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQ
+VMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGK
+CSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA
+ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEP
+EMVAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKAD
+LMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEITEPLLRIECYDISHSQGTNV
+VGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE
+GDDQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEF
+PVVLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHF
+GSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000929.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000929.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78f8585be64004782768063f0af39e27c1117321
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000929.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01120
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE
+>GCF_003691675.1_00839
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE
+>GCF_005280335.1_01773
+MSEESLRPEKPPTSEVLVITGMSGAGRTTAAHALEDHGWYVVENMPPPLFITLADLVARS
+PEAFPRLAIVVDVRSRAYFPELHAALQQLENNGVEYRMVFLEADEHVLVRRFEAGRRPHP
+LQGNASLLDGIRAERDMLAELKARADVVVDTTELNVHGLATEITELFSVSGPVTLRLTLM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAEVSDYVLTRPGVEDFLRSYTAM
+LAPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVQVQHRDMGRE
+>GCF_020097155.1_01666
+MSADEHLQPDKPPSSEVLVITGMSGAGRTTAAHALQDHGWYVVENMPPQLLGTLSDLVAR
+SPEAFPRLAIVVDVRSRSYFNELRTALQQLESTGVEFRTVFLEASDEVLVRRFEAGRRPH
+PLQGNARLLDGIQAEREILSELKERADIVVDTSALNVHGLATEVTQLFSEDGPVTVRLNV
+MSFGFKYGLPSDANFVADMRFVANPHWVPELRSKTGLDPEVSGFVLGQPGVQEFLSNYLA
+ALGPVVEGYRRENKHYATLAVGCTGGKHRSVAVAEELARRVAQWPRVSVHVDHRDVGRE
+>GCF_023573625.1_01070
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000932.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000932.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6eb314b6a76bcec3f7738715e881f4f808241b85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000932.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01123
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
+>GCF_003691675.1_00842
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
+>GCF_005280335.1_01770
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAARDADDFAAVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEHFGSFDKFRAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARQGASGLILPA
+>GCF_020097155.1_01663
+MTEFVLPELDYDYAALEPHISAKIMELHHSKHHATYVKGANTALEKLAAAREAEDFASVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEFFGSFDKFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQQRFEAARNGASGLILPA
+>GCF_023573625.1_01073
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000935.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000935.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f8e8f3a07d7dd50e73f88f60055beac04695eef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000935.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01126
+MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLSDADHDQEAVEVAVFPPFTGLRSVQ
+TLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV
+ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV
+WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD
+GALVGGASLDADEFAKIVRFDQA
+>GCF_003691675.1_00845
+MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRSVQ
+TLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV
+ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV
+WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD
+GALVGGASLDADEFAKIVRFDQA
+>GCF_005280335.1_01766
+MAETAARVPLIAGNWKMNLDHREAVTLVQRLAWLLTDADHDHEDVEVAVFPPFTDLRAVQ
+VLVTGDRLDVAYGAQDLSPEDSGAYTGDVSGAFLAALGCRYAIVGHSERRTIHGEDDALV
+ARKAAAALRHGLSPVVCVGEGLDVRQAGRHVAHTVAQLEGSLVGLSAEDVARTVVAYEPV
+WAIGTGEVAGAGDAQEMCAALRARVGELHGDDVAAGLRILYGGSVKSTSAPELLAQPDVD
+GALVGGASLDAEEFARIVRFDQA
+>GCF_020097155.1_01660
+MSVVQPVRVPLIAGNWKMNLDHQEAVTLVQRLGWLLGDADHEQGNVEAAVFPPFTDLRSV
+QTLVAADRIGVAYGAQDVSAEDSGAFTGEVSGAFLAKLGCAYAIVGHSERRTLHHEDDAL
+VARKAAAALRHGLVPVVCVGEGLDVRQAGRHVEHTVAQLRGSLDGLSSEDVARVVVAYEP
+VWAIGTGEVASAADAQEMCAALRADLAERHGAEVAERVRVLYGGSVKSSSAPELLAQPDV
+DGALVGGASLDADEFARIVRSDAAH
+>GCF_023573625.1_01076
+MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRAVQ
+TLVTGDRLDLAYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV
+ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV
+WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD
+GALVGGASLDADEFAKIVRFDQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000936.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000936.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9fc45b1d34d8e07c2cbba7936039b187bfe210ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000936.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01127
+MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV
+GSVVAWGVVIALLGVLPRLTMES
+>GCF_003691675.1_00846
+MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV
+GSVVAWGVVIALLGVLPRLTMES
+>GCF_005280335.1_01765
+MDMLTLILQILVVVLSVVIVLLVLLHKGRGGGVSDMFGGGVTTSMSSSGSAQRLLTRLTV
+GTVAAWALLIVTLGVLPRLAMES
+>GCF_020097155.1_01659
+MDILTLLLQIAVVALSVVIIMLVLLHKGRGGGVSDMFGGGVTTSMSSSGSAQRLLTRVTV
+SATVLWGLAIVALALIARFSVES
+>GCF_023573625.1_01077
+MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV
+GSVVAWGVVIALLGVLPRLTLES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000938.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000938.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35014f0435780c21af8861f2296965899fc4e60c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000938.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01129
+MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA
+FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL
+DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV
+QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE
+AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA
+SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP
+>GCF_003691675.1_00848
+MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA
+FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL
+DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV
+QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE
+AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA
+SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP
+>GCF_005280335.1_01763
+MPGESKAAARNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPS
+FSLVGFGRRDWSDEEFAEYVRAAVEASARTTFDETVWDQFRGGLRFVSGAFDDEAAYVRL
+GEVLGELESSRGTRGNTAFYLSIPPDWFEDVSRHLADQGLADRSQPADGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPPDAVFRIDHYLGKETVQNILAFRFANRMFEPIWNAEHVDHV
+QITMAEDIGIGGRAGYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRTEKEKILE
+AVQVPDTPAGLEAASARGQYTSGWQGGERITGFLDEEGFNPESVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHEGDEFGQNVIVIRVQPDEGVTIRFA
+SKVPGTQSEVRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRAWRRP
+>GCF_020097155.1_01657
+MRPEPGGPARRNPLRDPRDRRLTRIAGPSALVLFGVTGDLARKKLLPAMYDLAHRGLLPP
+SFSLVGFGRRDWSEAEFADYVRAAVEAGSRTAFNETVWDQFRGGLRFVSGAFGDADAYAR
+LDEVLTELESSRGTGGNTAFYLSIPPDWFEDVSRHLADQGLADRSQPADGPWRRVVIEKP
+FGHDLASAHELNAVIERVFPPDAVFRIDHYLGKETVQNILAFRFANRIFEPLWSAEHVDH
+VQITMAEDIGIGGRAGYYDGVGAARDVIQNHLLQLLALTAMEEPISFDAAHLRAEKEKVL
+AAVRVPCTPEGLEAASARGQYTSGWQGGEQVTGFLDEEGFNPASVTETFAALKVDIGTRR
+WQGVPFYLRAGKRLGRRVTEIAVVFKSPPHLLFPVHPGDEFGQNVIVIRVQPDEGVTIRF
+ASKVPGTQHEVRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQEEVELSWAIV
+DPFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRTWRRP
+>GCF_023573625.1_01079
+MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA
+FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL
+DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV
+QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE
+AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA
+SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000939.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000939.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5309781ee14b49f117c9a369e9a82e5dbe38491
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000939.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01130
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
+>GCF_003691675.1_00849
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
+>GCF_005280335.1_01762
+MSTLGLSATGSALEAIDRHLPTLLEDRVASRLGAQDAGLWGEAAREESARRLGWIDLFED
+SRALVRHIDALSRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVMEAAFREAGIDPRSRLVAVTDPGSPLHAECES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLTADDADNPGLQ
+LGAALGGTAPLRDKLVFTDHGSGIDGLPAWAEQLIAESTGKDGTGLLPVVVADGDPETGW
+DAPDMLQVQLVGEDAPAAPAHGVQVSGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KTAARSLLDAPARERTADRTVDGVELSGPEAVVSAADLAGVLRATADLVPENGYLAVHAY
+LSRHDDAELEEVRADLARLAGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQVTGDADLDV
+EVPGRPFSLGRLIAAQAAGDARVLVEHGRPVVTLHLPHRAAGIDAIRTAARAR
+>GCF_020097155.1_01656
+MSTFGLTATGAALDAVDRHVPALVAERFASRLAAEDADLWGPDARDEAAKRLGWISLFEE
+SRTVAAEAAALAEELRGQGLTRVVLAGMGGSSLAPEVIAATAGAELEVLDSTDPQQVAAV
+LDHDLERTVLVVSSKSGSTVETDSQRRIVEAALAAEDIDPASRIVVVTDPGSPLEEASVE
+AGYRAVFTADPTVGGRYSALTAFGLVPAALAGVDVESLLDEAEDVLDLVTADDADNPALQ
+LGAAIGGTEPLRDKLVIQDLGSGIDGFGDWVEQLIAESTGKDGTGLLPVVVRPGDPETAW
+EAPDLLKVTLVSESEESPAGGDGVRLHGSLGALLLTWEAATAVAGRLLGINPFDQPDVEA
+AKAAARELLDSPAEEAEPGTVIHGVEVSGPESVTSADDLRGVLAAVRELVPEDGYLAVHA
+YLDRHADVDLAGIRADLASALGRPVTFGWGPRFLHSTGQYHKGGPRNGVYLQVTGDAALD
+VEVPGRPFTLGRLIAAQAAGDADVLRRLGRPVVTLRLRDRSAGIAALRTAAREA
+>GCF_023573625.1_01080
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPHIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000941.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000941.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63168813bf27aaab5c2bf88d4923dae19a0c3aad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000941.fa
@@ -0,0 +1,69 @@
+>GCF_002008305.4_01132
+MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV
+AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ
+EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH
+GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEVAFQAWREANP
+ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYVGT
+FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD
+GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT
+RGLL
+>GCF_003691675.1_00851
+MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV
+AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ
+EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH
+GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEVAFQAWREANP
+ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYVGT
+FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD
+GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT
+RGLL
+>GCF_005280335.1_01760
+MTDAQHPSTAPALDRTAPARDFVYSEQDRRMVDTLKVLSADAVEQAGHGHPGTAISLAPV
+AWQMYQNVMHLDPQDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLELEDIRALRTEGSK
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRLRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVSARYEAYGWHVQ
+EVDWTNGALGHAVTEYTEDVEALYEALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGVH
+GSKLGAEELAGLKEGLGFDPAESFDVDPEVLANSRSIAERSAAYRRTWEGAFQAWREAHP
+ENARLYDRLAGRELPEGFAEAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+RSNNTTMKGEPSFIPARRSTATWQGDEHGRTLHFGIREFAAGAIVNGITIGGLTRAYMGT
+FLTFSDYMRPAVRLAALMGTPSVYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLENRDRPAGMVLSRQNLPVLPRDTDGFASAEGVARGAYVLVDAVGGS
+GAPAPARVLLIATGSEVSVAVHARELLQAEGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTAVSRGARVSLEHYGESADGARLMEKYGFTGEAVAQAA
+RGLL
+>GCF_020097155.1_01654
+MTDTASTALDRTLPARDFVYDEQDRRMVDTLKVLAADAVEKAGHGHPGTAISLSPVAWQL
+YQNVMHLDPSDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLELEDIAALRTEGSLTPGH
+PEYGHTHGVEVTTGPLGQGLAMAVGFAYEQRRLRGLMDPDAAPGTSPFDHHVFVLASDGD
+IQEGVSSEASSLAGHQELGNLVVVYDANRISIEDDTDISFTEDVAKRYKAYGWHVQEVDW
+SNGAQGHEVTEYTEGVQDLYEALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIHGSKL
+GGDEVVGLKEALGFDPQKSFDVDPEVLAHARSISERSAAYRETWEAAFAAWREAHPENAR
+LYDRLASRELPAGFEDAFPSWDADEKGVATRAASGKVLTALAPVMPELWGGSADLAGSNN
+TTMEGEPSFIPAHRSTAAWQGDPFGRTLHFGIREFAAGAIVNGITIGGLTRAYMGTFLTF
+SDYMRGAVRLAALMGTPAVYVWTHDSVGLGEDGPTHQPVEHLAALRAIPGLDVVRPADAN
+ETAWAWRTILQHRDRPAGLVLTRQNVPVLPRGTEGFAPADGVARGAYVLVDGADASGAAA
+PARVVLIATGSEVSVAVGARELLQAEGVPTRVVSAPCLEWFAEQDEAYRAEVLPDGPGAP
+VRVSVEAGIAMPWHELTVTQSSRGARVSLEHYGESADGPHLLKKYGFSPENVADTARGLL
+>GCF_023573625.1_01082
+MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV
+AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ
+EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH
+GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEAAFQAWREANP
+ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYMGT
+FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD
+GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT
+RGLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000942.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000942.fa
new file mode 100644
index 0000000000000000000000000000000000000000..152454a94310d2dbf4f616877e59d358a6a3fb5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000942.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01133
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRGTVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
+>GCF_003691675.1_00852
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRGTVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
+>GCF_005280335.1_01759
+MSSSLESSSAARVETAPPGVVDRSKPSLSRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMAATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILVLGFGANWLAAALGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIAW
+AAVRGTVEWPAIVLFTVIFLWTPPHYWPLSMKYKRDYQEADVPMLGAIASARHVSNQVVL
+YAWATVVCSLLLVPMGWAGIVYTCVALVVGGWFVWESHVLHRQARREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGEPLMRFGA
+>GCF_020097155.1_01653
+MSSSVESTSPATAAPGAAAPSARPPMTVGRKARAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDLLTMIATLVGGALAAGASGAFNCYIDRDIDRVMKRTARRPLVTGEVTPREALVFSW
+TLAVVSVLVLGFGANWLAAALGVAAIFFYVVVYSLILKRRTEQNIVWGGIAGCFPVVIGW
+AAVRGTVEWPAIVLFTVIFLWTPPHYWPLSMKYKRDYQEAEVPMLGAVASARLVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVAVGVGGWFVWESHVLQREAQRPDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGGPLMPAVTGS
+>GCF_023573625.1_01083
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRETVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000943.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000943.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54da851cf2dc27af7db8d6345e54784588a25ebe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000943.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01134
+MSTTTPAAGTAPAGLAARLPQRLTKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW
+PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL
+AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG
+ATTVRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRIHVIPVYLL
+LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA
+LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG
+>GCF_003691675.1_00853
+MSTTTPAAGTAPAGLAARLPQRLTKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW
+PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL
+AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG
+ATTVRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRIHVIPVYLL
+LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA
+LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG
+>GCF_005280335.1_01758
+MASLASEIGIIVTGGAVRLTGSGLGCPTWPKCTPESLTNTPEMGIHGYIEFGNRTLTFVL
+VVIAAAMFLSLWRLRRTHRSPFWLSVGLLAGIPAQAVVGGIVVLTELDPWWVAGHFIVSS
+VMVAVATLLVIRIGAERRAGRAGVRIVDGVTTGASRAAAWAAFAFTWAAVYLGTVVTGTG
+PHGGDPDAPRHAFDPLLVTRVHVIPVYLLIAAALVLLFTVRRAEGASRLQRAAVLRLLLA
+IAVQAAIGYTQHFTGLPVVLVILHMLGSALLVAAATEVWDRQRSRYVTAGPAALLDADPT
+PVTANAR
+>GCF_020097155.1_01652
+MTASPTTARPAAGGSSARRPPDRVTGVTVGLALASLISQMVIVVTGGAVRLTGSGLGCPT
+WPKCTPESLTTTAEMGIHGIIEFGNRTLTGVLGVIALLMIATLWRLRRSHRQAFTLSLLL
+LAGIVLQAVVGGVTVWMHLDPRIVGVHFVISGALIALATMLWVRLRAEHRHGAGAPVADG
+TTTPASRTASRVAYAALWLALVVGTLVTGTGPHSGDPAAARHGFDALMITRLHVVPVYIT
+VAATLVLLWQVLRTPGSGAGQRVAAWSLLGAVLLQGLLGYWQHFTGLPVGVVAAHLAGAT
+VAVVAGTLAWQRQTSRYRAPAVA
+>GCF_023573625.1_01084
+MSTTTPAARTAPAGLAARLPQRLSKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW
+PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL
+AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG
+ATTGRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRAHVVPVYLL
+LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA
+LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000944.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000944.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd903aadd294ddd9c760cfa65345790b6c5b115e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000944.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01135
+MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH
+VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV
+AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR
+PEATLAVANLLWVLFGAVGGTVFPARVPGVDLLPSGALGTALRAALLDGAWSPVPLLVLT
+LWGAVAVAAALRWFRWRP
+>GCF_003691675.1_00854
+MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH
+VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV
+AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR
+PEATLAVANLLWVLFGAVGGTVFPARVPGVDLLPSGALGTALRAALLDGAWSPVPLLVLT
+LWGAVAVAAALRWFRWRP
+>GCF_005280335.1_01757
+MSAPIAPGSAEPRTAGQVPEPGTAPHAGAAPLATRVLRQAAYETGTALRNGEQLLVTVVL
+PLLALVGVHVTGLLDEPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALAT
+TPLGTLGLVAGKALSVVALLLVQVAVIGGVGLALGWRPEAAGILPAVVALALGAAAFTAL
+GLLLAGTARPEATLAAANLLWVLFGAVGGTVFPSRVPGVDLLPSGALGSALRAALVDGAG
+APIPLLVLALWCAVAVAAALRWFRWRP
+>GCF_020097155.1_01651
+MSAPAAPIPASHAGAAPLGARILAQARYETVTALRNGEQLLVTLVLPLLALVGVHVTGLL
+DAPGRNGLDLAVPGVLALAVISAAFTATAISTGFERRYDVLAALATTPLGTGGLVAGKAA
+AVAAVLLLQTIVIGGVGLALGWSPDPAGIPPAVVALLLGAAAFTALGLLLAGTARPEATL
+AVANLVWVLLGALGGTVFPSRWAWMDLLPSGALGTALRSALQDGAWAPSALAVLAAWTVM
+AVAAALRWFRWRP
+>GCF_023573625.1_01085
+MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH
+VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV
+AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR
+PEATLAVANLLWVLFGAVGGTVFPARVPGVGLLPSGALGTALRAALLDGAWSPVPLLVLT
+LWGAVAVAAALRWFRWRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000945.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000945.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2d8ca722f39715c3fa063c693cd6f21befa4979
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000945.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01136
+MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM
+DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP
+LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV
+REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAEGDVVDVDFGDA
+SPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL
+RLEQILRETAA
+>GCF_003691675.1_00855
+MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM
+DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP
+LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV
+REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAEGDVVDVDFGDA
+SPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL
+RLEQILRETAA
+>GCF_005280335.1_01756
+MVPRPVLTPDPAPRDEPVLRLRDVHRSLGRGRARTPVLRGVDLTARAGAVTVLLGPNGAG
+KSTTLGLCHGMDRPDAGAVRVFGADPWRAPADLRARIGVMWQEGGLPPSVPARRFVGHVA
+SLYRDPMPVEPLLERLLIADVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLD
+PETRPVVHEVVREQTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGSLADLTRVAE
+GDVVDVDFGDAAPEAVRAWADALPEPLRAAGLAEPARLRVAGVHGPAELAALAASWHRHA
+LMPTRFERAGLRLEQILRETAA
+>GCF_020097155.1_01650
+MPETSPHPDAPALRLHEVRRTLGRGAARTEVLRGVDLEARRGAVTVLLGPNGAGKSTTLA
+LCHGSDRPDSGTVRVFGRDPWRADADLRARLGVMWQEGGLPPSVTARRFVRHVASLHGDP
+LDPDALLGRLRIDRVADRPIRRLSGGQRQRVALAAAVVGRPDLLFLDEPTAGLDPETRPV
+VHDVVREHTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGTLAELTRVQDGDVVDV
+RFDEARAADVRAWVAAAPASFRAVASAGAPAARVAGVRSPADLEALAASWTRAGLFPTRL
+ERAVLRLEELLQSPDADTPSPERSR
+>GCF_023573625.1_01086
+MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM
+DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP
+LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV
+REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGPLSELTRVAEGDVVDVDFGDA
+SPDAVRAWADTLPAPLRAAGLGESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL
+RLEQILRETAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000948.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000948.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cebe2ab23512d3d2ee66775191d9ddd4c31c2791
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000948.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01139
+MTDTVENTQRTMIPGMGEEGEKLTAAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVTVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEGDAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGIGDVEDELTAVMEDELRIAQL
+>GCF_003691675.1_00858
+MTDTVENTQRTMIPGMGEEGEKLTAAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVTVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEADAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGIGDVEDELTAVMEDELRIAQL
+>GCF_005280335.1_01753
+MTDTVENTQGSMIPGMGEEGEKLTVAQTSAPRAGAPERNAAGSRADRVSSYELADFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPSVTVAEQVGVRVETVARDDARVGSVLTP
+DDRVSAAAWNSVAQATVVTVSGEVAEPVRIDVVGSSAEPAAMHLTVIVEENAQADVVLAH
+RGTAVLAQNVEFDVRRDARLNVVSLQAWEDDAVHVSAQQASVATNARFKHVAVSHGGSVV
+RLTPTSRFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPRCVSNVLYKGALQGADARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGVRDVEDELTAVMEDELRIAAL
+>GCF_020097155.1_01647
+MENTERNMIPGMGEEGETLAGGQDAGAPVATRGQGQSRADRVSSKDLADFPVLTGREEDW
+RFTPLERLGGLHLPGGDDARLTGAAPAVTVSETAGVSVETVGRDDARVGSVLTPDDRVSA
+AAWTSFAEATVVTVSGEPGEPVRIEVTGSGVEPAAQQLTLIAEENAHADVVLTHRGSAVL
+AQNVEFEVRRGASLNVVSVQAWDDDAVHVGAHQASVARDAHLKHVTVTHGGSLVRLTPTA
+RFSDERGEAEMYGLYYADAGQHLENRLFVDHNRPNCVSNVLYKGALQGQDAHTVWVGDVL
+IRTEAEGTDSYEKNENLLLTDGARADSVPNLEIETGVIEGAGHASATGRFDETQLFYLMA
+RGIPESEARQLIVRGFLNEILQKIGIADVQDELTAVMEEELRVTAL
+>GCF_023573625.1_01089
+MTDTVENTQRTMIPGMGEEGEKLTVAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVAVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEGDAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGIPETEARRLIVRGFLNEIIQKIGVGDVEDELTAVMEDELRIAQL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000950.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000950.fa
new file mode 100644
index 0000000000000000000000000000000000000000..869900cc1affb8d1538ec54de5bc7b05a7cbd362
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000950.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01141
+MTETANQVPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI
+>GCF_003691675.1_00860
+MTETTNQAPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI
+>GCF_005280335.1_01751
+MTETANQVPTEDVREALKDVIDPELGVNVVDLGLLYGLHYAEDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI
+>GCF_020097155.1_01645
+MTDTAAQTPVEDIREALKDVIDPELGVNVVDLGLLYGLHYAEDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGKDQMRALGFNI
+>GCF_023573625.1_01091
+MTETTNQAPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000951.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..844db32530adc4b84956c5fea261bfff7706a079
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000951.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_01142
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVVATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHATSTVDPESGEPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSAQQEP
+DIRQCDTFRAPSLDI
+>GCF_003691675.1_00861
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVIATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHAASTVDPESGAPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSSQQEP
+DIRQCDTFRASSLDI
+>GCF_005280335.1_01749
+MGGRGLAIGGGGGLLALLLAIFAPGLAGQLGIDTGGSTGQSQYQQQGAGGTQPVSDEECS
+TGADANRNTDCRVIAATEAADQFWGEYMSQFSDVDWRQPQLTLFAGSVSTGCGSASSAMG
+PFYCPADESMYFDTSFFETLQSDFGAEGGPLAEQYIVAHEYGHHVQHVTGYLQYSRDGST
+GPESGAVRAELQADCLAGMWAGAATTTVDPESGEPYLQPISREQLRQAIDAAAAVGDDRI
+QEMSTGRVNPEAFTHGSSEQRMAWFLRGYETSQQEPDFRQCDTFRASSLDI
+>GCF_020097155.1_01644
+MSFNENVQINAGRARGGGGGGMGGRGLAIGGGGGILALLLAIFAPGLAEDLGIGGAGTGT
+GSSYQQQLPQSGSGTSTQPVSQADCSTGADANQNTDCRVIATTESADAFWGDYMGQYSNI
+QWRQPDLTLFTTSVSTGGCGSATSATGPFYCPADESMYFDTAFFSTLESDFGATGGPLAE
+EYIVAHEYGHHVQNVVGWLQYAQDGRTGAASNAVRSELQADCLAGMWAGHAATTKDPETG
+EAFLQPITQEQLAQAIDAAGAVGDDRIQEQYQGRVNPEAFTHGSASQRQAWFMRGYETTS
+QQSPDINQCNTFQAATLDI
+>GCF_023573625.1_01092
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVIATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHAASTVDPESGAPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSSQQEP
+DIRQCDTFRASSLDI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000952.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76e241d03b468de09e1d3cb77a4e4aa9b3a80e42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000952.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01143
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIL
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLGIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILHALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA
+>GCF_003691675.1_00862
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILHALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA
+>GCF_005280335.1_01748
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKILAGGGQPTAGSVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDHTIRRMREAEAGMAAVDDVERQRAMDRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYPGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAADRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEEAPDTGEVQEGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILGALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNEDYKDLITLA
+>GCF_020097155.1_01643
+MLTVTDLELRVGARLLMDEVSFRVAKGDKVGLVGRNGAGKTTLTRVLAGITQPTAGSVTV
+SGRLGYLPQDPKVEDMDQSGRDRILAARDLDQTIRRMRAAEADMASEDDAARQKAMDRYS
+RLQAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADTM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDAMRQTIDVYNM
+NWKNYQAQRQQDEARRRREFANAEKKASALLAQAEKMRAKATKATAAQNMIKRAERMMRG
+VEGERAQDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGTESPDTGEVIAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QCRTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILNALRQYEGAVVLVTHDEGAVEALAPERVVLLPDGDEDLWSDDYLDLISLA
+>GCF_023573625.1_01093
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILNALQQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000953.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000953.fa
new file mode 100644
index 0000000000000000000000000000000000000000..422f34eeab0cc1fbd75411b6acc2d29a85d5d631
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000953.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01144
+MSIPAPMTDPTARDAERLPALRFGFLATGPWILGFVVCVLFAFLCHALAQWQWDRRVEVQ
+HRVNRVLENYDDDPVPFAEASRLFTAFQTDDEWTPVTLTGEYLVDETLIVRNRPRAGQPG
+YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP
+DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVEPMPQKLVEPTLDEGPHLSYAIQWY
+LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE
+DALFD
+>GCF_003691675.1_00863
+MSTPAPMSAPTARDAERLPPLRFGFLATGPWILGFVLCILFAFLCHALAQWQWDRRVEVQ
+HRVNRVLENYDDDPVPFAEASRLFTAFQTEDEWTPVTLTGEYLVDETLIVRNRPRAGQPG
+YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP
+DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVESMPQKLVEPTLDEGPHLSYAIQWY
+LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE
+DALFD
+>GCF_005280335.1_01747
+MTAPAPATGFRRDPGSARPPRLRFDFLATPPWILGFVLCILFAFACHYLAQWQWERRVQV
+QHQVNRVLENYDDAPVPFAQASRMFTDFDAQDEWTPVTLSGEYLAEETLVVRNRPRAGRP
+GYEVLVPFRTDEGPVVVVDRGWLPVGNTPGRPDAVPAPPAGPAEVVVRVKPGEPALDRDA
+PEGQVPSIDLAEIRGHVGGPVADTAYGIMVEEDPAVQDLPQKLVEPTLDEGPHLSYAIQW
+YLFAAMGFGVWGYSAWMRARNDRADALEGVRDDGMLTARRAPRPKPVRRRRDGRPTDEEA
+EDALFD
+>GCF_020097155.1_01642
+MTPAPAPTDTPDAPGAERLPPLRFGFLASGPWILGFVVCILFAFLCHGLAQWQWDRRVQV
+MHDVNRVLANYDDDPVPFAEAPRLFTDFDSEDEWTPVTLTGRYETDETLVVRNRPRAGAP
+GYEVLVPFVTEEGVTVIVDRGWLPIGSQPGRPDAIPAPDPAAGEVVVRVKPGEPALDRDA
+PEGQVPSIDLAAIERILGRPIADTAYGLMVSESPAAATVPNQLVAPTLDEGPHLSYAIQW
+YIFAAMGFAVWGYSAWMKARNDRADALEDAEDDGLLAARRAPRPKARRRRRGGRPSDEEV
+EDALQEDVLRDRPGQASEIRSR
+>GCF_023573625.1_01094
+MSTPAPMSAPTARDAERLPPLRFGFLATGPWILGFVLCILFAFLCHALAQWQWDRRVEVQ
+HRVNRVLENYDDDPVPFAEASRLFTAFQTEDEWTPVTLTGEYLVDETLIVRNRPRAGQPG
+YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP
+DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVESMPQKLVEPTLDEGPHLSYAIQWY
+LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE
+DALFD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000954.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000954.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26aa0c6bc9d1ec97e821714c1eeb09568165395d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000954.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01146
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMRVYLVQMLVRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDDTAAPEPVV
+LTGDLVDDPRDRAPRALGRGSSSAGSPGLPGRGGA
+>GCF_003691675.1_00865
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDDTAAPKPVV
+LTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA
+>GCF_005280335.1_01746
+MTSSAAGSRAGRPARAGRSTGPQVQGVTTASAARSEDREARMKVYLVQMLIRTVCFGAAL
+FTTGWWQLLFILGAVALPYVAVVQVNNAGPRQAGSLRAVPAEGPELTARPADAPGPASPV
+VLTGDVVDDPREVGPRALPPGSPSEGARRLPGRGAA
+>GCF_020097155.1_01640
+MAAIVREPDAVQGVTTAAAPRSADRDARTRVYVVQMAVRTACFIAALFTHGWWQILFILG
+AVVLPYVAVVRVNNTGPREAGRRRDVARTAPAVPALPAEPSPVPTGPVVLVGEVVEDDDP
+AARRALPAGSPGETGRGRP
+>GCF_023573625.1_01096
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLHAVPAQGPALAPRPDDTAAPKPVV
+LTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000955.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000955.fa
new file mode 100644
index 0000000000000000000000000000000000000000..520eee4ecabeed13b8704d79ade4f4529d824578
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000955.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01148
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFTEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREGLEVGHTE
+LVGGAEDFLGQD
+>GCF_003691675.1_00867
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFAEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREDLEVGHTE
+LVGGAEDFLQQN
+>GCF_005280335.1_01744
+MTEKDLTGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQKIEEAGGRA
+VAVGGDVTSAEDRAALLDAAVESFGSLDVLVLNASGGMESQFGEDYAMKLNRDAQAALAD
+AALERMSAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFEAKGVGF
+AVVSGDMIEGTITATLLDRAEPGAIDARREAAGRLYSVEEFAAEVAALVGRDDLEVGHTE
+LVGGARDFLARGEG
+>GCF_020097155.1_01638
+MTTQDLAGKGVVVTGSSRGIGAETAQLLAARGAGVVVNYRQKAPRANKVVQAIEAARGRA
+VAVGGDVTVAEDRAALLDAAIDNFGSLDVLVLNASGGMESQFGEDYAMTLNRDAQAALAD
+AALERMSAGGQIVFVTSHQAHFIDEVATMDAYEPVARSKRAGEDALRERIPAFEAKGVGF
+VVVSGDMIEGTITATLLNRAEPGAIEARREAAGKLYSVEEFAAEVAALVGRTDLEVGHTE
+LVGGAQDFLGQD
+>GCF_023573625.1_01098
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFAEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREDLEVGHTE
+LVGGAEDFLQQN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000956.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000956.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f756766dda1e08bb1e7fdaa6185686040549fb9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000956.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01149
+MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL
+TVPATVAAAPAPLVVTDVDSTLIRQEVIELLAAHAGREAEVAEVTERAMRGELDFAASLH
+ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG
+VHAYCANELEVQDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL
+LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL
+>GCF_003691675.1_00868
+MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL
+TVPATVAAAPAPLVVTDVDSTLIRQEVVELLAAHAGREAEVAEVTERAMRGELDFAASLH
+ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG
+VHAYCANELEVRDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL
+LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL
+>GCF_005280335.1_01743
+MSTLRRLVVTADPALLADRTPPAGVPDDAERLLEDGLLGWRFAADEWAAAPEPGPGWAVH
+TLPAAVAEAPVPLVVTDVDSTLIRQEVIELLAAHAGREAEVAAVTERAMRGELDFAASLH
+ARVEALAGLPVGVVDDVVRAIRPTAGALALIEAVTAAGGRVCAVSGGFSQVLAPLAQAWG
+VHAYCANELEVHDGHLTGRVAGDVVDRAAKAAMLRAWAEDAGLSPEQAVGVGDGANDIDL
+LDAAGAGVALCAKPVLREHADVVVDVPSFTPLRWLLGL
+>GCF_020097155.1_01637
+MTQARHLLYRAVPAGTDSPVAPAWAPLPADAEHLAADGLAGLRWEGSVPSAEEATALPED
+WALASLPQSVAAAPTPLVVTDVDSTLIQQEVIELLAAHTGREAEVAAVTERAMRGELDFA
+QSLHARVEALAGLPASVVDDVVARVRPTDGAVELIAAVNAAGGRVCAVSGGFTQVLAPLA
+EAWGVHAYCANELEVRDGHLSGKVLGDVVDRAAKAAMLRAWAEDAGLSPEQAVGVGDGAN
+DIDLLEVAGCGVALCAKPILREHADVVIDVPSFTPLRWLLGL
+>GCF_023573625.1_01099
+MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL
+TVPATVAAAPAPLVVTDVDSTLIRQEVVELLAAHAGREAEVAEVTERAMRGELDFAASLH
+ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG
+VHAYCANELEVRDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL
+LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000957.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000957.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da145b76b98f615c409797d98abc483df248432a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000957.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01150
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEEVPPGFTHALLLRDGGVVAA
+GPIESTLTEEHLSAAFGTDLKVTRTGGRYTAVAR
+>GCF_003691675.1_00869
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEDVPPGFTHALLLRAGGVVAA
+GPIESTLTEEHLSSAFGTDLKVTRTGGRYTAVAR
+>GCF_005280335.1_01742
+MTLPAPSDDWFLPDEDAVLQMRRVRVRRGQTDILGPLDWTVRAGERWIVMGPNGAGKSTL
+LQIAATRLHPTGGEVAILEEVLGAVDVFELRPRIGLSSAQLAAQVPHEEKVQDAVVTAAY
+GVTGTWRESYEDEDRMRALGLVSSWGLSRLAHRRFGTLSEGERKRVLIARSLMTDPELLL
+LDEPAAGLDLAGREALVAQLSELARDEDAPALVLVTHHLEEVPPGFTHALLLRDGHAVAA
+GPIEQTLTEGHLSAAFDTPLRVTRTGGRYTAVAQ
+>GCF_020097155.1_01636
+MNTAPQDPSPRPVVEHDVFTPDEDAVLQLRDVAVRRGAKQILAGIDWTVRAGERWVVMGP
+NGAGKSTLLQIAASRMFPTSGDVAILDEVLGAVDVFELRPRIGLSSALLANQVRDDETVQ
+DAVITASYGMTGRWREEYEVEDRARALGLVSEWGLSRLAHRRFGTLSEGERKRVLIARAL
+MTDPELLLLDEPAAGLDVAGREALVGQLSELAADEDAPATVLVTHHLEEVPPGFTHALLL
+ADGAVVQAGPLEETLTAEHLSTAFGTPLRVTRADGRYTAVAA
+>GCF_023573625.1_01100
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEDVPPGFTHALLLRAGGVVAA
+GPIESTLTEEHLSSAFGTDLKVTRTGGRYTAVAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000958.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000958.fa
new file mode 100644
index 0000000000000000000000000000000000000000..792227fbf7a3e651ca5a27ec6f685f87dcefb5de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000958.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01151
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQGWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
+>GCF_003691675.1_00870
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQRWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
+>GCF_005280335.1_01741
+MIDVLGADVLGLELWQVVLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQISNA
+IGLVAAGFSGVFGYRRELKESGAVLPVLTVASLLGGVLGAFLLILLPAEVFGVAAPVLIV
+VALAFVVLQPRLQAWVRRRSAAREDGVVDVPARPSRPVSPVLWVLVFLAGVYGGYFVAAQ
+GVLLMGILGVFLVGGTLVHANAIKTWLSLAVNLVAATSYLLFAFDRIDWTAVLLIAASSM
+VGGLVGARIGRRISPTVLRIVIVVVGLAGLVSMVLRLVDGG
+>GCF_020097155.1_01635
+MDLLTAPVLGMDLWQVALVLLAGFWAGTINSIIGSGTLVTFPVLVAVGFPPVTAQVSNAM
+GLVASGFSGTYGYRRELRESRALLPRLTLASFLGAVIGATLLTVLPPTVFASVAPCLLVL
+ALTIVVLQPRIQAWVRRRSAGEHGHVPGADSPVPVGPASPALWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVMLVGGTLVHANAVKTWLSLTVNLTAAVFYLVFAFDRIDWRAVLLIAVSSL
+VGGSVGARIGRRMSPTALRVTIVVIGVAGLVSMLSRLAGA
+>GCF_023573625.1_01101
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQRWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000963.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000963.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97e33cdbacb05c048adbebfa85c45661eb8f490e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000963.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01158
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR
+>GCF_003691675.1_00877
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELIAELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR
+>GCF_005280335.1_01731
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGEPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANMAGHLGKLMHGVPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAEKTAYLGADAVIAVSDGMRRDILACYPEVDPEKVHTVHNGID
+TEAWTPQTETDALEKYGIDPTRPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTPELAHEVNGLIAELRRTREGVVVIEGMIPRREVTQILSAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPIEQVADGTGAPADEDAFAADFAAALTRVLE
+DPERATAMGEAGRARAIEHFSWEAIAERTIEVYEAVLR
+>GCF_020097155.1_01629
+MRIDIVTKEFPPTIYGGAGVHVAELTRVLSSRADVHVHAFGGAREPDYHGATVTSYAQPA
+GFESANGAVQTLVTDLDIVGDLDGADVIHSHTWYANMAGHLGGLMHGVPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAESTAYHGAAAVIAVSEGMRRDILRCYPDVDPAKVHTVHNGID
+TQLWTPQTGTDALTKYGIDPDRPSVAFVGRITRQKGVPHLLRAALQLPEDVQLVLCVGAA
+DTPELAREVEGLIGRLRAEREGVVVVEGMIPRGEVTQILSAATVFACPSIYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVDDGVTGLLVPVEQADDGTGTPVDEEKFAADLAKALSTVLA
+DPERATAMGEAGRARAIEHFSWETIADRTMEVYAAVAR
+>GCF_023573625.1_01108
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000964.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000964.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cda9599eae965cef5666e3f42121c266c9630c99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000964.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_01159
+MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK
+DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD
+PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT
+ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR
+RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ
+EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQFVGKRLLTDYSKEFGRLNVGA
+VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA
+GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL
+RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR
+MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG
+>GCF_003691675.1_00878
+MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK
+DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD
+PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT
+ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR
+RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ
+EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQLVGKRLLTDYSKEFGRLNVGA
+VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA
+GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL
+RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR
+MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG
+>GCF_005280335.1_01730
+MTVHEKLAPQSPTHTTEVPSDVAEIAPEHPEPGSLDSAALQDALLGAWAEDRRTARALVR
+DPRLHRDPLLGMDEHRERVLGQLGVLVENGAVHRMFPKEFGGDDNHGGNIAAFADLVLGD
+PSLQIKAGVQWGLFAAAILHLGTEEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIGTT
+ATYDEAAGEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITKGVNHGVHCFYVPIRDED
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFDQVRVPRTNLLNRYGDVAEDGTYSSPIESPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGAIAYGEQRRQFNASDPEREEVLLDYQNHQR
+RLVDRLARAYADAFASNELLERFDGVFSGRADSDADRQELETLAAAIKPLATWNALDTLQ
+ETREACGGAGFMARNRIPQMRADLDVYVTFEGDNNVLLQLVGKRLLTDYSHEFGRLNVGA
+VSRYVVAQASDAIHRAGLHKAVQSVSDGGSERRSANWFKDPEVQRDLLTDRVRAKTADIA
+GTLAGVRGKTQAEQAAAFNTRQHELIEVARNQGELLQWEAFTRAVQATRDESTRTVLTWL
+RDLFALRVLEEDLGWLVAHGRLSSQRARSLRGYVNRLAERLRPFALELVEAFGLEPEHLR
+MDIATQAEAERQAEAHAWFEARRAAGEEPEDEKAVRAREKAARGRRG
+>GCF_020097155.1_01628
+MTDIRTDAASAAEALPATDAVPHDVAEIAPEDPTPGALDAAALQDLLLGSWAEAHRTARG
+LVKDERLHRDPALGMDEHRARVLDQLGILVEEKAVHRAFPADLGGQDDHGGSIAAFANLV
+LADPSLQIKAGVQWGLFSSAILHLGTREHHEKWLPGAMDLSMPGAFAMTEIGHGSDVASI
+ATTATYDEATQEFVIHTPFKAAWKDYLGNAALHGRAATVFAQLITKGVNHGVHCFYVPIR
+DESGAFLPGVGGEDDGLKGGLNGIDNGRLHFDHVRVPRTHLLNRYGDVAEDGTYSSDIAS
+PGRRFFTMIGTLVQGRVSLSLAASIASFMGLHGALAYAEQRRQFGGPEGSETLLLDYQNH
+QRRLIDRLARTYADLFAANELLEKFDHVFSGAGDTDKDREELETLAAAIKPLTTWNALDT
+LQEAREATGGMGFMAGRNRLPHLRADLDIFVTFEGDNNILLQLVGKRLLTDYSAEFGKLN
+VGAVSRWAASEASDALHRVGLHKAAQSVHDRGDQRRAANWFKDPQVQRDLLTDRVRTRVA
+DIASTLGSARGKSKAEQAAAFNSRQHELIEVARHHGELLQWEAFTRQVESLPAGQTRTVL
+TWLRDLFALRLIEDDLGWLVAHGRVSSARARVLRGYVNRLAERLRPFALELVEAFGLEPE
+HLRMEIATDAESVRQQEAADWFAARRAAGEEPVHEKTLHAGKR
+>GCF_023573625.1_01109
+MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK
+DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD
+PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT
+ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR
+RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ
+EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQLVGKRLLTDYSKEFGRLNVGA
+VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA
+GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL
+RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR
+MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000965.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000965.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69edd1763926671c2182c66a3819b1a36bcd195e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000965.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01161
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTMKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQTQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR
+>GCF_003691675.1_00880
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEAVGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLTTAKTMKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPVFGRQLGDEATMTAGNSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR
+>GCF_005280335.1_01729
+MTQPETTARPAVAGGALRPAVVVGGNRIPFARANTAYAEVGNQEMLTAALEGLVARFGLQ
+GERVGQVSAGAVLKHPRNFNLTREAVLGSALASDTPAADLQVACATGMEAIGTLADKIRL
+GRIDSAIGGGVDSISDAPVSLSDGARRALLRLNAAKTMKDRLAALKDLRPGHLAPEPAGA
+GEPRTGMSMGDHQALTTHRWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFRGLDRD
+NNLRPDSTPEKLAGLKPAFGRHLGEEATMTAGNSTPLTDGASAVLLSSEDWAAERGLPVL
+AEFVDVENAAVDFVDGDEGLLMSPAYAVPRLLARHGLTLQDLDFVEIHEAFAGTVLSTLA
+AWEDEEYCRERLGLPGALGSVDRAKLNVHGSSLAAGHPFAATGGRIVALLSKMLHEKGEG
+SLGLVSVCAAGGQGIVALLRGR
+>GCF_020097155.1_01626
+MSTESPRVPAETARPAIAGGELRPAVVVGSNRIPFARAFTAYAEVGEQEMLTAAIDGLVA
+RLGLQGERLGQVSAGAVMKHPKDFNLTREAVMGSALSSETPAADIQVACATGMEAIGTLA
+DKIRLGRIDSAIGGGVDSISASPMTVSESARRVLLQLNSAKTVKDRLKALSSLRPGQLVP
+EPAAAGEPRTGMSMGEHQALTTHQWGITRQAQDELAAASHRNLGASYASGYQDDLVTPFR
+GLAKDNNLRPDSTVEKLAGLKPAFGRHLGDEATMTAGNSTPLTDGASAVLLSSEDWAVQR
+NLPVLAEIVDMENAAVDFVDGEDGLLMSPVYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LATLAAWEDEEFGRTRLGLPGAYGSVDRAKLNVNGSSLAAGHPFAATGGRIVGLLSKMLH
+EKGEGSLGLVSVCAAGGQGIVALLRGR
+>GCF_023573625.1_01111
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLIA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTTKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000966.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000966.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8084411ee9b628889c073ed561fe0b20a48b971
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000966.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01162
+MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA
+SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE
+AATDPTLRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA
+YVSGQFVPVATADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA
+AGEALAEVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDAVVHNAGITRDRMLANMD
+AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGQGLRIVGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA
+ETVAWLASDAAGGTNGATLRVCGQSKLGA
+>GCF_003691675.1_00881
+MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA
+SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE
+AATDPALRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA
+YVSGQFVPVSTADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA
+AGETLAKVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDVVVHNAGITRDRMLANMD
+AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGHGLRIVGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA
+ETVAWLASDAAGGTNGATLRVCGQSKLGA
+>GCF_005280335.1_01728
+MTDRYGAFAASALGRRLTGALGLPQPVELRRHAPGEPVLHGSVLVLGAGPAAADARTLLA
+SWGLEVADAPREGARLAGVVACFDDAAAPGDLGETVLQIGGALRSLGASSRVVTVSVDPE
+AAAEPAVRAARQGVQGLTRSLAQEMRRGGTANGIVLGEGVPLTAPGAAGALAFLLSGRSA
+YVSGQFLPVTTRDGATPADAARPLADKVAVVTGAARGIGAAIVRTLARDGATVVGVDVPV
+AGESLAAVVNEVGGTALALDITAPEAGARILEHCRARHGRMDVVVHNAGITRDRMLANMD
+AARWDSVIAVNTASQLAMNEAFLADDAREVTGEGLRIIGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPALAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNSLQQGGLPQDVA
+EAVAWFASDAAGGTNGATLRVCGQSKLGA
+>GCF_020097155.1_01625
+MPANDPYGDLVRTRLGRRLTGALGLPQPAELRRHTAGDPAVRGTVLVLGATSAADAARAL
+VTAEGARAVAHPAEGERLAAVIACFDGVAAPGDLSDTALALGGALRSLEPSAHVVTVVED
+PEEAEVPAVRAARAGVMGLTRSLAHEMRRGGVANGLLLRGGARLGDAGPAGALRFLLSGR
+AAFVSGQFLPAAAGAGSAPASADARPLEGRVAVVTGAARGIGAAILRTLARDGATVVGVD
+LPAAGEDLVRIVNELGGTALPLDITAPDAGARIVEHARARHGRLDVVVHNAGITKDKLLA
+NMDAARWDAVLAVNTASQLAINEVLLSAEAADVVSPDIRIVGLASISGIAGNRGQTNYAA
+SKAGVIGLTAATAPDLAARGGGITAVAPGFIETEMTAKIPLVTRELGRRVNSLQQGGRPE
+DVAEAVAFLSSPAASGINGTTLRVCGQSMLGA
+>GCF_023573625.1_01112
+MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA
+SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE
+SATDPTLRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA
+YVSGQFVPVATADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA
+AGEALAEVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDVVVHNAGITRDRMLANMD
+AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGQGLRIVGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA
+ETVAWLASDAAGGTNGATLRVCGQSKLGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000968.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000968.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4cc8e68c0c679799866f2b721f5bd57680cea554
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000968.fa
@@ -0,0 +1,101 @@
+>GCF_002008305.4_01164
+MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAV
+EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR
+LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA
+AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR
+RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV
+HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR
+VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV
+PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF
+RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV
+LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA
+QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA
+LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA
+SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR
+VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA
+DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE
+VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL
+RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE
+GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY
+AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV
+TAVPRRSPGLDA
+>GCF_003691675.1_00883
+MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAV
+EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR
+LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA
+AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR
+RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV
+HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR
+VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV
+PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF
+RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV
+LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA
+QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA
+LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA
+SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR
+VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA
+DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE
+VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL
+RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE
+GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY
+AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV
+TAVPRRSPGLDA
+>GCF_005280335.1_01726
+MSRRFLSALLVHVPDIPEFASLPAAEQDELRAAGAAVQARLERSGTIDRPAVAAALWPAL
+RRVHAVPRSPEREAAYAAFRAEAGPGLDDFALWSALRTADDVPGPDLADPAWAPGGEHAE
+RVRTERADEVDLHRWVQWVAAEQLAAVQQRARAAGMRMGVMVDLAVGATRETADAWMLGD
+VLVPGMSVGAPPEVFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRDAGGIRMDHVL
+GLFRLWWIPVGAGATQGAYVEYDHEAMLAVLTLEAERAGAVVVGEDLGTFEPWVQRRLAE
+AGVLGTSILWFEQRDGEPLPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTV
+DVAQERRRSADEVEAFLGAAVRRGLLDARDARVRPDDAAQREAQTVALHRLLAQAPSALH
+SVSLVDAVGERRIQNQPGTTQDQYPNWTLPLGDREGRMLRVEDLASSASAARLFDAVEEE
+LRASVPVGIGVSLHTSPLAQPGRGDAGGLNVYVRHAALALARRGVRMILLTRAEEPVGPE
+SARVTRLEAGGEAPAVTVVELAVGPAAPLPKAELAALTDEFTAAARAWLASDAVPGGPVL
+APQGLDGRGPGAPAAPPVAFVHGHYWLSAPTAAALAAATGAPHLHTMHTTAAVKMLEDPE
+LREPGARIEAEGAVVREADLLVVNSPAEVVDLREALGVPRARTRVLPPGADLATFTPEGP
+ALWPGDPDDDGALRVLFAGRIQRHKGPHLLVEALAVLRERAGGPGADPGVRLHVNGAPSG
+EEGLDLPGLALERGVADLVTFSEPVRAEELAAQLRAADVVAMPSASETYGLVALEAQACG
+TPVLAHRVGGLVHAVIDGASGRLVTEGSPEAWADALAAVLADRPAWDALAAGAVRHAAGH
+SWEAYADGLLEAAAGLARRQDGA
+>GCF_020097155.1_01623
+MPENARALLRRLARAHGVQTEYVGQDGSDQSVADETLVRVLSALGVEVDADGVAGLTEAL
+DAVDAAPWRDVLPPTVVARQGHRSTVPVHVARGAAVQVRLVQEDGRVVDLPTREAVGATL
+VVDGQERVRHDLDLPEDLPLGWHRLEAVSETGSVARATLVSAPAALTTAAPFLARRGWGV
+AAQGYSVTSSGSWGVGDAHDAGSLAELAAPHGADFLLLHPLHAVEPAGAPADSPYSPVSR
+RFLSAFLIRVTDIPEFAALPAEEQKRLAAAGRAVQEAVLTGGTIDRAAVAEVLWPALEAV
+WRAPRTSERDADYAAFRDRQGTGLDDFAAWSVLRRDALRAGVAGPDPTDPAAGPGSDGVR
+RVRAERADELDFHRWVQWIADEQLAAAQERAREAGMRMGVMLDLAVGATRGSADAWMLGD
+VLVPSMSVGAPPEVFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTLMAHAGGLRMDHVL
+GLFRLWWIPEGLGAPQGAYVHYDHEAMLAVLTLEAERAGVVVIGEDLGTFEPWVQRRLAE
+AGVLGTSILWFEQEDGVPTPPEQYRRLCMAAVNTHDLPPTAGYLEGVHIDLRERLGLYTA
+DVAAERRRSAAEVEAFLGAARKRGLLEATGPDGVETVEDRVVALHRLLAQAPSALHCVGL
+VDAVGERRIQNQPGTLQEQYPNWTVPLGDADGRVLTVEDLAGTASVSRLFDAVAAELDAS
+VPVGIAVAFHTSPLAQPGQGDAGGLNVYVRHSARALARLGVRMLLLTRAESPVGPSGVRV
+TTLPQGEGAPDVTVVELAAGPQEPVAKEELPAHREAFTAAAREWLASADVPGGPLLGAAG
+AAAARVRFVHAHYWLSGDTAAAVADDLGAPRVQTMHTTGAVKSAGDPGHPEPAERLAAEA
+DLVRRADLLVVNSPAESRDLQELLDVDRDRVRVLPPGVDLESFTPEGPSRWPGGDAVGAD
+ALRVLFAGRVQEHKGPHVLVAALAELRARAADGDPRVVLHVNGEQSGPADLDLPALAARL
+GVADLVTFSPPVPPVELAAQMRAADVVALPSASETYGLVAVEAQAAGTPVLAHRVGGLVH
+AVQDGVSGRLVIPNTASAWADALAAVREDRQAWDAMAPAAVRHARAHAWSGWAEGLLDAV
+AGLPRP
+>GCF_023573625.1_01114
+MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAL
+EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR
+LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA
+AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR
+RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV
+HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR
+VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV
+PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF
+RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV
+LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA
+QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA
+LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA
+SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR
+VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA
+DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE
+VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL
+RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE
+GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY
+AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV
+AAVPRRSPGLDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000969.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000969.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a122cb77a63c565282c1adbed967319fd57bc4cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000969.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01166
+MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDEADPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPEVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE
+RVPVDALEFGCRVLERMLEPR
+>GCF_003691675.1_00885
+MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDSEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE
+RVPVDALEFGCRVLERMLEPR
+>GCF_005280335.1_01723
+MIQNAHDTPVSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAALCARLMEEAGMRPRL
+FESSPGRVSVVGHLPGWDEDAPGLVVHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLSVLLHLTRTGRRPRRPLTVAFFADEEAGGVYGARWLVEHHPELFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGIAWLNLRAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDEQDPTPQLDALGQARSWVAGTLRTSSNPTGMT
+SGYKHNVIPSTATGTVDARLLPGEEEAALATLQELAGPGVSIEPEHRDVALETPFSGDLV
+ELMVASLQAEDPGAEVLPFMLGGGTDNKSLARLGITGYGFAPMRLPADLAFTSLFHGIDE
+RVPVDALEFGCRVLERMLEPR
+>GCF_020097155.1_01621
+MDASTPSTAPSTADADVVEICRDLIRIDTTNHGGGRSVGEPEAAELCAAWMRKAGMEPEL
+IESAPGRVSVVGRLEGWDPEAPGLVLHGHTDVVPAEPDEWTVDPFGAEFRDGMIWGRGAV
+DMKGMDAMILSVLVHLARTGRRPRRPVVVAFFSDEEAGGVFGAQWLVAHRPELFAGCTEA
+ISEVGGFSTDVAGTRAYLVQTGEKGLAWLNLRAQGAPGHGSAPHTDNAVTRLAGAMERIG
+RHPWPLTYTKTTRQLLEEVAEITGTPFDERDPTPQLQALGHARDWVAGTLRTSSNPTGLT
+AGYKHNVIPSTATGTVDVRLIPGEEEQTLAELADLAGDGIEISPEHQDTGLEVPFSGDLV
+ERMASALDAEDPGAHVLPFMLGAGTDNKSLHRLGIAGYGFSPLQLPSGLEFTRLFHGIDE
+RVPVESLRFGCRVLEHVLEPRA
+>GCF_023573625.1_01116
+MVENIENPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMTEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHGIDE
+RVPVDALEFGCRVLERMLEPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000973.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000973.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67f1330da40588cb9451b01a552ff8c97751968e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000973.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01170
+MKSWSTPAPPAVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLAEAAADPLPVVDVVAALLGLR
+LR
+>GCF_003691675.1_00889
+MKSWSTPAPPTVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGIEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPLALEALDAWAAGTLPGLAEAAADPVPVVDVVAALLGLR
+LR
+>GCF_005280335.1_01719
+MKSWSTPVPPAVPTRPDRLRLHDTATGAVRHPGNDAREASLYVCGITPYDATHLGHASTY
+VAFDLLNRYWRAAGLEVAYVQNVTDVDDPLLERADATGVDWRELARDQTDLFRTDMAALE
+VLAPDHYVGATEAIDLVVDAVEAMLAAGLAYRVPGDADAPDGDVYFDVRAAEAAGDWRLG
+QVSAMPLDEMAAVFPERGGDPQRPGKRDPLDPLLWRVHRDGEPAWDGRSLGEGRPGWHIE
+CSVISRAHLPSPFTVQGGGSDLRFPHHEFSAAHATAVDGRPLARHYAHTGMVALNGQKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEDVLARAQERVARWRAALEGPH
+AQAGSAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLDAAADAAPVAVADVASALLGL
+RLR
+>GCF_020097155.1_01617
+MKSWSTPAPRALPVQPDRLRVFDTATQALRHPGNDARTASLYVCGITPYDATHLGHATTY
+VSFDLLQRYWRAAGLEVAYTQNVTDVDDPLLERAEATGVDWRELAREQTDLFRSDMEALN
+VFAPDHYVGATEAIDLVVRAVEAMLEGGTAYRVPGTDGEPDGDVYFDSAAAQARGGWTLG
+SVSAMDRAQMEEVFPERGGDPGRPGKRDPLDPLLWRVHREGEPAWDGGALGSGRPGWHIE
+CSAIAREHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGRPLAHTFLHSGMVALDGQKMS
+KSLGNLELVSRLRARGVEPVAIRAAILDRHYRSDWEWSEDLLTAAEERVARWRSALDGPH
+ADAGAAVLAAAHTALSEDLDAPAALRVLDAWADGTLDGLSTTAEPLPVADVVDALLGLRL
+R
+>GCF_023573625.1_01120
+MKSWSTPAPPAVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLAEAAADPLPVVDVVAALLGLR
+LR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000974.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000974.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b46c57e1fa7214fb9c6d0598fe1c0c1f88d2b11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000974.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01171
+MTDATSEDQPDDALGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR
+EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEAFLDREGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWRAFLEELFTAADAHDVDAVVTLGALLADVPHTRPLRARPTS
+PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL
+VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+SIAREFERYLRGRGGR
+>GCF_003691675.1_00890
+MTDATSEDQPDDVLGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR
+EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEALLDREGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWRAFLEELFTAADARDVDAVVTLGALLADVPHTRPLRARPTS
+PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL
+VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+SIAREFERYLRGRGGR
+>GCF_005280335.1_01718
+MTDASSADQPDDALGPLRTHLTATVDDLEAGLRAPTVLLLAFEGWNDAGDAASGALDALR
+EQWDAAEAGRICDGEFYDYQVTRPVVRRDADGLGTLEWPAVRLHEAQLDAQGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWQAFAEELFAAAAARQVDAVVTLGALLADVPHSRPLRARPTS
+PLVDVRVAVGADRPAYEGPTGIVGVIADEAARRGLPSVSLWGAVPHYVAQAPSPKTLLGL
+VEAIEDLLHVSVSTCELEDDAQAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+AIAREFERYLRGRGGR
+>GCF_020097155.1_01616
+MDEQTDPGSLDGAPSPEDRLGALRAHLTATVPEVEDGSRPPAVLLLAFEGWNDAGEAATG
+ALAELSAQWEAAPAGVVCDGEYYDYQVTRPVVHRDADGLGTLEWPALRVHEARLDAHGAP
+VPDGEAVPADGLRVLLASGVEPNVRWRAYVEELLRWAEAEGVDAVLTLGALLADVPHSRP
+LRARPTSPLVAVRVAVDAGLPAYEGPTGIVGVVTDEAARRGTASLSLWGAVPHYVAQAPS
+PKTLLGLVEAVEDLLHVELLTHALRDDAQAWQRGVDELAREDPEVASYVRRLEESQDAQE
+LPEASGEAIAREFERYLRGRGRD
+>GCF_023573625.1_01121
+MTDATSEDQPDDVLGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR
+EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEALLDREGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWRAFLEELFTAADARDVDAVVTLGALLADVPHTRPLRARPTS
+PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL
+VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+SIAREFERYLRGRGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000977.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000977.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fdcaa299f0b4af1442e52660fd2a91390047cfe1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000977.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01174
+MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV
+VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL
+SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG
+SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET
+LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFRAEDVEAWQPA
+DEARWTPEALGERPITDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD
+>GCF_003691675.1_00893
+MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV
+VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL
+SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG
+SVDRVVLDMLAPWECLDTVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET
+LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFKAEDVEAWQPA
+DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD
+>GCF_005280335.1_01715
+MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV
+VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL
+SMSLLRAVGDHGRLHSYERREEFADVARANVEAFFGAEHPAWSIHLGDAQEQMTRVHEPG
+SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET
+LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLATGEEALRLKKRSKVSEFKAEDVEAWQPA
+DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAERGVDAYGGSIQEQDQD
+>GCF_020097155.1_01613
+MSDATAPETPAAPTTPDTAAPAGRPAGVTARRGPLRAGQRVQIKDAKGRLNTITLLPGGE
+FHSYQGVLRHDDLIGGPEGIVVQNSSGHAYQVLRPLLNDFVLSMPRGATVVYPKDAGQIV
+QQADIFPGAVVVEAGVGSGALSMSLLRAVGDAGRLHSYERRAEFAEIARGNVESFFGGVH
+PAWSIHLGDAQEEMPKVHEPHSVDRVVLDMLAPWECLDAVATVLAPGGVWLNYVATATQL
+SRVAEAIRASGKFTQIEATETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLAAGEDALV
+MKKRLKVSEFTTEDVEAWTPSDGARWTPQALGERTVTDKKARKAAKEARLTARRARAALE
+GRDPRTVGQDKD
+>GCF_023573625.1_01124
+MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV
+VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL
+SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG
+SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET
+LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFKAEDVEAWQPA
+DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000982.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000982.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0e1e70a280e91d9f4380af822b64a90dfb57c98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000982.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01179
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQRLDSLLDEIDSVLESNAEEFVKGFVQK
+GGQ
+>GCF_003691675.1_00898
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQRLDSLLDEIDSVLESNAEEFVKGFVQK
+GGQ
+>GCF_005280335.1_01710
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQGLDSLLDEIDSVLESNAEEFVKGFVQK
+GGQ
+>GCF_020097155.1_01608
+MAQEQIRPRPAGGPEDEGAAAQAQAKAAPQDTGLDGLLDEIDSVLESNAEEFVKGFVQKG
+GQ
+>GCF_023573625.1_01129
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQGLDSLLDEIDSVLVSNAEEFVKGFVQK
+GGQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000985.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000985.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51e200c13544464442fcd64d424af13c3467da9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000985.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_01183
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDTAFEKLFQRDRR
+VLRAVGVPLETLEPAGLDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWYLTLVRGRWYLTGWDLDRGAERSFRLTRMEGEPRRVERATDAPGRPEDHD
+HAGLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGRAVPSAAHPDLTDRVRAGLAAAAEAHAGPADPALLEVPLAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGITDERLDADLETLRYCGMPERDFPGF
+QFEVAEVGGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAPRARPARWRVHPDDTAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAA
+VAAALVGRHGGAVEVLAPADLRTSVADALGDALAALPAR
+>GCF_003691675.1_00902
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDAAFEKLFQRDRR
+VLRAVGVPLETLEPAGFDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWFLTLVRGRWYLTGWDLDRAAERSFRLTRMEGEPRRLERATDAPGRPEDHD
+HADLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGCAVPSAAHPDLTDRVRAGLAAAAESHAGPADPALLEVALAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGITDERLDADLETLRYCGMPERDFPGF
+QFEVAEVGGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAARARPARWRVHPDDAAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAG
+VAAALVGRHGGAVQVLAPADLRASVADALGDALVALPAR
+>GCF_005280335.1_01705
+MAPPASRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLSDAAFEKLFQRDRR
+VLRAVGVPLETLEADSFEEEAQGVRHRVVRDAMLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFAPTPDLAADDELAGYHALTPRADPRLEALTQAVAEEAVLRFPYRDARG
+RESRRTVRAWFLTLVRGRWYLTGWDADREAERSFRLTRMEGEPRRVERAASLPGRPADHD
+HADLVARLAGQADAERVRVWLAPGRGQGVRAVGARVDPRAEDGAAPGDGWELWEAPAGTH
+EDGLAAEVGGLLGRAVPSAAEPDLARRVADALAAAARAHAGPAAPALLEAPLAPPVRRRA
+RDSSEDLVGRLLDIVGLANRADGVDRAELRARLGVTEERLDADLETLRYCGMPERDFPGF
+QFEVDEEGGRVHVRRAADLAGPVRLTRPEGHSLVAALQTVADLPVLDDADRAAARSAQRR
+IAEAVLDAGGAAASAADDEALAEAEAGTAPTPAPGGAVAAHWDVAVDPETVRTLLAAIAE
+RRVLRLDYRSVHADALSERDVEPLAVVQDGARLYLRAWCRSAGEDRVFRVDRIGAATATG
+EAFAPRARPARWRVHPDEAAGTPAVLRWAHRVRDAASGYRPEAQADLPDGDRLTRVRLTD
+ADVAAALVGRHGGAVEVLYPAAMRAHVKDALDRAVDALAAR
+>GCF_020097155.1_01604
+MSAHGSTAEPAERIISLLWLLLHEPLGYTREQIRRLVVGYEGLTDGAFEKLFQRDRRALR
+AVGVPLETVGDPDDEAGPRLRVDRDALLLQDVDFTVDERRALVRARRLWGDSPLRDDVVR
+AVGVLFHPGEVGGDDALEGFRTVMPRTDPRVAALSEAAAEQSVVRFSYRDAAGALTERTV
+RAWLLTLVRGRWYLTGWDADRAAERSFRLTRMESDPVVLDAGAASPAGEAPTLPAGHDHA
+ALRARLAGRAEAETVRVWLAPGRGQGFRVAGRPVPATAADGPAPGPDWELWECPSGPSED
+GAVAEAAVAVGQVLFSTVEAAAGRALAADLAAAAAVHAGDPDPAWRDVPLTAPTRRRSRA
+SSEDLVGRLLDIVGLANRAEGIGRDELQERLGVTARELDADLEVLRYCGMPEREFPGFQF
+DVEDEGGRVRVHQSSELAGPVRLTLPEAHALVAALQTVAEMTVLTPEDREAARSAQRRIR
+ASLADAGQSHAGSADAEAPRDGTGKEPGAVVAHWDVVADPDTVRTLLDAVAERAVVHLRY
+HGVRSDAVTERDVEPLAVVQDRTRLYLQAWCRRAGGPRVFRVDRIGALHRTGETFRARRV
+PAWDPRPAGDGVEAVVRWAHEVRDAADAYAPAAAATLDSGDRLTRVLLADDDAAVGLAAR
+HGGRVEILAPAALRGAVRGRLEAAARRAAGAVA
+>GCF_023573625.1_01133
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDAAFEKLFQRDRR
+VLRAVGVPLETLEPAGFDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWFLTLVRGRWYLTGWDLDRGAERSFRLTRMEGEPRRVERATDAPGRPEDHD
+HAGLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGRAVPSAAHPDLTDRVRAGLAAAAETHAGPADPALLEVALAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGVTDERLDADLETLRYCGMPERDFPGF
+QFEVAEVAGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAPRARPARWRVHPDDAAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAA
+VAAALVGRHGGAVEVLAPADLRTSVADALGDALAALPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000986.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000986.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fff56ebda567ef029c9a6c47fc716c60c863fc1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000986.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01184
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR
+>GCF_003691675.1_00903
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR
+>GCF_005280335.1_01704
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEDKGAKDGKDAR
+SGSGSTAADEPVEGRVVERDETDVRPRDER
+>GCF_020097155.1_01603
+MRFTPTHLIVLIIVVLLLFAAPKLPALARNLGQSMRIFSSEVKQMKEENTTKKAEGAATA
+DAPSQGAGSTAAEPVEGRVVDRDVRDDR
+>GCF_023573625.1_01134
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000987.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1f67f82de7148c8c7d767f7e213866e0685d9a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000987.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01185
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSALAVAVGMVIGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRSGQREVDVEAELAEGPKPLDQI
+>GCF_003691675.1_00904
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSGLAVAVGMVVGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRQGQREMDVEAELAAGPKPLDQI
+>GCF_005280335.1_01703
+MSEVEEVARRTRRRRRRDNPTGEMPLREHLTELRNRVIKAGVAVLLGMVVGFLIYQPVMA
+ELFRPVNELSRDGRISAIAYDTVASPFDLMLKVSLFIGLIVSSPVWLYQIWAFIVPGLKK
+AEKKYALGFIAAAVPLFLLGMGLGWLVMPQAVQFFVGFTPEGGATLPTASVYISFVTRLY
+LAFGVAMVLPVLLVGLNMLGVLPGRTIVKHWRITVFLIMLIAAIAAPGADAISMVYMAVP
+LVLLFGVAIALCLWGDRRRARRAVRREQDVEAELASGPKPLHEI
+>GCF_020097155.1_01602
+MTSVDEEAAGARGRRKGRKPKNPNGEMPLREHLKELRDRLIKSVLAVVLGAVAGFALYKP
+VMEVLTRPMVEARERGVNAALAFDTVSSPFDMMLKVALFIGIVVSSPVWLYQAWAFVVPG
+LTKSEKKYAVGFLGTAIPLFLAGLYLAWLVHPQAVQFFIGFTFDGTAALPTASNFLTFSI
+TLFLVFGVSMVLPVFLVGLNLLGVLPATTILKHWRIVVFLVALIAAMAAPGSDVISMFYL
+AGPLLLLFGISILVCWLNDRRRARRSRDTAEDLEAEIAAGPRSLDEL
+>GCF_023573625.1_01135
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSALAVAVGMVIGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRSGQREVDVEAELAEGPKPLDQI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000989.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000989.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52bd76c3120f1b083ef6925e3e4d632d41fb436a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000989.fa
@@ -0,0 +1,39 @@
+>GCF_002008305.4_01187
+MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF
+VEPLARPADARDALSRGTAVVTVLAGPEDTGAAPADEDVQTVVYRHADRVDAEAAGVWLP
+VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR
+VRHRLVVTHPVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVTVCLGAGPAGDP
+WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAARLSVAPRLSVSAPAVFGVWD
+ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA
+ATPA
+>GCF_003691675.1_00906
+MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF
+VEPLARPADARDALSRGTAVVTVLAGPEDTGAVPADEDVQTVVYRHADRVDAEAAGVWLP
+VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR
+VRHRLVVTHSVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVSVCLGAGPAGDP
+WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAAGLSVAPRLSVSAPAVFGVWD
+ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA
+ATPA
+>GCF_005280335.1_01701
+MGRVTAHLLTTGIIHSVTDPYAQALLVRDGVIAWLGADDSAERVADPADARTDLDGAVVV
+PAFVEPLARPEDARDALSRGTAVVTVLAGPAGDVAPAEGVQAVVYRHAEGPAEGAVGVWL
+PVAADADAADLAAALAEATRAGEQAYLVPAADAAGHGDAEAPAAAQAAAIAALRRVAEEL
+GAPALGRVRHRLVVTSPVTAEDRAFLASVAVSATVVPAADGTLRAPVASLLADAVPVALG
+AGPGRDPWAAVRAALSHPEEAERISARSAFAAATRTPLRALPDAADADLVAAPRLAVSAP
+GVFGVWEAEAVAVQSPDGRVAAWSTDTRAGTPLLPALDDQTPLPRWRATWVGGRIAAEAA
+DGDARGTGDHA
+>GCF_020097155.1_01600
+MSSTLFLNGIVHSASDPYATAALVSDGVVAWLGDDSSADRVADPDVPRVDLAGAVLAPAF
+VEPGGPSVDPAQALRHGVAIVTVLAEPGQTAQALQAAADPALQTVVYRAADTVDAEAAGV
+WLPAEGEALAALVVASTRAGEQVHLVPPAGGDPSEGQAAALAALRSAAEELGAPALGRVR
+HRVVLTAPITAEDRALLAAISASVTVGPEADGLLRAPLGTLLAEGVPVCLSTAGEAGPWA
+AVRAALSHPDEAERISARSAFTAATRTPLRVLPDAPGATVQAAPRLTVSAPATFAVWEAD
+AVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRPAAVEVADA
+>GCF_023573625.1_01137
+MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF
+VEPLARPADARDALSRGTAVVTVLAGPEDTGAAPADEDVQTVVYRHADRVDAEAAGVWLP
+VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR
+VRHRLVVTHPVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVTVCLGAGPAGDP
+WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAARLSVAPRLSVSAPAVFGVWD
+ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA
+ATPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000991.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000991.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf5fd1c9c512ac235071d6dff7c8ae21de9ab761
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000991.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01189
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA
+>GCF_003691675.1_00908
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEDVDA
+>GCF_005280335.1_01699
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAEAEGKPVRTHWDMLRERRSLEELQETYALQLNKLRASRGEDVDA
+>GCF_020097155.1_01598
+MSDRSLRGMRLGAQSLESEAGVEPAPRQRVEYRTEDGEQVFVTFAQEAEVPTTWTSKTGK
+EALRVDGEKPEENPGKPVRTHWDMLLERRSMEELEETFQIQLKKLHASRGEAV
+>GCF_023573625.1_01139
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000992.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000992.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98b0a0c525b82526f76f2faf6fae63099c111c14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000992.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01190
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQANTMFVVPAELTRALQGLGEAFAPGDGDRPTPEHAPR
+RRDSGDRAGEPGAEHSGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH
+>GCF_003691675.1_00909
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQATTMFVVPAELTRALQGLGEAFAPGDGDRPTPERAPR
+RRDSGDRAGEPGAEHVGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH
+>GCF_005280335.1_01698
+METIIILVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTMIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDEATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQALPKIADGESNTMFVVPAELTRALQGLGEAFSPAGDGESRRPSPSG
+ARGEAAERAGEHGGASPERPRRPRGSRPTTADALRSSGVMDAMTAGAVTAQEMPQTSLDE
+ALATPKELDPDPSAGRAPGRRPAGETDGNGVGH
+>GCF_020097155.1_01597
+MEFLIVLAVLAVLVGVLLASSVKIIPQARTANVERLGKYQRTAGAGLTLIIPFIDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDAINSQLRGVLDDATSRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSAILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIAEGTSNTMFVVPAELTRALQGLGEAFSPGSPSAAGTGSSDT
+SDDAAPAAGRAATGPGGRRRGRASEGARPTTAEELRSSGLLDAMTAGALTADRMPQTSLD
+EALQTPPEAEPAPVRREPGMP
+>GCF_023573625.1_01140
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQANTMFVVPAELTRALQGLGEAFAPGDGDRPTPEHAPR
+RRDSGDRAGEPGAEHSGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000993.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000993.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab0b5fad8c2914481e2f2a20ebdef93824cfb4c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000993.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01191
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADGA
+>GCF_003691675.1_00910
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPDVAPGDEVTVLRIDGATLVVRPLPRIDWQADGA
+>GCF_005280335.1_01697
+MDWIEANAGWLWLVAAAGLIGVELLTLDLVFLMIAAGAGAAGVVALAGGPLPLQLAAFAV
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITAEAGTLTVDGDTWSARV
+EDGAPDAAPGAEVTVLRVEGATLVVRPLPQIDWEDGRS
+>GCF_020097155.1_01596
+MEWIEANADWLWLVLALGLVGAELLSLDLVLAMLAAGALSAGVAALAGAPLGLQLGVFVV
+VSLLTLVAVRPAAMRRLHPDPAVGASWLDGLSGRRLTATGPVTDEGGRIDVDGETWSARV
+EPGAAPAAHGQGVTVLRVEGAHLILRPDPVIDWDAPAHD
+>GCF_023573625.1_01141
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000996.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000996.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85436f77dd16b08484ccf81f070c710b0328cd15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000996.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_01194
+MVSVHLVPIRPTAATADDAQRLSAALLDDPRPGAAVISAAWHIDETDAAPGDGELAVTLD
+GMAAGVGLALWAVRSGSWAVLLDTEGNYDKQSALSHITAGERRRARRAPGRLVLPHGRRP
+GRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGISQQAV
+HSRLRHGLWHESRTAVAAVLPLLERLSADPGE
+>GCF_003691675.1_00914
+MVFVHLVPIRPTAATADDARRLAAVLLDDPHPDASVAAAVWRGDEGNPDADAAPGDGELA
+VVVESMAAAVGLALWAVRTGSWAVLLDPEDALDKDSLLSYLTPAERRRARRAPGRLVLPH
+GRRPGRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGIS
+QQAVHSRLRHGLWHESRTAVAAVLPLLERLSADPGE
+>GCF_005280335.1_01693
+MIVLHLLPLTAPDAADAAWTRVGDELNRPGAVSSLVMPFDRQGEGSEARLVGGMDSGVEA
+VGILLSLVRSGAWAVVVEVAEGRAAGESLLQREAERARRANGHCAVLGPSGPSAAWIEPA
+LQLLGALERRRSEPQQDAGRRVEAGASQREVAAELQVSQQAVHARLRGGLWNETRALAGA
+TADALDVLARRGDRVSDGGASPSTSERG
+>GCF_020097155.1_01591
+MVPVAVRCGSAGAAGRWAASIPGARRLGREGGRDLIVHADDAAAAVALMLAVRRAGAGAV
+GAGVAIEQVEGALRRARRRPGGIAVSRVPGSTGTEEERGLLEAGLGVLLTLESRRSAPQQ
+AAGVLIEAGRSQREAAADLGVSQQAVQQRLRAGLWEETRTLLDALLPMARRVLEA
+>GCF_023573625.1_01148
+MVSVHLVLIRPTTATAEDARRLATALRDDPRPDAAVTAAMWLGDESDPVDDDAAPHDGEL
+AVVLDDAAAAVGLALWAVRTGSWAVMLDPEGGSDKDSALSYLTPAELRRARRAPGRLVLP
+AGGRPGRASESGREADLRCAEATLQLVAAVERRRSADQHAAGRLVEAGASQREAAAELGI
+SQQAVHSRLRHGLWHVSRTAVAAVLPLLERLSTDPGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000997.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000997.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c8d3f548a637e7b11f50e523e80ff1c1f919153
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000997.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01195
+MTSSPTARRAAPAEHRDPRGALPALAVDLLLTLLFVALGQGQHSTERGPLGLLVTAAPFL
+AGLLLMTGVTAGHRTWARAWPHGVIVWLGTVAVGMLLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
+>GCF_003691675.1_00915
+MTSSPTARRAVPAEHRDPRGAQPALAVDLLLTLLFVALGQGQHATERGPLGLLVTAAPFL
+AGLLVMTGLTAGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
+>GCF_005280335.1_01692
+MADTLSENRSETMAQTGGMTDSPTRRHSPASPPSPLWAATALAVDAVLVVVFVALGQDQH
+TTDRGLGGLLATALPFLLGLVAATVLTAGHRTWHRVWPHGVAVWLGTVAVGMALRVLWDQ
+GGAPLSFVLVALGVLGVFLLGRRAVTAWVIRRRARV
+>GCF_020097155.1_01590
+MSTTPLPQDSSPAAHPSDRRRGSAPWVAFALDAALVVLFVALGQREHATDRGGLALVTAA
+APFLLAWVAGTALAGGPRTWARVWPQGVVVWAVTVAAGMGLRVLWGLGGAPVPFVLVASA
+VLAVFLLGRRWASTLLAHRATDRASRAS
+>GCF_023573625.1_01149
+MTSSPTARRVVPAEHRAPRGALPALAVDLLLTVLFVALGQGQHSTERGPVGLLVTAAPFL
+AGLLLMTGLTSGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000998.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000998.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5bf3c8b449f33bbfafa80541b435ffc7fb6385df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000998.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01196
+MVTAIVLIKTDKSSIPETAETLAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVDGIQDTETMLAFRAYSSEDLGEGWALGFDS
+>GCF_003691675.1_00916
+MVTAIVLIKTDKSSIPETAETLAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVDGIQDTETMLAFRTYSSEDLGEGWALGFDS
+>GCF_005280335.1_01691
+MVTAIVMIKTDKSSIPETAETLAALEGIGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVEGIQDTETMLAFRTYSSEDLGEGWALGFED
+>GCF_020097155.1_01589
+MVTAIVMITTDKSTIPETAQAIASLEGVSSVYSVTGAWDLVAMVKLKRYEDLADVIADQL
+SKVDGIEDTETMLAFRTYSTEDLEEGWALGFDG
+>GCF_023573625.1_01150
+MVTAIVLIKTDKSSIPETAEALAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVDGIQDTETMLAFRTYSSEDLGEGWALGFDS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000999.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000999.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54b242367178c5dd4f69138fd009dd6c7963067f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0000999.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01197
+MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVTAQALGCSSQAMVPLLAQVLADRGVRGFVFRGADGRDKITT
+SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV
+LLNAAAGLTAWDRGADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS
+>GCF_003691675.1_00917
+MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVTAQALGCSSEAMVPLLAQVLADRGVRGFVFRGADGRDKITT
+SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV
+LLNAAAGLTAWDRDADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS
+>GCF_005280335.1_01690
+MSIPNTTAAAPETTWPDVFRALTFGEDLSDEAAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAARPVQVTGETLDIVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPREKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVSAQALGCSSEVMVPLLARVLADRGVRGFVFRGSDGRDKITT
+SGPSTVIEVRHEVTAHELDPRDFGIELAPVEALAGRDGAYNATLVHALLAGEKGPIRDAV
+LLNAATGLTAWDTEAQGPLADRLAANMARAAESLDSGAARDVLDRWVAFSRS
+>GCF_020097155.1_01587
+MRETVTHTWPEVFRRLTLGQDLDDAAAEWAMGEMMSGDATEGQVGAFLLALAAKGETVPE
+LRGLTDAMVAKARRVHVSGETLDIVGTGGDRLGTVNLSTMSSLVAAGAGARIVKHGNRGA
+SSTAGAADVIEALGVDLSMPPAKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQLGVPTV
+FNFLGPLSNPAQASAQALGCSSEEMVPLLAQVLADRGVRGFVFRGSDGRDKITTSGPSTI
+MEVRGGVTAHEIDPRDFGIELAPVEALAGRDGAYNATLVRGLLAGEHGPIRDAVLLNAAA
+GLTAWDVEAEGPLMDRLRTNMARAAESIDSGAAADVLERWVQFSRS
+>GCF_023573625.1_01151
+MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVTAQALGCSSEAMVPLLAQVLADRGVRGFVFRGADGRDKITT
+SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV
+LLNAAAGLTAWDRDADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001001.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03120393fd3210c3e94596198a994bd5c4d53fb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001001.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01199
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF
+NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA
+QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
+>GCF_003691675.1_00919
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF
+NANCASCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA
+QLAAYVASLGAGPAIPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVDEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLTLGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
+>GCF_005280335.1_01688
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF
+NANCATCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA
+QLAAYVASLGAGPAIPEDEYLDINNEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKFA
+PSLQGVEEKYIYEAMETGPQNMPVFSDANIKPEDKRDIIAYLKTIENQGSPGGLSLGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
+>GCF_020097155.1_01585
+MKALSQNRRHPLVGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAAAADDITAGEKLF
+NANCASCHNMGATGTADGPSLVGVGAAAVDFQVGTGRMPMQMNGPQAQRKPNQFSEEQTA
+QLAAYVASLGAGPAVPADEDLDPNAEGVNIAKGGDLFRINCAMCHNAAAAGGALTRGKFA
+PSLEGVSEKHIYEAMETGPQNMPVFSDANLKPEDKRDIIAYLKTIEANGSPGGLQLGSLG
+PVAEGLFIWTAGLALIVGFMVWLTSRSS
+>GCF_023573625.1_01153
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF
+NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA
+QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001002.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001002.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a37948f4eb0628c683ed788ed644b0b8680ddf07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001002.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01200
+MGEKGLEGTERRSGSLEHAGEDAPRYAIDDPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVRITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG
+>GCF_003691675.1_00920
+MGEKGFEGTEHRSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
+>GCF_005280335.1_01687
+MGEKGFEGTEHGSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTLLFFVGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEADRVAATGMISEILDESQIKRRPLLRNTLIGAAVLAPLPFIAVFRDL
+DDSDNFSDEETHNFGPERLRHTMWSEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG
+>GCF_020097155.1_01584
+MGEKGYEGAERHSDALEHAGEESPRYAIDNPGLPPHRPRLADEDPRAAKRAERQVSVFFL
+ISVIGTVLFFIGYFGVGQVGNGESTSVLYLQNLLLGLGVALAMFGIGIGVVHWAKTLMPD
+HEVVEERHEIRTEADRAAAQGMIADILDESQIKRRPLLRNTLIGAAVLAPLPFIAAFRDL
+DNTDNFSDEAAKNFGPERLRHTMWHEGVRLVRDPTGSPIKASDVTLGSALHVIPDGLNDL
+EHGKLNEKAKAVVLVMRLDPSKVKISPGRENWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLAQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
+>GCF_023573625.1_01154
+MGEKGFEGTEHRSDSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDEEIHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001003.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001003.fa
new file mode 100644
index 0000000000000000000000000000000000000000..189a1b0fd8316b8089715d4da9e36e7c4b9b1c14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001003.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01201
+MSTTVNEFQPATSTGRIANFVDTRTGMSPIVKFFARKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTFFFDPSMSEVVYNGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM
+CAWPWIERWITKDDTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFHLSL
+NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRP
+LTDYELYRLVAFEDRRPVPAIPGRNGKVGALEKARAGLNRMFYQERVAPVSREELVEART
+HGQHGHEEHPVELGHGSDAPRLER
+>GCF_003691675.1_00921
+MSTTVNEFQPATTTGRIANFVDTRMGMSPIVKFFGRKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTLFFDPSMSEVVYDGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM
+CTWPWIERWITKDNTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFRLSL
+NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRQ
+LTDYELYRLVSFEDRRPVPAIPGRNGKVGMLEKARAGLNRMFYQDRVAPVSREELVEART
+HGQHGHEEHPVELEHGSHAPHLDR
+>GCF_005280335.1_01686
+MSTTVNEFQPATSTGRIANFVDTRMGMSPIVKFFARKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTFFFDPSMSEVVYNGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALL
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPIVGTYLSAFFFGGEFPGHSIIGRLYALHIMVVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTENNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDFSFLWNIPMPWGSSVSLPMGVLVPLIPIGVLIVGM
+CAWPWIERWITKDDTEHHLLDRPRNAPTRTGIGVAAVIWYCVMWAAASSDLIATHFRLSL
+NDVLYALRTLFFLGPVIGFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPDGGFHERHRQ
+LTDHELYRLVSFEDRRPVPALPNRSGKVGMIEKARAGLNRMFYQDRVAPVTREELVEARA
+HGHHGVEDGGHHELGADPSSHNPKIDG
+>GCF_020097155.1_01583
+MSTATHEYQPATGTGRLANFLDTRVGLSPIVKFFGRKTFPDHWTFMFGEVALYSFVILLL
+SGAFLTFFFDPSMSHVTYDGAYAPLRGIEMSAAMASALDISFDIRGGLFMRQLHHWSALL
+FVASMSVHMLRIFFTGAFRRPRELNWVVGCFLLMAGWAAGFTGYSLPDDVLSGNGLRIID
+GILKAMPLVGSYLSAFLFGGEFPGYSVIGRLYALHIMIVPAIILLLIAVHLFMVVVHKHT
+QYPGPGRTENNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINSIWIYGPYDPSPVS
+AGTQPDWYIGPFDGALRLMPGMIGDFSFLWNIPMPWGSRVSLPMGVLTPLIPVGVILVGM
+ISWPWIERWITKDDREHHLLDRPRNAPARTGIGVGMMIMWCTMWAAASSDLIATHFHLSL
+NDVLYFLRALFILGPILGFIVTRRICISLQRRDRETVLHGHESGVVEMSPEGGFSERHRQ
+LTDYEMYRLVSFEDRRPVPATPGRNGKVSGAERMRAGLNRMFYQERVAPVSREELVEART
+HGHGEHVGAVQGGSHSAELGH
+>GCF_023573625.1_01155
+MSTTVNEFQPATTTGRIANFVDTRMGMSPIVKFFGRKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTLFFDPSMSEVVYDGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM
+CTWPWIERWITKDNTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFHLSL
+NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRQ
+LTDYELYRLVSFEDRRPVPAMPGRNGKVGALEKARAGLNRMFYQDRVAPVSREELVEART
+HGQHGHEDGGHHELGADPSSHNPKIDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001004.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10b993fd9ff7ccf1a9802214ac891cb7dfc3ad58
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001004.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01203
+MKVAANIFWVIGLFFVGAGTLYGFWNEWTEWAGIPAIYALGGMSWMIAWYLNAAERKYGV
+GPADDEDGQIVEYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWVFVIGIIAGAYFTF
+GWVYEFSRGKFAH
+>GCF_003691675.1_00922
+MKVAANIFWIIGLFFIAAATLYGFWVEWTEWAGIPAIYAVGGMSWMIAWYLNVTERKYGV
+GPADDADGQIADYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWIFIIGVIAGAYFTF
+GWVYEFSRGKYAH
+>GCF_005280335.1_01684
+MKVAANIFWIIGLFFIAAATLYGFWVEWTEWAGIPAIYAVGGMSWMIAWYLQSTEKKFGL
+GPADDEDGEITDYAGTYGTFAPWSWWPLGLGVACAILITGLAVGWWVFIIGAVAAAYFTF
+GWVYEFSRGKYAH
+>GCF_020097155.1_01582
+MKIASNIFWIIGAFLVAVATLYGFWVKWTEWAGIPAIYALGAMCWMIAWYVQSTDKRHGL
+GPADDEDGEIVEYAGTYGTFAPSSWWPLGVAVACAMLVTGLAVGWWIFALGVIAGVYFTF
+GWVYEFSRGKYAH
+>GCF_023573625.1_01160
+MKVAANIFWVIGLFFVGAGTLYGFWNEWTEWAGIPALYALAGMSWMIAWYLNAAERKYGV
+GPADDEDGQIVDYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWVFIIGVIAGAYFTF
+GWVYEFSRGKFAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001006.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6efdbeadfcc802f319a0bd4a52efda2306d040d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001006.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01205
+MGTTALLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLVWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILTVFTLWGFTDRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQEDGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVVHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVQRLEEMESGQVGEEYSRNPNNNPDGAGTMERDLQTPRGGGSH
+>GCF_003691675.1_00924
+MGTTSLLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILMVFTLWGFTNRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVAHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGESHSEMLFNVEVVDE
+AEFVQRLEEMEPGQVGDEYSRNPNNNPDGAGTMERDLQTPRGGGSH
+>GCF_005280335.1_01682
+MGTTALLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTIIPILMVFTLWGFTNRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVVEANYSGIQAQLDGTEGVRDTLPVLYLPKDVPVHFELKS
+RDVAHSFWIPQFLQKRDLIPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVDRLAEMEPGLVGDEYSRNPNNNPDGAREMERDLQTPRGGGSH
+>GCF_020097155.1_01580
+MRAQNDAGRRTRRRLTAGALGATALVALTGCSAEAQRGWLPGTDNTTNHNAQLTDLWVNS
+WIAALAVGLIAWGAMIWCMIAYRRRKNDQGFPRQTAYHMPIETMFTVIPILMVFTLWGFT
+DRVQAEVDTPIDDSPLTVTVYGKQWSWDFNYSYEKDGQTREAHFQGVQAQLDGSDGKRET
+LPTLYLPKDVPVHFELKSRDVAHSFWIPQFLQKRDMLPGKTNNLYLTPQEIGRFDGKCAE
+LCGEFHSEMLFNVEVVDEATFVQKMNEMEPGLVGDELNRNPNQNPDGARNMEVDLQTPRG
+GGNH
+>GCF_023573625.1_01162
+MGTTALLVLTGCSAEVQRGWYPGTRETTNHNAQLTDLWVNSWIAAMAVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILMVFTLWGFTDRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVAHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVQRLEEMEPGQVGDEYSRNPNNNPDGAGTMERDLQTPRGGGSH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001007.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be64aca9e4abbdf86c8a5d2a803503144adf0869
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001007.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01206
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
+>GCF_003691675.1_00925
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
+>GCF_005280335.1_01681
+MALSADETGVEIGATQDSEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVQVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV
+GSCACGDSFH
+>GCF_020097155.1_01579
+MALSAEETGVEIGATEDATGLPPHEVELTDVAAAKVRALLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV
+GSCACGDSFH
+>GCF_023573625.1_01163
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYIMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001008.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99993b9d2ca28f11ed0dce23fa0158d76573508e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001008.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01207
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRAQLERSAEAVA
+GLLREAGLQDVEIVSEIRDDGRPGGPAVIGEKPGTSDKPTVLFYAHHDVQPIGDEDLWDT
+PPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSMRLGPGMEPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSAPAAAAMMAALEDAWGVEPRAIGMGGSIPFTADLAE
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA
+>GCF_003691675.1_00926
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSAEAVA
+GLLRAAGLQHVEIVTETRDDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEDLWDT
+PPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMDPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSATAAAAMMAALEDAWDVEPRAIGMGGSIPFTADLAQ
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA
+>GCF_005280335.1_01680
+MTETTPPVRDDAALVAAVRDAVDARFPQTLQTLTDLVAIPGIAWDSADRAQLERSSEAVA
+ALLRQAGLQGVEIVTETREDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEALWDT
+EPLVATEKGGRLYGRGAADDKAGIMVHLAALAALKDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLENHRARLEADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRRSASLDYPEDVFRADAGVLDSVTLAGRGPV
+ADRLWNAPALSVIGIDVPSVAESSNTIQPQARAKFSLRLGPGMDPAEAFEALKAHLEAQS
+AAVLGAEITVEAGEFGQPFDTDTSDPLAAAMMGALGDAWGVAPKEAGMGGSIPFTADLAE
+VFPDATILITGVEDPDSRAHSANESLHIEDFRRAVVAEALWFARLAG
+>GCF_020097155.1_01578
+MTQSTQNTPVGAAPDPELVSAIRAAVDRRFPETLQSLKDLVSIPGIAWDSMDREPLERSA
+AAVADLLRTAGLEGVETAVEERADGRPGGPAVIGGRPAVGDKPTVLLYAHHDVQPLGEEG
+LWDTPPLVATERDGRLYGRGAADDKAGIMVHLAALAALDEVCPDAGVGVRVFIEGEEEAG
+SPTFRPFLERHRDRLAADAIVVADSSNWAVGEPALTTSLRGVVSATVTVRALDHAVHSGM
+FGGPVLDAVVLMSRLIATLHDADGAVAVPGLEPRHHADVDYPEDAFRADSGILPGTRLAG
+RGALADRLWNGPALSVIGLDAPSVDTSSNTIQPAARAKISLRLGPGMDPAASLDALRAHL
+EAQSDAVLGAEITVEPGELGQPFSTDTSAPAAAAMMGALGAAFATPARETGLGGSIPFTA
+DLKELFPEATILITGVEDPDSRAHSANESLHLEDFRRAIVAEALWLAAMGA
+>GCF_023573625.1_01164
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSAEAVA
+GLLREAGLQEVEIVTETRDDDRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEDLWDT
+PPLEATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMEPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSAPAAAGMMAALEDAWGVEPRAIGMGGSIPFTADLAE
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001012.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28cbbd79636b71ef7b2ae0dc491926be6512cf67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001012.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01211
+MSADRAPQPPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDVDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPDSASVADGGA
+>GCF_003691675.1_00930
+MSADRAPQSPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDIDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPASDADGGA
+>GCF_005280335.1_01676
+MSGSGPSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIVEALTPEHGLVRAVAKGVRKT
+SSRLGSTVEPFMHTTLQLARGRGELLTVTQAQLLHPYATMLAADYDAYAVAGALAEAVER
+IPAVDEAGRRAQYRLLHGALAALARRRHDPRLILHSFLLRTLAQAGWAPTFDRCARCGAP
+GPHSAVHVALGGAVCPECRPPGAAHPAPQTLALLAALAAGDWATADSSDAAARREAAGIV
+AAYLQFHAERRLVSPVRPGPGPRPPRPARREETMRADRAPQSPPPHPSGAVAPRIDPRFV
+PRHVAIVMDGNGRWANQRGLPRTEGHRAGEAALLDVVAGAVELGVGHVSAYAFSTENWRR
+SAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWNGRAPRLWTPVIRELQEAEELTRHNTGT
+TLHMCVNYGSRAEIQDGVQALAEEVRAGRMRPADITEDVITRYLDRGFRAGQDVDVVPDV
+DLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWPDVDRRTLWEAVETYARRDRRYGGAVDT
+AQPAPSSGAPDSASDADGGA
+>GCF_020097155.1_01574
+MSDVPKVSPPPHPSGAVPPKLDPRFVPRHVAVVMDGNGRWANQRGLPRTEGHRAGEAALL
+DVVAGAVELGVGHVSAYAFSTENWSRSAEEVRFLMGFSKDVLRRQRDTLDSWNVRIRWNG
+RAPRLWTPVIRELREAEDLTRDNTGTTLHMCVNYGSRAEIVDGVQALAEEVAAGRMRPRD
+LTEDVITRWLDRGFRAGDRDVDVTPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDELWP
+DVDRRTLYAAVLEYAHRDRRFGGAVDAPAAD
+>GCF_023573625.1_01168
+MSADRAPQPPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDVDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPDSASVADGGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001013.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001013.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45cef053cfd9a106767906cf3878efc65a39c3cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001013.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01213
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLRGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLLLSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA
+>GCF_003691675.1_00932
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVITEAPRWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLKGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA
+>GCF_005280335.1_01675
+MSAHLQKPSGMKFHKYVPYQDQIQVSLPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFESLEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLKGTQI
+TYEYSPESYTGTELEFARRISDEVAQVLEASTDRKMILNLPATVEMATPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+FSQGVDPMIDFSDMDHIKRTVEYCNQLPVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+ADAKAAGKTVDEIDWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQEMADAQGGEVSGADLWTAFQDEYLPAEAKDEQWGRYRLRSVTSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRMLGEDDMDVRVLDYTEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRAVRA
+>GCF_020097155.1_01572
+MRNLQKPSGMKHGKYVPYHEQIEVHLPDRTWPDKVITEAPRWCAVDLRDGNQALIDPMGP
+ERKLRMFQLLVQMGYKEIEVGFPSASQTDFDFVRQLIEGDHIPDDVSIQVLTQAREHLIE
+RTFESLEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLTGTEIT
+YEYSPESYTGTELEFARRISDEVATVLEASTDRQMILNLPATVEMATPNVYADSIEWMHR
+NLEHRDSIILSLHPHNDRGTGVAAAELGYLAGGDRIEGCLFGNGERTGNVDLVTLGMNLF
+SQGIDPMIDFSDMDHIRRTVEYCNQLPVPERSPWGGDLVFTAFSGSHQDAIKKGFEAMEA
+DAAAAGKHVDEIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHKLDLPRR
+AQIEFSHVIQELADAHGGEVSGADLWTAFQDEYLPAENKEEAWGRYRVRSVSSESGENGA
+FRMTAEIFVDHEPQTRTAEGNGPIDAFLKILGEDGQDVRVLDYTEHALSEGGSAMAAAYV
+EAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRSLRA
+>GCF_023573625.1_01170
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLRGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001014.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2861124b14bc48f783e0499863edf3738fb8d031
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001014.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01214
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYPDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVMVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
+>GCF_003691675.1_00933
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYPDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVVVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
+>GCF_005280335.1_01674
+MTDLVDPARAADGHRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGQRLNDLVAETLGEVDAVGFCLPADEAIGPGDRFIAQQL
+AHLHRTPVVAVVTKTDKVGPEQLMAQLLAVTALGEEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLEVLRGLLPEGPPLYPDGELTDEPEAVMIAELIREAALEGVRDELPHSVAVVVEEM
+ALREGRPDDRPLMDVWANLFVERDSQKGIIIGKGGSRLREIGARARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
+>GCF_020097155.1_01571
+MTSLLDPAVPEGHRSGFACLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVHR
+PDFQLVLVDTPGLHRPRTLLGERLNALVQETLSEVDVVGFCLPADEKIGPGDRFIAQQLA
+ALRRTPVVAIVTKTDKTDPQRVAEQLLAVTALGDEVLGPENGGRGFAAVVPVSAVAGRQV
+EDVESVLAQLLPDGPPLYPDGELTDEPEAIMVAELIREAALEDVRDELPHSVAVVVEEMN
+PREGRPEERPLLDVYANVFVERDSQKGIIIGKGGSRLRAIGTQARTGIERMLGTPVHLDL
+RVKVAKDWQRDPKHLNRLGM
+>GCF_023573625.1_01171
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYLDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVVVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001017.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b781b387f7308f875af5eb1f6893a580672905e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001017.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01217
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
+>GCF_003691675.1_00936
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
+>GCF_005280335.1_01671
+MVRTLGPQDALLRILGGVFPAVDLTVRDQRLEMAGPVPDVASVRRVVEDLRSIARRDQAV
+TPEVMEQVVTHVRGAAAGRGAGQLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGI
+GPAGTGKTYLAMAKAVQALQAKEVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYD
+ALHDMIEPESIPRLMEAGTIEVAPLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGF
+GARMVVTGDTSQVDLPRGTRSGLSQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYD
+AARGAEPAPRGGRGHRGR
+>GCF_020097155.1_01568
+MIRPIVSDPSSHVVLPPVSVPGAESVSFESAELMVRTLGAHDALLRILAGVYPDVEVTVR
+DQSLGMSGPPRHVAQARRIVEDLRSLARRDAPVTPDVVEQVVSLVRDGETGRASGTLHLD
+SILSGRGRKIRAKTLHQQDYVEAIDRATIVFGLGPAGTGKTYLAMAKAVQALQAKEVTRI
+ILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMESGTIEVAPLAY
+MRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGVRSGLAEAV
+EVLEGVDGLEMVRFDSSDVVRHSLVSAIVDAYDGARGSGSAADPRPAGRGAQRGRSGRGR
+>GCF_023573625.1_01174
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001018.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001018.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63fd931ed2ab6d5fd109860d3c86f00f8abd9a2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001018.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01218
+MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA
+AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAAKARQKWADTARAAAKQARRARVPAVRDHVSGTAVAGLARDDDGGRLVLVLHE
+DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP
+AALAVLQHRLGRW
+>GCF_003691675.1_00937
+MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA
+AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAAKARRKWADTARAAAKQARRARVPAVRDHVSGTAVAGLAWDDDGGRLVLVLHE
+DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP
+AALAVLQHRLGRW
+>GCF_005280335.1_01670
+MTAPLFHLEPGALTGAVPGAEVSFGGPEARHAAASMRLAPGESVLLADGSGVRGHGTVLA
+AAPDAVTVRLDAVDEEPAAVPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAEKARQKWADTARAAAKQARRARVPEVRGHVSGTGVAGLASAPDDGARLVLVLH
+EDAERGLSEVPVERLREAAEIAVVVGPEGGVGPAELEACTAAGAVPVRLGPHVLRASTAG
+PAALAVLAHRLGRW
+>GCF_020097155.1_01567
+MTAPLFLLDAGALAGVAPGAEVAFTGAEARHAAASMRLGAGESVLVADGSGARASCVVVD
+AAPSAVTVRVESLEHDAAPRPALVLVQALAKGDRDLMAVQASTELGVDAVVPWEAERSIV
+RWKGAKAAKAHQKWEDTVRAAAKQARRARVPEVRPVVSGTAVAALAGPDRLLLVLHEDAD
+LGLGGLPDADLEAAAEVALVVGPEGGVSPAELDACTAAGAVPVRLGPHVLRASTAGPAAL
+AVLQHRLGRW
+>GCF_023573625.1_01176
+MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA
+AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAAKARQKWADTARAAAKQARRARVPAVRDHVSGTAVAGLAWDDDGGRLVLVLHE
+DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP
+AALAVLQHRLGRW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001019.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001019.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75fcd732739645511ff34d1a3003cb6cf8f0c246
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001019.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01219
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL
+>GCF_003691675.1_00938
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL
+>GCF_005280335.1_01669
+MTDHYATLGVSRDASTEEIRRAYRKLARTHHPDVNPDPESAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQSGFPGGFGGGGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+APIDLEDAVFGGEQTITLDTAVRCKRCEGSCCEPGTEPETCQTCQGHGMIQRPMRSLLGT
+VMATEACPACQGFGTVIPDPCHECAGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPHETFRREGDHLATTVTVPMAAAALGTTVTLATLDGEQTVRLEPG
+VQSGHVETLAGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRELLERLAELRGEEVVHGT
+PPARGMFARLRENLRNL
+>GCF_020097155.1_01566
+MADHYATLGVSRDASAEEIKRAYRKLARQHHPDVNPSEEAAEEFKRISHAYEVLSDEDKR
+RVYDQTGNENGTAGGFGGGGFGGAGFGGFADIFETFMNAAGTPGGGRGPMPRARRGQDAL
+VTARIELRDAVFGGEATLQLDTAVTCERCSGTCCEPGTHPETCSTCQGQGMTQRPVRSML
+GTIMAAETCPVCRGFGTVIPHPCTECSGQGRVRVQQPLTIRIPAGVDDGTRIHLAGRGEA
+GPGGGPNGDLYVEVQVRPDEVFRREGDHLATTVTVPMAAAALGTSVTLETLDGPQEVDIE
+PGTQSGHVETLRGLGVGRLRGAGRGDLKVDVVVTTPTDVTDEQRALLEQLAGLRGEEVVH
+GAPPQSKGMFARLRENLKNL
+>GCF_023573625.1_01177
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPGPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001023.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001023.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f629c5e53ccc015adaf044a84d14b5a9c8d199e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001023.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01224
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCDPEDVLRVSGKTG
+VGVEELLDRVVRAVPSPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTKGLAVGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFGLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQAADLVKVDILLQGEQVDAFSSITHKDNAYTYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK
+>GCF_003691675.1_00943
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCEPEDVLRVSGKTG
+VGVEDLLDRVVRAIPGPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTNGLAAGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFDLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHRDNAYAYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK
+>GCF_005280335.1_01664
+MSPLASNPPVPAATEPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWELDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELATLIGCEPEDVLRVSGKTG
+VGVEDLLDRVVRSIPAPEGEADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKIRMM
+STGATHELLEIGVSSPEPTPTKGLAVGEVGYLITGVKDVRQSKVGDTVTNHAKPAAEELG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFNLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKIHEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLRGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHKDNAYSYGVMMTGKLKELIPRQQFEV
+PIQAAIGSRVIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADSAAKK
+>GCF_020097155.1_01561
+MSEAPEPIKDVPVSPLASKPPVPAATDPAVIRNFCIIAHIDHGKSTLADRMLQATGVVQP
+REMKAQYLDRMDIERERGITIKSQAVRMPWEVDGVNYALNMIDTPGHVDFTYEVSRSLAA
+CEGAILLVDAAQGIEAQTLANLYLAMENELEIIPVLNKIDLPAADPDRYAAELATLIGCE
+PDDVLRVSGKTGQGVEALLDRVVERLPAPQGVADAPARAMIFDSVYDTYRGVVTYVRVVD
+GMLSPREKIRMMSTGATHELLEIGVSSPEPMPTKGLSVGEVGYLITGVKDVRQSKVGDTV
+TNSSRPATEQIGGYEDPKPMVFSGLYPIDGSDYPNLRDALDKLKLNDAALVYEPETSVAL
+GFGFRVGFLGLLHLEIVRERLEREFDLDLISTAPNVVYEVKREDKTVVTVTNPSEFPEGK
+VLEVKEPMASATVIVPAEYIGAVMELCQTKRGHLKGMDYLSEERVEIRYWIPLAEIVFDF
+FDQLKSRTKGYASLDWKADGDQVADLVKVDILLQGEQVDAFSAITHRDNAYSYGVMMTGK
+LKELIPRQQFEVPIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKR
+MKMVGRVEVPQEAFIAALSSDGAEPAKK
+>GCF_023573625.1_01182
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCEPEDVLRVSGKTG
+VGVEELLDRVVRAIPGPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTKGLAAGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFDLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHRDNAYAYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001025.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f7ad0c0cb679c75b60726dc808ec8fb929b6b9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001025.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01226
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEPEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>GCF_003691675.1_00945
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>GCF_005280335.1_01662
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>GCF_020097155.1_01559
+MANIKSQKKRILTNEKARQRNIAVKSELKTAIRAVDKAVAAGEQDAAVEALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>GCF_023573625.1_01184
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001026.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e284f2a659789fcab2d8c52f94a83294029b8bbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001026.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01227
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGTRGKRLLDAVAKAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVSVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>GCF_003691675.1_00946
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGNRGKKLLDAVAQAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVTVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>GCF_005280335.1_01661
+MSAARSPRSGRAGRVDPLAWRKAEPAPLMLLKGPEDHAARWVTDKVTAALRERHGELEVH
+SLRAGEYQAGQLATAASPSLFAEPTLIKVDGLESMNDAFLEDALRLVQHGPGADDVTLVL
+RHAGGSRGKRLLDAVAKAGTVVDCVPLKKDEERLAFVLAEFRDRRRRIEEDAARSLLRAT
+GASLTELAAACAQLVDDTEGTVTAAMVDTYYGGRVEATSFAVADAALEGHAARAVSLVRH
+AMATGVHPVMVTAALALKARQVARMIDAHRPAGELAALLGVAPFQVRYIQQAARHWTPAG
+IAQAMEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>GCF_020097155.1_01558
+MSAARSTRSARGARGVDPLAWRRAEPAPLMLLRGPEEYAARWVADRVVATLQARHGSLET
+HRLRASDYQAGQLALAASPSLFAEPTLIRVDGLESMNDAFLEDALRLVAQGPGADDVTVL
+LRHTGGSRGKRLIDAVAAAGVVVECPALKKDEDRLALVQAEFREARRRIDEDAARALVRA
+TGASLTDLASACRQLIEDVEGTVTPQTVETYYGGRVEATSFAVADATLEGHAARAVSLTR
+HALATGVHPVMITSALAVKARQVARIIDARAGQGELASILGVAPFQVRFIQQAARHWTPA
+GIARAVEWIAQADAEVKGAARDADFAVERAVIRVATAVSR
+>GCF_023573625.1_01185
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGNRGKKLLDAVAQAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVTVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001028.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9cd1c572dd8d645c7b55c387811e2617704c6ea5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001028.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01229
+MSPSHRLCDDPPAFAPDPAAVPDVDTAGPHAASRWERTPPRGPVLRWRPALLAVTVLLVA
+AAAWWAVAWLTTPAPPAAVPAAAAGAGIPQTGAPSAASTAAGTDARTPEAGPSGEASGSA
+GSTPLRVHVVGEVARPGVVSLAPGSRVADAVRAAGGPTRHARAERINLAAPLDDGQQVLV
+PSAHTPQDALDRVAGAAQAQPTPTTGGAGATGEPGGAEPRGTVDLNTADAAGLQTLPGVG
+PATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDLVSW
+>GCF_003691675.1_00948
+MRDAPDSATGPQTARMSPSHRLCDDPPAFAPDPAPAAAPDVDTAGPHAASRWERTPPRGP
+VLRWRPALLAVTVLLVAATAWWAVAWLTTPAPPAAIPAAAAGAGIPQTDAPSTAPSAAGT
+DARTSEAGPSGEASGPAGSGPLRVHVVGEVARPGVVSLAPGSRVADAVGAAGGPTRHARA
+ERINLAAPLDDGQQVLVPSARTPQDALDRVAGAAQAQPTPTTGRAGGGGEPGGAESGDTV
+DLNTADATELQTLPGVGPATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDHVSW
+>GCF_005280335.1_01659
+MSHPHRLAPDAALSDDPRRGRPASDLVPVPPALAARGPSAWERVPPRGRVLRWRPALLAV
+TVLLVAAAAWWAVAWLTSPAPPSPAPAASAVEARVEPETEDGPDAADAAPPSDGAGPAAE
+PSGGSGPVATLLRVHVVGEVERPGVVSLAPGARVADAVRAAGGATREARTERINLAAPLA
+DGRQVLVPSARTPEEDLARVAGGQDGPGGPEGGAAGTAPDAAASAPAGPARAGGSGGAGA
+GPVDLNAADAVALQTLPGVGPATAEKIIAHRETVGPFTGLQDLDAVPGVGPAALERLRDR
+VTW
+>GCF_020097155.1_01556
+MDTKTLTPAVDEPDWEDPPPRGPLLRWRTAGAGLTLVAILGLTWWLVAWLTAPAPPDAVP
+AGAVGSASAAGSAAHEASAAPLRATAATPEGQDGGGRSAAAANPSGRVRVHVVGQVRRPG
+VVELPAGARVADAVAAAGGARELARTDRINLAAPVVDGQQVVVPDAQTAVEPAAVAGEAP
+DGGPTPRTGSGASAADGSGGGPATVDLNTADLAALQTLPGVGPATAEKIIAQRESVGPFS
+GLQDLDAVPGIGPATLDRLKDHVTW
+>GCF_023573625.1_01187
+MSPSHRLCDDPPAFAPDPAPAAAPDVDTAGPHAASRWERTPPRGPVLRWRPALLAVTVLL
+VAATAWWAVAWLTTPAPPAAIPAAAAGAGIPQTDAPSTAPSAAGTDARTSEAGPSGEASG
+PAGSGPLRVHVVGEVARPGVVSLAPGSRVADAVGAAGGPTRHARAERINLAAPLDDGQQV
+LVPSARTPQDALDRVAGAAQAQPTPTTGRAGGGGEPGGAESGDTVDLNTADATELQTLPG
+VGPATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDHVSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001029.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb9e3d9ad5c67e26c5fafae2b305554cccdd25c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001029.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01230
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTVYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAADAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELAVERAGEDPVRIAVHEYGDPETAMQLAERLQPISTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD
+>GCF_003691675.1_00949
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD
+>GCF_005280335.1_01658
+MATIEQWRDDALVRLRSRRSQLVGRARYGLKPPRRDRTAVVTDSAAALPAAALGHSLAAG
+IRQVPLPVMVGDQIHAEGTDDLALELPLALAAGTAVRTSRPSPGAFRSVYAQLAREGYAR
+ILSVHLSGELSGTAEAARLAAVDAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMTVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLIGTLLHVRPVLAVDDGAISLVDRPR
+SAARAVDRLVELATERAGDVPVRIAVHEYGDPETAAALAERLTPVSTTPVPVVELPAVLA
+AHLGLGALGVVVCPLESPTGGSGD
+>GCF_020097155.1_01555
+MASTSQWLEDAVERLRARRGQLVGRARYGLKPARRDRTGIVTDSAAALPVEVFAHPFAAG
+IRQVALPVMVGEQIHVEGDADLDLELQLALAAGTPVRTSRPAPGAFRAAYADLAQAGCAR
+ILSVHLSGELSGTVEAARLAAADAPVPVVVLDSRTAGLALGHAVLDAAVEAGFGRPLDQV
+AAIAQACADQSSVLFTVPHLEQLRRGGRIGAVPSLLGALLQVRPVLGLQDGSVHLVDRAR
+TSPRALERMVDLARERAAGGPARIAVHEYGDPAGATALAERLQSASATPVPVVPLPAVLA
+AHLGLGTLAVVLSPLEPVPSTSSSPAQAN
+>GCF_023573625.1_01188
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001030.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a09115497fd7955e2861c0d03c5c987c27baec6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001030.fa
@@ -0,0 +1,75 @@
+>GCF_002008305.4_01231
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPEAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNDGKAMSK
+SLGNGVDLGDQLDQFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGTPAGTDPADGAVALRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVIRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAQIVKVIVREPKLVNLVIR
+>GCF_003691675.1_00950
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPDAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGDQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGAPAGTDPAGGAVTLRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVVRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAEIVKVIVREPKLVNLVIR
+>GCF_005280335.1_01657
+MFPYPSGDLHMGHAEAFAMGDVVARHWMQRGYDVLHPIGWDSFGLPAENAAIKRDAHPAE
+WTYANIETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRKGLAYRKDSPVNWC
+PQDQTVLANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLA
+MQRNWIGRSEGAHVDFQIEDGPQITVFTTRPDTLHGATFMVVAADAPLAAELADESVRAE
+LEAYREELKKVSDIDRQATDRPKTGVFLGRHAINPLNGERLPVWASDYVLADYGTGAIMA
+VPAHDQRDLDFARAMGLPVRAVLDTGEENPAVSGVATTGDGTLVNSGELDGLDKTAAIAR
+AIEIVEGRGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCEACGEVLVPEDQLPVTLPTDL
+NGEQLAPKGQSPLAAATSWVEVACPDCGGPARRDTDTMDTFVDSSWYTLRYASPNDDTQV
+FDPEAVRRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNG
+GRAMSKSLGNGVDLGAQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRL
+ARDVREAGTPADADPATGSVALRRVTHRSVHEAGQLLDDGKFNVVIAKTMELVNAARKEI
+DGGAGAADPAVREAAEAVAVLLSLVAPYTAEDMWVMLGHEPSVVRAGWPAVDESLLVEDT
+VTAVVQVKGKVRDTLEVPADITAEDLEARARASQKVRTFIGDAEIVKVIVREPKLVNLVI
+R
+>GCF_020097155.1_01554
+MSQTPESAAPATPQVPEDAEYAFSEVEARWAGYWEQAGTFTPRGDGSATRTVVDMFPYPS
+GDLHMGHAEAFAMGDVLARYWLQRGYDVLHPIGWDSFGLPAENAAIKRNAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRKGLAYRKDSPVNWCPQDQTV
+LANEQVVDGKCERCGAEVTKRELNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPAVTVFTTRPDTLHGATFMVVAADAPLALELVDDEHRAALEAYRE
+ELKKASDIERQATDRPKTGVFLGRHAVNPLTGERLPMWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMDLPVRTVVDTGEEDPAVSGVATTGEGTLVNSGELDGLSKADGIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPEHGEVLVPEDQLPVLLPTDLKGGQLA
+PKGQSPLAAAEEWVNVPCPECGAPARRDSDTMDTFVDSSWYFLRYASPWDEQQVFDPELV
+KTWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGQQLDEFGVDAVRTTMVFASPPEDDVDWADVAPAAAGKFLARAWRLARDVRA
+AGTPAGDPAQGSAALRRVTHRTVHEAAALVEDHKFNVVVAKTMELVNATRKEIDGGAGAA
+DPAVREAAEAVAILLSLVAPYVAEDMWAMLGHEPSVVRAGWPAVDESLLVEDTVTAVVQV
+KGKVRDQLQVPADVSAADLEAAARASAKVRAFIGDAEIVKVIVREPKLVNLVIR
+>GCF_023573625.1_01189
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPDAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGDQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGAPAGTDPAGGAVTLRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVVRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAEIVKVIVREPKLVNLVIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001031.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001031.fa
new file mode 100644
index 0000000000000000000000000000000000000000..971afcac3c5997f7bd059d7df99db9b6fbdaf11b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001031.fa
@@ -0,0 +1,43 @@
+>GCF_002008305.4_01232
+MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI
+LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW
+AGSTLMTLLVLVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ
+ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTALLLMAST
+LLYLGYAEIGRADVPMLRLFASIAPWLGWAMVVVIYLMIFNTAIGMFYALGRRLTADRPG
+RYRPVFAGVTLLAFAVSFVGFGDLINVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL
+RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPDAVTEALEDEVAQVLEEDDALTS
+EGARPGPDAGPERPAGGSHSA
+>GCF_003691675.1_00951
+MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI
+LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW
+AGSTLMTLLVLVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ
+ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTVLLLMAST
+LLYLGYAEIGRADVPMLRLFASIAPWLGWAMVVVIYLMIYNTAIGMFYALGRRLTADHPG
+RYRPVFAGVTLLAFAVSFVGFGDLMNVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL
+RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPGAVTEALEDEVAQVLEEDDAVTP
+DEVHPGPDAGPERPAGGSHSA
+>GCF_005280335.1_01656
+MVFRSVSHPVMARILDVTVTVTLFAIGFVMLAGAGSTLAQQLGWPTWAGAGLMTALVLVT
+GMLDVEKVSAIISLITPLIILAVVAGFVHVLLTHEGSFTANEALAVQAATPVAPWWLSSV
+NYFGLVVVMAVSMCLVIGGSITNPREAFAGGLTGGVLYTVLLLLASVLLYLGYAEIGRAD
+VPMLQLFASIAPWLGWTMVVVIYLMIYNTAIGMLYALGRRLTAERPGRYRPVFIGVTLLA
+FAVSFVGFGDLMNVVYPALGYLGIVLALVLIAWWVLHRRQISAESGLRLRLRALLRLREH
+PEKTFTAQHAVLLQEAADESVAATAVVTEAVEEEVVQAIEADEPYGDPRRS
+>GCF_020097155.1_01553
+MQKSAALRSVQLALAFVGLLVGAGFATGAEVIQYFVGFGEVGIGGALLAGVLVAVGGAVA
+LQLGSLFLAADHKVVFRSVSHPVMARILDAVVTVTLFAIGFVMLAGAGSTLAQQLGWPVW
+AGAALMTAMVIVTGMLDVEKVSAIIGMITPLIIIAVVAGFAYVVATHEGPFTVNDSLAVQ
+AVTPVSPWWLSSINYFGLVVVMAVSMCVVIGGSTSSPREAFVGGLVGGVVYTVLLVLASV
+LLYLGYAELGTADVPMLQLFASIHPALGWAMVVVIYLMIYNTAIGMFYALGRRLTAERPG
+LYRPAFVGVTLAAFAVSFLGFGDLMNYVYPALGYLGIVLAVVLLVWWAAHRDDIAAESGL
+RLRLLALLRLREHPEKTFTRQHAVILQETAEESVAPTETVTEMMEADAVAVIEAEDPDLL
+PAADETAGRGGADHGGADGSAAARG
+>GCF_023573625.1_01190
+MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI
+LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW
+AGSTLMTLLVVVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ
+ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTALLLMAST
+LLYLGYADIGRADVPMLRLFASIAPWLGWAMVVVIYLMIFNTAIGMFYALGRRLTADRPG
+RYRPVFAGVTLLAFAVSFVGFGDLMNVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL
+RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPGAVTEALEDEVAQVLEEDDALTS
+GGARPGPDAGPERPAGGSHSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001032.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25ac79e321545698d52fae6fdbb5241cbe2d74f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001032.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_01233
+MPVPTPPAAPGPPVRLRDLLRPPAAPADPRVLTGHVARTPRRRTLAVPDPVRRTPSSVAV
+WEYAPVPEAAPGSRGAPEGDPAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG
+DSEPFPHAEHTVAHHADAVAAGVAALGLPAAPVLVAHSYGTTVAAELAVRDPSRWARLVL
+LNPIAEPALQASASVTSRVLAAVAEGYYEVAARLPERPARLLLGAPPVVWVTTLATTRTR
+DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS
+VPAQKALAAAIDAGGGTAELHVLDGVGHLLHYERPAACAALIRDWLRRAGR
+>GCF_003691675.1_00952
+MPVPTPPAPPGPPVRLRDLLRPPAAPADPRVLTGHPARTPRRRTLAVPDPVRRTPSSVAV
+WEYAPVPVAAPGSPGALEGDAAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG
+ASEPFPRAEHTVAHHADAVAAAVVALGLPAAPVLVAHSYGTTVAAELVAREPSRWGRLVL
+LNPIAEPALQASASATSRVLAAVAEGYYEVAARLPERSARLLLGAPPVVWATTLAMTRTR
+DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS
+VPAQEALAAAIDAAGGTAELHVLDGVGHLLHYERPAACAALIRDWFRRAGR
+>GCF_005280335.1_01655
+MHGFRGDHHGLALLADALPERAITSIELPGFGDSEPFPDAEHTVAHHADAVAAVLAAMPP
+SQRPVLVAHSYGTVVGAELVARDPGRWDRLALLNPIAEPALDASASWTSRGLAALARGYY
+ELAARLPERAGRLVLGAAPVVWVTTLAMSRTPDRRVLAYTHDQHRRYFSRFASARMLSES
+YRASSTGTVADAADRLRLPVLLVAGREDPLGSVPAQEALAAAIEAGGGRAELHVLDGVGH
+LLHYERPGECAALLRAWAARGR
+>GCF_020097155.1_01552
+MPAPHDADPASPAGPRPIRPWHRLRIPAPTTPPRALTGHDVRVPRRRDVAVPDPISGAPL
+SVAVWQHDAAPSSGASVAGAARPHLVFVHGFRGDHHGLQLLADCLPEFGVSSVELPGFGA
+SDPFPDAEHTVAHHADALAAAVAALGLDAPPVLVAHSYGTVVAAHLVQRDSGAWPALALL
+NPIAEPALDASGSRADRLLAGVAEAYYEAAARLPERVSRLLLGAPPVVWVTTQAMSRTRD
+RDVLAYTHDQHRRFFSGFASARMLSESYRASSTGTVAQAADRLDLPVLLVAGREDPLGSV
+AAQEALAARIAAAGGVPELHVLDGVGHLLHYERPAACARLLREWLAAGA
+>GCF_023573625.1_01191
+MPAPTPPAAPGPPVRLRDLLRPPAAPADPRVLTDHPARTPRRRTLAVPDPVSGTPSSVAV
+WEYAPVPEAAPGSPSGLKGDTAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG
+ASEPFPHAEHTVAHHADAVAAVVAALGLPAAPVLVAHSYGTTVAAELVARDPSRWGRLAL
+LNPIAEPALQASASVTSRVLAAVAEGYYEVAARLPERSARLLLGAPPVVWVTTLAMTRTR
+DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS
+VPAQEALAAAIDAGGGTAELHVLDGVGHLLHYERPAACAALIRDWLRRAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001034.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001034.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52d29f3855893987a805a550810462c5ab634568
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001034.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01235
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPKIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLETREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
+>GCF_003691675.1_00954
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
+>GCF_005280335.1_01653
+MTDAAQPSPARHADPYTGVGGGELRLFTSESVTEGHPDKICDQISDAILDAILAADPAAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVTRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRQENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHDWVGQEQLRKDVEEH
+VIRPVIERSGLDTSGMRVIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTAVVPEER
+IIQAVNEVFDLRPAAIVKELNLLRPIYRKTAANGHFGRDDADFTWERTDRVERLRAAAGL
+>GCF_020097155.1_01550
+MSDTPTPTPSAAAQPYRGVGGGDLRLFTSESVTSGHPDKMCDQISDAILDAILAADPSAK
+VAVETLSTTGLVQVAGEVNTSAYVEIPHIVRETILDIGYDSSANGFDGAQCGVNVSIGQQ
+SSDIFAGVSRSLEAREQGSADEVDEQGAGDQGIMFGYATNETPSYMPTPIYLAHRLSERL
+TAVRRQENTPMPYLLPDGKTQVTVGYDADHRPRTVETVVVSTQHHDVVTQEQLRADVAEH
+VIRPVIERSGLDVSNARFIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYALRWVAKNVVAAGLAGRAEFQVAYAIGSARPVGLYVDTFGTNAVPEET
+IIAAVNEVFDLRPAAIVKSLNLLRPIYRKTAAHGHFGRDDADFTWERTDKVEELRRAAGV
+>GCF_023573625.1_01193
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEKH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001035.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c2483d7ff18eeae94abdc841c16f981d78ceac9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001035.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01236
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF
+EAVDEVNHVRLGRHADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATAANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR
+PRASGSGTEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGAIV
+RFIAGSMSVPAPEGVERVVQVESTQDLLEAVLAEAADADVLVMAAAVADFRPAEVSDAKM
+KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDPTSSVLEYGRAKLA
+RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDQAAAAVVQAIVDDLAGR
+DPAGASGR
+>GCF_003691675.1_00955
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF
+EAVDEVNHVRLGRRADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATVANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR
+PRASGSDAEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGATV
+RFVAGSMSVPTPEGVERVVPVESTQDLLDAVQAEAADADVLVMAAAVADFRPAEVSDAKM
+KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDATSSVLEYGRAKLA
+RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDEAAAAVVQAIVDDLAGR
+DPVGASGR
+>GCF_005280335.1_01652
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGTATWEALSGRPVRTGTF
+EAVDEVNHVRLGRQADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATVANVALLRERGVTVVEPAVGRLTGADSGARRLPEPDEIWELAQAAAADPAARR
+PRATTSRPGPAAAGAAPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGVALARAALA
+AGARVRFIAGSMSVPVPEGVERAVHVESTAELLTAVLEQAADADVLVMAAAVADFRPAEA
+SESKMKKGDDGSSPVIVLERTEDVLATAVRTRAAGGPMAPLIVGFAAETGDAESSVLEYG
+RAKLARKGCEMLVVNEVGRDKVFGRDETAVTILFADGSPAVEAAGSKDEAAAAVVGAVVD
+RLAASAPGSASAR
+>GCF_020097155.1_01549
+MEVVLGVGGGIAAYKAALLLRLMKEAGHGVTVVPTDNALRFVGAPTWEALSGRPVRTDTF
+TDVPEVSHVRLGREADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWRHPATVANVALLRERGVHVIEPDSGRLTGADSGPGRLPEPARIWAEAQDAAARAGGRA
+GREAAVTAAEPGAASPLAGRTVVISAGGTREALDPVRFLGNRSSGKQGTALAEAVLAAGA
+RVRFIAGPMSVAPPAGTEVTAVESTQELLEAVLSEAADADVLIMAAAVADFRPAQVATSK
+IKKTDDGGAPTIVLERTPDVLATAVQTRDAGGPMAPVIVGFAAETGDEHTTPLEYGRAKL
+ARKGCDLLVVNEVGDGKVFGQDATEVTVLSADGAEPVTRTGSKAEAAAAVVEALERVLAS
+REAGGAPGR
+>GCF_023573625.1_01194
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF
+EAVDEVNHVRLGRRADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATVANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR
+PRASGSDAEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGATV
+RFVAGSMSVPTPEGVERVVPVESTQDLLDAVQAEAADADVLVMAAAVADFRPAEVSDAKM
+KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDATSSVLEYGRAKLA
+RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDEAAAAVVRAIVDDLAGR
+DPVGASGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001036.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001036.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08256fcfcc39c7bbae409c72c9d40f0dede2baf8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001036.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_01237
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEAGLLESHEAVEATPEAELAAEDFGDFSLPGEDDPFATLESSDAHQPT
+GDPAAIEEAAETVRAEEGISEDAPEA
+>GCF_003691675.1_00956
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM
+GDPAAIEEAAETVRAEEGTSEDATEA
+>GCF_005280335.1_01651
+MTEQYDGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIETDLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLEPSDAGQPV
+GDPEAIEEAAEAVRAEEGTSEDAPEA
+>GCF_020097155.1_01548
+MTPPPPPDGPPPAAPCVPTHGQKTTREQTLETYVTDQYEGIVNPPIDSLLERVDSKYALV
+LFAAKRARQINAYYSQLHEGLFEYVGPLVDTQLNEKPLSIAMREIESDMLVMAETAAVEP
+AIELAEEEFGDFALPGDDDPFVAEPTAEGVSPEEYGAPVTTGDDDAVEDILSGADVADED
+A
+>GCF_023573625.1_01195
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM
+GDPAAIEEAAETVRAEEGTSEDATEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001039.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001039.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecbdf632760e5cadcf6d6da9ade8dade20870153
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001039.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01240
+MTTTATGGAGPRAPFGRRLAHAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEVGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR
+>GCF_003691675.1_00959
+MTTTATGGAGPRAPFGRRLAQAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEAGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR
+>GCF_005280335.1_01648
+MAQAGPLCLGVDPHPSLLRQWGLPDTPAGLEAFSLTGLEAAVGPDGPRVAAIKPQVALYE
+RHGSAGLAALERLLAEARDAGVLTIADAKRGDIGSTMDGYAAAWTSDASPLAADAVTLSP
+YLGFGTLVPTIEAAHAAGRGVFVLALTSNPEGREVQHVGRDAGEGAVARRIAAAAADLNA
+ALRAEDEWGPVGLVLGATVAEDAERLGLDLPGLAGPLLAPGFGAQGATAAGMREGFGRAW
+PQVLATSSRGILAGGPTVAALVERIERDRADLG
+>GCF_020097155.1_01545
+MSVPAASMTREPFGRRLAAAMAAAGPLCLGIDPHPSLLQAWGLPDTAAGLESFGLTALEA
+AAGDGAARVAAVKPQVALFERHGSAGLAVLERLLAEARDAGVLTIADAKRGDIGSTMDGY
+AAAWLDDASPLAADAVTLSPYLGYGTLTASIERAAAAGRGVFVLALTSNPEGASVQHVGA
+SEGQGAVAARIVTSAAADDARLAGLDGWGPVGLVVGATVAGHARELGIDLAALRGPLLAP
+GFGAQGATGAGMREAFGAAWPQVLATSSRGILAAGPTVTSLTRAIDAARADLGVEGPDPR
+HAAGRDA
+>GCF_023573625.1_01198
+MTTTATGGAGPRAPFGRRLAHAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEAGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001040.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61f0ff60c0e81c3fe99ba8fc9101c865bc7aabcb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001040.fa
@@ -0,0 +1,100 @@
+>GCF_002008305.4_01241
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL
+AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV
+TSLQEHDARLQQAVAGPEAAA
+>GCF_003691675.1_00960
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL
+AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVAHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV
+TSLQEHDARLQQAVAGPEAAA
+>GCF_005280335.1_01647
+MPKRPDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLHRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPADGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPRELL
+RRARTATTDRLAQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADQIRDAEVLDES
+LLRHAKRHGFSDAQIGSLRHMGADVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGRSVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVLGVYVQLGGQTPLKLAQQLADAGVPILGT
+SPEAIDLAEHRGEFARVLDRAGLVAPKNGTAVSFEDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGERMYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATEQIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAAMIGVGKSIADLQAEGVLPTAYDGATLPLGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHYDTAFAKSQAAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQIVSTGGTAEVLRRNGIPAETVAKIAEAGGEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRAYEWSV
+TSLQEHDARLQQAVEASA
+>GCF_020097155.1_01544
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVILVNSNPATIMTDPEL
+ADATYVEPITPEVVAKIIEKERPDAVLPTLGGQTALNTAIALDKDGVLEKFGVELIGANI
+AAIELGENRELFKGVVERAGGESARSHIVHTMEEAFAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLRRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPEDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADATLTTTMKSVGEAMAIGRSFSEALQKALRSLEQKGSELSFDRDADPASLL
+ASARTATTQRLAQTQRALYAGATLEEAFEATAIDPWFLDQLMLINEVADEVREAPQLDEA
+VLRRAKRHGFSDAQIGSLRHMDPAVVRGLRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLESEVDEHAAPSVVILGSGPNRIGQGIEFDYSCVHATLALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEATGGVAGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPEAIDLAEHRGEFARVLDEAGLIAPKNGTAVSFEDARRVADEIGYPVLVRPSYVLGGRG
+MEIVYTEEALAHYVTNATEITPTQPMLVDRFLEDAIEIDVDALYDGHELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVRTATEKIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAAMIGMGRTIAELRAAGTLPTAFDGASLPMGASVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHFDTAFAKSQAGAGGPLPTEGRVFVSV
+ANRDKRAVVGQAKRLVDLGFEIVSTGGTAEVLRRNGVPAEVVAKIADASDADGAGTVLEQ
+LHEGRVDLVLNTPSGGEARTDGYEIRAAATSLGVPVITTTAEFAACLQAIEAMRTYEWSV
+TSLQEHEERLAQAVAAEASA
+>GCF_023573625.1_01199
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL
+AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV
+TSLQEHDARLQQAVAGPEAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001041.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98a618f99be6b71205a3c85e2b767f0b86acdef4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001041.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01242
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA
+>GCF_003691675.1_00961
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELETFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVDAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA
+>GCF_005280335.1_01646
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDTDRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVYSGEHAGRPEAELLAEVREQPSMAGARLAETVTTEQPYVIEPAA
+HGWEGEPLAEIAALDLGIKAATPRHLASRGIRVHVLPATAGLEEIRAVSPDGVFLSNGPG
+DPATADAQVALLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVMDNATG
+RVAITSQNHGFAVDAPLGEPVEAPETRYGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVRMLTEHRDAAAPAATEGA
+>GCF_020097155.1_01543
+MSTPTPETALLVLEDGTVHRGRAYGARGSTLGEAVFTTGMTGYQETLTDPSYARQIVVQT
+APHIGNTGVNDEDAESRAIWVAGYVVRDAARRPSNWRSQRTLDEELAAHGVVGIQDVDTR
+AITRALRTEGSMKAGIFSGEAAQRPEAELLAEVREQPSMAGARLAETVSAPSAYVVEPSD
+HGWDGEPIADVAALDLGIKAATPHHLAARGIRVHVLPADSDFAAIQAVRPDGVFMSNGPG
+DPATADAQVAVLREVLDAGLPYFGICFGNQIFGRALGFGTYKLPFGHRGPNQPVMDKATG
+RVEITSQNHGFAVDAPIGEVVEAPEARYGRVEVSHWSLNDDVVEGLRLLDRPAFSVQFHP
+EAAAGPHDSLGLFDRFAHTLTERRAAAPSATPEGA
+>GCF_023573625.1_01200
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001043.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da509d32a563b9b02a72523e1defbc8cb1879eef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001043.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01245
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLTGMRVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>GCF_003691675.1_00964
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLTGMRVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>GCF_005280335.1_01643
+MRHLLSTAGLSRADALAVLDTAEEMDAVNRREIKKLPALRGRTVVNFFFEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLAGMHVVIVGDILHSRVAR
+SNVWLLATLGAKVTLAAPPTLLPVGVSAWPCEVTYSLDEALDARPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDERFARLTAGSGALLSEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>GCF_020097155.1_01540
+MRHLLDTADLTRAEALAVLDTAEEMAAVNAREVKKLPSLRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVISFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAAAQLAASGWV
+DSAVVNAGDGTHAHPTQALLDAFTLRHHLAAHDGVAPTGTDLTGMHVVIVGDILHSRVAR
+SNVWLLTLLGARVTLAAPPTLLPVGVASWPARVTYSLDEALADAPDAVMMLRVQAERMGG
+AYFPSAGEYTRLWGLNPARFERLTRQSGSRLDTPLVMHPGPMNRGLEICDAAADSPQNTV
+LEQVANGVSVRMAVLHLVLNQDPALAPQEARP
+>GCF_023573625.1_01203
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGQDLTGMCVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001045.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001045.fa
new file mode 100644
index 0000000000000000000000000000000000000000..789dcb11efd3e1bd54d4c9a74f47a22c77b1298d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001045.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01247
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>GCF_003691675.1_00966
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>GCF_005280335.1_01641
+MTEPASAASGAKRGTTARSRSRQRAVEILFEAEQRGATVAEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAVSEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>GCF_020097155.1_01538
+MTDTPSASDAKRGTTARSRSRQRAVEILFEAEQRGTDVLQGIRTRRESTDLQVNAYTQRL
+VEGVVADQERVDEALTSYSRGWSLDRMPAVDRAILRVGAWELLFEDEVPDAVAVSEAVAL
+AAALSTDESPEFVNGLLGRLQQVKPTLLA
+>GCF_023573625.1_01205
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001046.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34c43e7838492096ed79cb2edb8e5a00c1b409bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001046.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01248
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
+>GCF_003691675.1_00967
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
+>GCF_005280335.1_01640
+MATSNDIKNGAVLKLEGQLWNVIEFQHVKPGKGGAFVRTKMKNITTGKVVDKTFNAGAKV
+EFATVDRSDYQYLYQDGSDYVFMDVKDYDQITVSESVVGDAAKYMLENTQVVIALNEGTP
+LYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQGTRVKVDTRTGD
+YLGRVND
+>GCF_020097155.1_01537
+MATTNDIKNGSVLNLEGQLWNVIEFQHVKPGKGGAFVRTKMRNITSGKVVDKTFNAGTKV
+EFATVDRSDYQYLYQDGEDYVFMDVKDYDQITVPAAVVGDAAKYMLENTQVVIAMNEGTP
+LYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQGTRVKVNTTNGE
+YLGRVND
+>GCF_023573625.1_01206
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001048.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..800010ea3ab42ec8a381f32fcbf4d446c1c3f287
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001048.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01250
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMTGALEARLTAAATVAAAADEDPAARPAR
+RVVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPTPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP
+>GCF_003691675.1_00969
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMIGALEARLTAAATVAAAADEDPAARPAR
+RIVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPAPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP
+>GCF_005280335.1_01638
+MPGPVSLCAWEAMTGALEARLATAAAAADGAPAPRIVLVGPMGAGKTTVGRALAATTGLP
+FVDADELFVQVHGPIPEFFAARGEAAFREEEARVIAHVLGRPSPCVLSCGGGAVLHPATR
+RALRGPGSDVVHLAVDEAVALRRVGGGAGRPVLAGDPAGTWRRILAEREPFYREVADLVV
+DTTGLTAAEAAWRIVEGVHRPRRSESHP
+>GCF_020097155.1_01535
+MSAQPAPTDGVPSWEAMVRGLDGRLAETSRDPGPVVVLVGPMGAGKTTVGRALAEATGRV
+FVDSDALFEDAFGSIPAYFTSRGEPEFRRQEERVIAHVLAHPAPCVLACGGGAVLSAATR
+ARLADPRAVVVSLQVAEPEALRRLGGGAGRPVLAGDPAGRWKAVLAERAPLYAEVADLTL
+DGTGHRPGDIASRIVEAIPTLPRRHTRP
+>GCF_023573625.1_01208
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMIGALEARLTAAATVAAAADEDPAARPAR
+RIVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPAPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001049.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001049.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5580ea88f4a484bf066f87686941b7529f49ab55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001049.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01251
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDADPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGLATAARRGSAAHDGIARGADGRPRRTSDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPAADVVADGPMGDPLP
+>GCF_003691675.1_00970
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDADPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGTAAHDGIARGADGRPRRTTDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPGADVVADGPMGDPLP
+>GCF_005280335.1_01637
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGLTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELEGLARNAALTRPRPGHADLTG
+MQKYGFDDARPLLERASARETAARVALGTVARAFLAQLGVRIVSHTTAFGEAALPEGHPF
+PLPEDQDRLDADPVRCLDPETSAAMVAEVDDAHKAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGSAAHDGIVRGEDGRPRRTSDRAGGIE
+AGMSTGEVLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAVLEKFGGDSVGETRRNMAAFQAAVPALPEPSADADASGHMGDPLQ
+>GCF_020097155.1_01534
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQEIQDALARRRLGYGRGARMKFEQDAVTVL
+GGIRHGLTLGSPVAIQVGNTEWPKWEQVMAADPVPEEELAGLARNARLTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLAELGVRIVSHTVAFGEAALPEPHAF
+PVPEDQDRLDADPVRCIDPETSAAMVAEVDAAHKEGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATASRRGSAAHDGIARGADGRPRRTSDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAVLEKFGGDSVAETRRNMEAFTAALPALPDAPAEQPAADHMGDPLQ
+>GCF_023573625.1_01209
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDAEPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGTAAHDGIARGADGRPRRTTDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPGADVVADGPMGDPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001050.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001050.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a75333999899b1a007fe4e45c3222e6c11ea531b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001050.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01252
+MRPVLRAAVLGRPIAHSLSPVLHAAAYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGAA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPAAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGANAVLFGVRDAARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPADAALPPLLDAAY
+DPWPSVLAAAWSREGGPVASGLSMLLHQGVEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
+>GCF_003691675.1_00971
+MRPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGTA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPSAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGADAVLFGVRDPARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPAGAALPPLLDAAY
+DPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
+>GCF_005280335.1_01636
+MGAPSDVRAEASAGAPAAPRLRAAVLGRPIAHSLSPVLHGAAYGVLGLDVDYRRRDLGED
+EVGAFVAGRLGAPRTADGGDAAARGEDWLGCSVTMPLKRAVVGCAGRVSERVRLLGTANT
+LVRDHPEHPGLVSAENTDVDGILGALASAGLAERGSGGAVGILGNGGTATAAVLAAATLG
+ADEVVFGVRDAARAAEVTALADALGLAWRTVGQPELAAAAPGLRAVVATLPPRAADPLAA
+HVPVGAALPPLLDAAYDPWPSALASAWTEAGGAVASGLSMLLHQGVEQVRLFTARPRAAA
+GMPEPDWAAVTRAAARALGPAAG
+>GCF_020097155.1_01533
+MAGATFRAAVLGRPIAHSLSPVLHAAAYRALGLDVDYGRADLGEEEVGPWLAARLGAPGS
+AARPAGPSGGDWLGVSVTMPLKPAVVPLADELSARVRELGVANTLVRDHPDHPGSLLAHN
+TDVDGIVRALAERGLDAGAGGGAVGILGNGGTATAAVAAASLLRAETVVLGVRDAGRARD
+VVALADRLGLGVRVEAQDALVRQAADLRAVVATLPPRAADPLADKVPAGVLPPLLDAAYD
+PWPSAIARAWSAAGGGVASGLSMLLHQGVEQVRLFTERPRRAAGGVEPDWAEVTAAASRA
+LGLPGR
+>GCF_023573625.1_01210
+MRPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGTA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPSAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGADAVLFGVRDPARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPAGAALPPLLDAAY
+DPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001052.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4dbea054607b606bf9bf7fe2144e213517c0f44d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001052.fa
@@ -0,0 +1,85 @@
+>GCF_002008305.4_01255
+MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD
+PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKEDNYWHTGQPGPGGPCSEIFYDRGP
+AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDVAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+ARIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFRALMAEQRDRARADAKAKKSGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVPSAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAESLSAGARSEVEDVVNIAIRDDHTVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLAAQAR
+DVTTSGGTSVRVLAHHAGDVAGDQLRSLALDLRARIESAGGNAAGTPVFVALTAEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALDAVVAAV
+RAA
+>GCF_003691675.1_00974
+MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD
+PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP
+AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDIAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFRALMAEQRDRARADAKAKKAGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAEALSAGARSEVEDVVNIAIRDDHAVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLAGQAQ
+DVTTSAGTSVRVLAHHVGDVAGDQLRSLVLDLRARIESAGGNAAGTPVLVALTAEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALEAVVAAV
+RAA
+>GCF_005280335.1_01633
+MKSQEIARRWIAFFESKGHQHVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRAV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKEKAIPMAWELLTTSVEDGGYGLD
+PERLWVTVYEEDDEAARIWEESVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP
+EYGADGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDVAGELENKNIDTGLGLERLAML
+LQGVENMYETDQVRPVLDRAAELSGREYTSTEDPTDPHYEDDVRLRMVADHVRSALMLIG
+DGVRPGNEGRGYVLRRLIRRVIRALRLMGVTEPVLPELLPVSRDAMKGSYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARTAGGGIAGADAFELHDTYGFPIELTLEIAE
+ESGVAVDEAGFRALMAEQRDRARADAKAKKSGHTDTALYQRLRAEGQTHFTGYTEHTTES
+VVRGLLLDGEEVASASAGTELEVILDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+RGLSVHRVKVLDGEVPAGAEALGAIDLQRRLDGEKAHSGTHLVHAALHQVLGPEATQSGS
+FNKEGYLRFDFRWAESLSAGARSEVEDVVNIAIRDDHTVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIAASMDRLKAAEKQIAELQAKALQAQAGELAAQAQ
+DVTTASGVSVRVLARHVGEVAGDQLRGLVLDLRSRIESAGGNAAGTPVLVALTGEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALDAVVAAA
+RAA
+>GCF_020097155.1_01530
+MKSHEIARRWTAYFEKQGHLVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRAT
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKEKAIPMAWELLTTSVEDGGYGLD
+PERLWVTVYEEDDEAARIWREDVGVRPERIQRMGKADNYWNTGQPGPGGPCSEIFYDRGP
+EYGVEGGPEADDTRYIEIWNLVFMQYRLSQVRSKYDFDVAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAELAGKSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFHALMAEQRDRARADAKAKKSGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGVITGDGFSLEVLDVQAPV
+KGLSVHRVKVLDGEVPVGAEAVGRIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAEAVSAMARSEIEDVVNIAIRDDHQVLTQEMSLDEARAMGAMSLFGE
+KYGDRVRVVEINGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSDLSEMFKAPADQLKDRITATMDRLKAAEKQVADLQAKALQAQAGTLAAQAQ
+DVTTTSGASVKVLAHHAGEVAGDQLRSLVLGLRSRIESAGGNAAGTPVLVALTGEAKGRP
+LVVVATNEAARGAGLKAGAMVKLATAALGGGGGGKDDVAQGGGQDVTAVAAALDAVLDAV
+RDA
+>GCF_023573625.1_01213
+MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD
+PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP
+AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDIAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFRALMAEQRDRARADAKAKKAGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAEALSAGARSEVEDVVNIAIRDDHAVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLVGQAQ
+DVTTSAGTSVRVLAHHVGDVAGDQLRSLVLDLRARIESAGGNAAGTPVLVALTAEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALEAVVAAV
+RAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001053.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3cf85ab052833067bae4ca2b42195826e923703d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001053.fa
@@ -0,0 +1,19 @@
+>GCF_002008305.4_01256
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA
+>GCF_003691675.1_00975
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA
+>GCF_005280335.1_01632
+MLRSLLLVTAGAASGWLAHRALGDRAAADAAPGRSDAGPQARPGRARLDPEHLARQAGQA
+VGDAAAAALNEGARRLADRVRAEAPWAAQFLPHTGPIIEGETVEPPSPSGPGGPRPQTTI
+PTTTTQKDTHA
+>GCF_020097155.1_01529
+MSRITSLLLVGAGTAAGWIAHRAVESGRRAVDQEAGRRLQETLDPTRLGRSAGQAVGDAA
+AEALAQSAQAFTERLRADAPPWVSQLIGPPRDTIEGEALDTPDTTATPSSARKDPHA
+>GCF_023573625.1_01214
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001054.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4cd4c644b97684b9fed7a5f14d5387b4b05a99b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001054.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01257
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR
+HIMVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
+>GCF_003691675.1_00976
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR
+HILVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
+>GCF_005280335.1_01630
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEMRLDALVLRAGFARTIQQARQLVVHR
+HIMVDGKRVDIPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
+>GCF_020097155.1_01528
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEMRLDALVLRAGFARTIQQARQLVVHR
+HIMVDGKRVDIPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIEKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
+>GCF_023573625.1_01215
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR
+HILVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001056.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..217f0cfde212b1e9cc53e088c948ebe2759b44af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001056.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01259
+MDDLFSAAHTGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLEDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTEEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVATAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
+>GCF_003691675.1_00978
+MDDLFSAAHNGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLQDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTDEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
+>GCF_005280335.1_01628
+MADLFSAAHESDDDGPSGTVAAPRASAPLAVRMRPRTLEEVLGQRHLMRPGSPLRKLAEP
+DPGSPAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRER
+DLYDRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLLT
+LRPLTDEDIVGLVERAVADERGLNGAVDLADDARDYVVRMAGGDARRALTVLEAAAGVAL
+DKARQAGADEDAGGDGGARAGAAAPVTVTEEDAAQAMDHHVQRYDKDGDQHYDVISAFIK
+SIRGSDVDAALHWLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLI
+GMPEGRIILGQAVTHLATAPKSNASYAAVNEALADVRAGGTGQVPPHLRDAHYPGAAALG
+HGKGYVYSHDEPHAVARQQYAPDPLVGKDYYRPKPIGAEKRLVDQVAALRRITRGE
+>GCF_020097155.1_01526
+MDDLFSAAHADPDDDAPVTASGRARASAPLAVRMRPRSLDEVLGQAHLKQPGSPLRKLAE
+PAASAQAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQARR
+EREMYDRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLL
+LTLRPLDDTDLAALVDRAVADERGLNGTVEPTPNARDYVVRMAGGDARRALTVLEAAAGV
+ALDRAEARGETTGPGSAPVEVTEEDAAQAMDAQVQRYDKDGDQHYDVISAFIKSIRGSDV
+DAAMHWLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRI
+VLGQAVTHLATAPKSNASYTAVNEAIADVRAGGTGVVPAHLRDSHYPGAKALGHGQGYVY
+SHDEPHAVARQQYAPDPLVGRDYYRPKPIGHERQLGPQVDALRRIIRGD
+>GCF_023573625.1_01217
+MDDLFSAAHNGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLQDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTDEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001057.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001057.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a81c94b98428a743350929433de7a2a476ca2177
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001057.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01260
+MSPAAPRADHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPESAAALAALDHGDGRPAGPDRTALEGRLLWTRCATGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPAGDRPRRTARGASGDVDIRGTPRAGRDVTVRSHPCDGVTPSSASLP
+>GCF_003691675.1_00979
+MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPSED
+>GCF_005280335.1_00445
+MSEHPASPTHVLLLRAVNVGGRNRVPKADLAELAAEAGLADVAVHLNSGNVLGTPDTGDH
+VDDVAARLRALLAERLGVDTSVHAAARTELSALVDGLLASDLLAPGETLDSVDPKTVHLV
+LLDTVPHPEAGEALAAVDAGDDRAVVVGRGVWVRYAGPSHSSHLGLPRIERAASGDAPPA
+QRRVGTARNLATVRVLAGR
+>GCF_020097155.1_01525
+MSRAAPRTDHTHVLLLRGINVGRSNRVSNARLAAWAEAARARDVTTHLASGNVLFRLPDA
+DDDAGPAFLRAFRDAALADDGPDVPLILTTPAELRGALAMHDRLPWSGGEAKLTQLTVLA
+ESPRDGAAEALAGLDHGSGRAAGPDRSALEGRFLWIRSPGRISDSPLTPARLEKALGVTG
+TARNLATVRVLAGMA
+>GCF_023573625.1_01218
+MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPSED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001058.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..565172373bee8a8e1af863df6e97cc9813896f70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001058.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01261
+MPRLARLATAVTAAALSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ
+>GCF_003691675.1_00980
+MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ
+>GCF_005280335.1_01627
+MRTLSRLAAATSMVALSAAVVAPLTVAAPAANPSGRSIELTAAGTHATGVFDASAAEIPA
+FDKTTGRLFVVNAQKGAIDVLTVGEDAEPAAESVLSVAGLPAADGSVTGAGAVVNSVAVA
+GAVMAATVEAEDKTGHGWLVFFDTRTLGFLGGVRVGALPDSVALAPNGAYAVVANEGEPA
+DDFSSDPEGTISVVSVPKNARQFARLGQDAVRTVDFRAYDEGAALPEGVRVFGPDVAVPS
+GHEEAGRIARNLEPEYASIDPTGRTAYVSVQEANAVVAVDLASASLADFWALHLTDWSTE
+GVLDVSDKDGAISPAYQPVLGVPMPDGLATYKHRGQTLVVTANQGDSREWGDFVDAERVK
+DLELCGDVFPHAKALQKNEALGRLNVLTDLGYDAERGCHTELHALGGRGFSIYTADGQRL
+FDSSGMLEEQIARLIAAGELPAHAFNANNDETPSFDSRSDDKGVEPESVVVGEVQGRQYA
+FVGLERIGGVMVFDITDPTDARYVDYINERAWDAVGEDGDAGLGDMGAEGLAFVPASDSP
+SGTALLIVATEVSGSTTVYEVDPVKGGKRT
+>GCF_020097155.1_01524
+MSRIVRLTRLGAAAGALALSAAVVAPSAVSAPVTATAAAANPSGKTVELSLAGTHETGVF
+GESAAEIPAFDAATGRLFVVNAEKGAVDVLRVGADGAPAAETVLSAEGLRTADGSVTDGG
+ATVNSVAVSGGVLAVAVEAADKTGLGWVAFFDTTTLSYLGGVRVGALPDSIAFSPDGAYA
+VVANEGEPADDFSADPEGTISVISVPKNVRQFARLTQAAVRTVDFRAYDAGTALPEGVRV
+FGPDVQVPEGQEPAGRIARNLEPEYVTIDDTGRTAYVSVQEANAVVAVDLKSATLKDFWA
+LQLTDWSKEGVLDASNEDKAITLRNQPVLGVPMPDGVDTYRYRGQDLVVTANEGDSREWG
+DFVDAARVKDLELCTAEYPDAKALQKKPALGRLNVVTDLGYDADRDCFSQLHAFGGRSFS
+IYTADGTRLFDSAGMIEEQIAQLIADGELPESAFNANNDETPSFDSRSDDKGPEPEAVVV
+GRVQGRTYAFVGLERIGGVMVFDITDPTKATYVDYVNERNWDAEGDDAAAGLGDMGAEGL
+TFVPANESPSGTALLVVANEVSGSTTVYEVNPVRR
+>GCF_023573625.1_01219
+MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001059.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e35f6042d652bd524e901d8d7164d98b0386cafb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001059.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01262
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
+>GCF_003691675.1_00981
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
+>GCF_005280335.1_01626
+MRAVLQRARSASVTVAGEVVGSFEGAGLVILLGVSTQDTGAEADALAAKVATLRMLDGEA
+SLVSAGAPALVVSQFTLYGDVRKGRRPSWTGAARPEHAEPLYERFAAGLEAEGVRVERGV
+FGAQMDVTLVNDGPFTLVVDTADLTGPRRG
+>GCF_020097155.1_01522
+MRAVLQRARSASVTVDGEVVGAFDGEGLVILLGVSTEDTEAEAVQLAAKVAGLRILDGER
+SLVEASAPALVISQFTLYGDVRKGRRPSWSAAARGDQAEPLYECFAGELGTAGVRVERGV
+FRADMDVALTNAGPFTLVVDTADLAGPRRG
+>GCF_023573625.1_01220
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001060.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001060.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7573627ce46a53d86a4fe7fb94bfe4b1517fa6ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001060.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01263
+MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL
+RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT
+PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI
+SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA
+DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGAALAY
+AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA
+EPEA
+>GCF_003691675.1_00982
+MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVREEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL
+RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKHT
+PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI
+SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA
+DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGAALAY
+AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA
+EPEA
+>GCF_005280335.1_01624
+MNPTISSGRSPDGEDAFVLRTHQLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDAS
+GFAQVVVRDEADFDPLRNEWVLQVSGVVERRPEGNENPNLPSGEIELIAETVTVLNTAAA
+LPFQVDEHVEVGEEARLRHRYLDLRRPEPSRIMRLRSEVNRTAREMLHGEGFTEVETPTL
+TRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADR
+QPEFTQLDIEASFVEQDDVIALGEKIVKAVWALVGVDVPTPIRRMTYAEAMEKYGSDKPD
+LRFGLELTDLTAYFKDTPFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAY
+VLIQEDGSLTGPVSKNISDEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGR
+RCELFTDAGNGVEAKDADWAFVWVVDAPMFEPAADAVASGDVAVGSGAWTAVHHAFTSPK
+PEFADTFDTDPGSALAYAYDIVCNGNEIGGGSIRIHRQDMQERVFSVMGLSQEDAQEKFG
+FLLEGFKYGAPPHGGIAFGWDRVVALLAGTESIREVIAFPKTGGGFDPLTAAPAPITAQQ
+RKEAGVDAKPEPKKAEGEKAEAAGQPQA
+>GCF_020097155.1_01521
+MLRTHHLGELNASLIGQTVTVTGWVAKRRDHGGVAFVDLRDASGRAQVVVRDEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPTGEVELIADDVVVLNTAAALPFQIDEHVEVGEEARL
+RHRYLDLRRPQPARIMRLRSEANRVARELLNEQGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGLEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEQIVKALWGLVGVEVQTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT
+PFRVFQNEYVGAVVMPGGASQPRRTLDAWQEWAKQRGAKGLAHVLIQEDGTLTGPVSKNI
+TDEEKAGLAAAVGANPGDCVFFAAGKAKESRALLGAARVEIGRRCELFTDAGDGVEAKDA
+DWAFVWVVDAPLFEPAADAVASGDVAVGAGQWTAVHHAFTSPKPEFMDTFDTDPGSALAY
+AYDIVCNGNEIGGGSIRIHRQDVQKRVFSVMGLSEEDANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTESIREVIAFPKTGGGYDPLTAAPAPITPQQRKEAGVDAKPEAKKAEG
+AASEGAEAQAKANDEKTAADEAQLR
+>GCF_023573625.1_01221
+MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL
+RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT
+PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI
+SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA
+DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGSALAY
+AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA
+EPGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001061.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..195c27fc523c92a017cc0670844adba60827b690
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001061.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01264
+MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA
+LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAVAATLGLYLVPDDA
+AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL
+GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT
+ALISGLGTSGLARSPAPVRELLETALGSGWGWVAVAGAALAAAGAMLTLLTGISRTALAM
+AREADLPRPLARVHAGTGTPWTAQLTVAAAVVLLLLTTDILTVVGFSSFGVLVYYAVANL
+SALTLRGDDHGHRPARPRPLRVPRAVNVLGLALCLLLAFSLPPMSVAAMAGVFLIGVGGR
+AFVRAGRRGG
+>GCF_003691675.1_00983
+MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA
+LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAMAATLGLYLFPDDD
+AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL
+GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT
+ALISGLGTSGLARSPAPVRDLLETALGSGWGWVAVAGAALAAAGAMLNLLTGISRTALAM
+ARESDLPRPLARVHAGTGTPWTAQLTLAAAVILLLLTTDILTVVGFSSFGVLVYYAVANL
+SALTLRGDDDGRRPARPRPLRPLRVPRAVNVLGLALCLLLALSLPPMSVAAMAGVFLIGV
+GGRAFVRAGRRGR
+>GCF_005280335.1_01623
+MLQRRLTLTHAVVIGLGSMIGAGVFTAIGLAAALTGGHPGLLYAALALALLTALCNALST
+AQLATVHPESGGAYVYGRRQLHPLAGFVAGWGFVTGKTASVAAMAATIGLYLFPDDAAAA
+RLTGVAAVVVLTAVAMAGVTRTAQATMAILVPVAAVLALAIGAGLALGAPSEADAFAGVA
+DSPVTGVLMGAGILFFAFAGYARVATMGEEVIDPRRSIPRAILIALGLTAGLYVLLTAAL
+FAGLGPTGLALSPAPVRELLETTLGATWGWAALAGAALAAAGAALNLLTGISRTALAMAR
+ESDLPRPLARVNARTGTPWVGQLTIAVAVILLLLTTDILTVVGFSSFGVLVYYAVANLAA
+ATLRGGEDGRDPALPRPLRVPRAVNVLGLVLCAVLAATLPPMAVVAMLAVFLVGVGGRAF
+VLAGRGRPGRRGAVAP
+>GCF_020097155.1_01520
+MTATSPAPRGLPLRGALAIGVGSMVGAGAFTSLGLAALLTGGHVGALAAALGLAVAVATC
+NALSTAQLAAVHPASGGTYVYGRRQIGPTAGFVAGWGFVTGKTASVAAMATTAGLYLFPD
+SPLAARLAGAAAVVILTAVALRGITRTAQATVAILVPVLAVLGLTIVAGLAGGRAAADTP
+VSAADPAGVLAAAGVLFFAFAGYARVATMGEEVEDPRRTIPRAVLGALAFTVVLYALLAA
+ALVAALGGTGLAASEAPVRATLEASLGAGWGWAAVVGAVLACAGAMLNLLAGISRTGMAM
+AREGDLPRPLARVDERTAVPWAGQVTVAVAVILLVLTTDVLTVVGFSSFGVLVYYAVANL
+SALTLRPEQRTLRVPRAVNVLGLGLCLVIAFTLPPASVAAMVGVFLIGLGGRWFVRSRRP
+DRIG
+>GCF_023573625.1_01222
+MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA
+LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAMAATLGLYLFPDDA
+AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL
+GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT
+ALISGLGTSGLARSPAPVRDLLETALGSGWGWVAVAGAALAAAGAMLNLLTGISRTALAM
+ARESDLPRPLARVHAGTGTPWTAQLTVAAAVILLLLTTDILTVVGFSSFGVLVYYAVANL
+SALTLRGDDDGRRPARPRPLRVPRAVNVLGLALCLLLALSLPPMSVAAMAGVFLIGVGGR
+AFVRAGRRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001062.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31401c127da4448456d8d24d8e2a3c90b47ba498
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001062.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01265
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGRREPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS
+DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG
+ARVHEVKDIRSGEQHAVDPADWTPPTEDLLPQITRTQD
+>GCF_003691675.1_00984
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGLRDPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS
+DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG
+ARVHEVKDIRSGEQHAADPADWTPPAEDLLPQVARAQD
+>GCF_005280335.1_01622
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGRREAKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGELSPRHDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLTDAAGVLRSIDKLEKIGADEVARLLQEEVGASPEQARQALALAAIRTE
+DVSFVEQVRALGVSDPLLEEGLAELADVVETLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQEMAQASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFLGRDDAG
+ARVHEVKDIRSGDQHPADPADWTPPSEDLLPQVTRTESTEG
+>GCF_020097155.1_01517
+MSRKQSLSGFHEWLPAERIVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDQEVAEGVREAKDPSDPKRLALHFDLTVPFARYVTENAGHLAFPFRRHQIQ
+KVWRGERPQEGRAREFTQADIDVVGDGELSPRYDADVALVMAEALGALPIGDFRIRVNNR
+KLAEGFYRGIGLEDAAGVLRSIDKLEKVGAEEVARLLQEEVGATAEQAAQALKLAEIRTP
+DTAFVEQVRALGVEDPLLEEGLAELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALATKGNRAFPGVGLSIGVTRLVMRMLSQEMAVASRAVPTVV
+YVALTHDDDWSRAQDVAAGLRGRGIAAEVAVSAEKFGKQIKYADRRGIPFVWFLGAEGAS
+DEVKDIRSGEQVPADAATWAPPAEDLVPQVTESPRAED
+>GCF_023573625.1_01223
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGLRDPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS
+DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG
+ARVHEVKDIRSGEQHAADPADWTPPAEDLLPQVARAQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001064.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001064.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f07116f995864ca2fb42f522d98ba29c3845fe0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001064.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01267
+MTTVTIEETAPAGALMLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGQLPWTLTQSDVAA
+DATGVAPAEQDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLTALDVPD
+>GCF_003691675.1_00986
+MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA
+DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLAALDVPD
+>GCF_005280335.1_01620
+MEGLILAGEPFTPAELQALGSRGVVVPLVPGVWARPEAARRPGVRAEALWMLGGPVLAGG
+WTAIGSSAAWVLTGGAVPERLHAAVPHFHRLPAGGSPLPWTLTQSDVAAGPDGRAPAEED
+VLRIGPLRVTTPERTVEDLLLSPDPDAARTAAAVIAAHGAAGLRERLARHSRRSGVVAAR
+RRLDVLLGALEAAG
+>GCF_020097155.1_01515
+MHQGHGSRGGAAWELAGMTFTEPELRLLAARGTLEAVLPGVYRPVDVPSEPAGRAAALGL
+LGGPVLASGWTAVGPSAAWVHVGGPAPHRLHAAVPHFHRLPAGGAAPAWRLVQSDVAAGP
+TGAAPAEEDVQVLEGVRVTVPARTVEDLLLTGDPDDARRAARVIAAHGAEGLRDRLDRPS
+RRPGSVGARRRLRMLLDALGADG
+>GCF_023573625.1_01225
+MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA
+DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLAALDVPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001066.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c14c4b226fd6c95f080f461eee7ae0f443ae2e8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001066.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01269
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL
+>GCF_003691675.1_00988
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL
+>GCF_005280335.1_01618
+MNRFADWGNALYSGRVSYPFVQRWRLWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTAATDIAAGERAVTDVLAGGHATVTNIAPGTVRVQTEQLDDAQTRQVAANLQDAYG
+VGQDQVTSTFVGPTWGAAVSQQALLGLVIFVVLVTLFMAFYFRTWKMSLAAVIGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGQEEDPERTFEQNVNL
+AVNQTLVRSITTSIVGILPVGSILFIGAGLLGAGTLRDIALAIFVGIIVGTLSTLFIQAP
+LYALLRRGDEDVRDHDARAAARAARENRGDTVTDPDVAPWEDGARL
+>GCF_020097155.1_01513
+MNRFADWGNALYSGRISYPFVRKWKTWFLIAAALLAVAFGLTALRGGFNLGIDFRGGSEF
+TVSDAASSELDPGRAAVTDVVAGAEPTVTQVAPGTMRVQTEQLDDAQTRQVAQNLQQAYG
+VTGDHVTSTFVGPTWGQAVSQQAVIGLVIFVVLVTLFMALYFRTWKMSLAAVVGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTRGVEEDPDRTFDGSVNL
+AVNQTLVRSITTSIVGLLPVGSILFIGAGLLGAGTLRDISLAIFVGIIVGTLSTLFIQAP
+LYALLRRGDADVVAHDARVGADHDEREQEEDLADARGAVL
+>GCF_023573625.1_01227
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001067.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0e2ca664c248a663729a29ac88c2cd646a7cd64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001067.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01270
+MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS
+TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD
+PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST
+NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ
+ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV
+YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP
+RTGLPAEASDEPADADDAAAADAPRPLAATGAPRAGSSARGGRRSRTAPPMTIAERRRAE
+RRRQEEDQ
+>GCF_003691675.1_00989
+MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS
+TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD
+PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST
+NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ
+ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV
+YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP
+RTGLPAEDSDEPADAAAADAPRPLVATGAPRAGSSARGGGRRSRTAPPMTIAERRRAERR
+RQEEDQ
+>GCF_005280335.1_01617
+MAKRTPTGSARRTLAWLAALTVALTAILGWGVASGAASWAPKLALDLEGGTQMVLAPETA
+TGESVTSEQLDQAVEIIRQRVDGSGVAEAEVATQGAENVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGSGEATPEDQRLPEDQLPQPEGEPADAYDPNWVTPALLTQYQALDCAAPRD
+PAAPPPPSDQAIVACERPADLGEGVQTPARKYILGPVVIPGTQIEGATNGLAQAQSGVST
+NQWVVNIDFDEEGAKTFSEVTQKLTPYPDGDPRKQFAILLDGDVISAPQSNAVITAGSAQ
+ISGPTLNEETTAQLAEQLNYGSLPISFSIESEQQISATLGQDQLFWGLIAGLIGLALVAV
+YQFFQYRALGLLTFASIVVAGILTYLAIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHSVPMAVHEGWKRAKRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPIMVLLAQTRFVGGGHRMSGLDPSLLDRQALYQGAGRLREPGGAR
+RTGSTAAPAADVAADDGARVPVPVGAAPADEASGEEGTATRGLRRPRPAQPMTIAERRRA
+ERRRQEEDQ
+>GCF_020097155.1_01512
+MAKTSPTRAAGRTLAWLAALIVALTAILGLGVASGQASWAPKLALDLEGGTQMVLAPTTA
+SGEQATPEQLQQAVEIIRQRVDGSGVAEAVVATQGDQNVVVSMPGVPDEETRRLIQASAD
+MQFRPVLQAVPGGQPTPQDQLVPKDQFPTPSAEPTDAYDPNWITPELADEFQRTDCTLPR
+DPNAAPPATDRAVVVCEPQQETPAGTMPATKYIVGPVVIPGTMIEKASNATAQSQTGVTT
+NEWVVNIDFDGEGTKRFTEVTQKLTPFAEGDPRKQFAIMLDGQVIAAPQSNVVITGGQAQ
+ISGPGFTEESTAQLAEQLNYGSLPISFTIESEQQISATLGRDQLFWGLIAGLIGLALVAV
+YQFFQYRALGLLTFASIVVAGALTYLAIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRSGHTLDAALHEGWKRAKRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLLVVFMFTHPLMVLLSRTDFVGGGHPMSGLDPRVLGVEPALYQGAGRFREPAAA
+RAARGGSHAADDDDAGSSAARRGRRSEQPMTIAERRRAERAGAAQTPAAQTPAGSAPAAD
+TEEDAL
+>GCF_023573625.1_01228
+MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS
+TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD
+PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST
+NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ
+ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV
+YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP
+RTGLPAEDSDEPADAAAADAPRPLVATGAPRAGSSARGGGRRSRTAPPMTIAERRRAERR
+RQEEDQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001069.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..871b9d43e7350f7b618d70e8d681a145923773c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001069.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01273
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLSTLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR
+>GCF_003691675.1_00992
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR
+>GCF_005280335.1_01614
+MIASLSGTVEHVALDRAVIAVGGFGVQFSATPQTLATLHEGRTGSVQTHLVVKEDALTLF
+GFADRHEREVFEVLITANGVGPRLALAVLSVHHPEAVRRAVTEEDENALTRVPGVGPKLA
+RKIIVELSGRLTPTGEQVPAPEEPAAPETPEAAWHADVVQAMTGLGWSEKEALKAVEATV
+AARPELDEARDVAALLRATLRDVGTAGTVRGGR
+>GCF_020097155.1_01509
+MIASLSGTVEHVGLDHAVIAVGGVGLSFSATPQTLSHLHEGRDGAVQTHLVVKEDSLTLF
+GFADRAEREVFEVLLGANGVGPRLALAILAVHRPEAVRRAVTDEDEKALTLVPGIGPKMA
+RKIIVDLAGRLAPTGEVEPEAAVVEPEAAADAWHADVVQAMTGLGWSEKEAAKAVAATVA
+THPDVDASGDVAALLRATLRDVGAAAAVRGGRRA
+>GCF_023573625.1_01231
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001072.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001072.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c442472d3942e7f444d0a9a54af494bb759b922
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001072.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_01276
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARVASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRADAEVAPWDWPALSAGYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDRADALGERPVVFTTMNVPAPAAGRPALLTLDETTTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVETGEPLPA
+GTLERLEAADLWGEGHRTVEYLGATLVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
+>GCF_003691675.1_00995
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEATTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPA
+GTLERLEAADLWGEGHRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
+>GCF_005280335.1_01611
+MTPTPASSVLPADHPLATPSELPYGLPDFSAVTDAQLAEAVRAGMAAQRAEVEQILGAAT
+APTFENTVRAFELSGQLLRRSAAMFFTLVSADGTDARQGLAEELSPELAAHEDALLLDPR
+LAERVAAIDGAGLTGEDARLLEVLRRRLDLAGAGLGEAERAELGRINTELAGLTAAYTRR
+LVADTAERAVLVTDRERLAGLSEDDLASAAAAAREAGHGGADGEGGDEAGPWLLTLSLFT
+SQPWLASLEDEALRREVFEASVGRGAAGDHETLSTAMEVVRLRLRKARLLGSASWAEHAL
+KDRAAPSTTAVEELLATMAPRAMANARTDAATAAAHAGRVGGAVAPWDWPALSAAYARER
+FAVDAGALRPHFELDRVLHAGVFAAATALYGITFEERPELAGRLYRPGIRVFEVRDEDGA
+GVGLFVADLFARSTKSGGAWMHTVRDAADALDERPVVFNTMNVPAPAPGRPALLTLDEAT
+TLFHEFGHALHGLLAKGEYVSLSGTHVPRDVVEFPSQVNEVWLREPALLAEYARHVETGE
+PLPAGTLERLEAADLWGEGYRTVEYLGATLVDWAWHSLTEDTVEAATADPAAFERRVLTE
+AGIDPELVPPRYGTGYFKHIFGNDYAAGYYSYIWAEVLDADAVEWFREHGGMTRENGRRF
+AEELLSRGETRDLLESYRAFRGRDAELEPLLRRRGLVDAAA
+>GCF_020097155.1_01506
+MTQITHRLPAGHPLLSPSPLPHGLPDFAAVSDADLATGMRQGMAEQRAEVEEILSSPEAP
+TFENTVRALELSGALLRRVAPMFSTLVGSDGTDARQALAEELSPELAAHEDAILLDPRLS
+ARVAAVDDAGLAGEDARLLERTRTRLEIAGAGLDEAGRAELARLNGELATLSAAYTRRLV
+ADTAARAVLVTDRERLAGLRADDLAAAAERAAAEAGHRRADAAEGAGPWLLTLSLFTSQP
+WLADLEDAGLRREVFEASVGRGSSGEHETLTTAMRIVRLRLEKARLLGAASWAEHALRDR
+AAPSVAAVEGLLGSLTGPAMANARRDAEAVAEGDAPVVPWDWPFLSAAHAREAFDVDAGA
+LRPWFELDRVLTRGVFAAATALYGLRFAEREDLAGHLYRPAIRVWEVTDEDGRGVGLFVG
+DFFARPTKSGGAWMHNVVDASAALGTRPVVFCTMNVPAPAEGRPALLTLDEATTLFHEFG
+HVLHGLLAEGEYPSLTGTAVPRDTVEFPSQVNEVWLREPSLLADYARHVETGAELPTGTL
+ERLEAADLWGEGYRTVEYLGATLLDWAWHTLTEDTVDAATADPAGFERRVLTEAGIDVDL
+VPPRYGTGYFKHVFGNDYAAGYYSYIWAEVLDADAVEWFREHGGLTRENGRRFAEELLSR
+GDTRDVLESYRAFRGRDAELEPLLRRRGLLPEGA
+>GCF_023573625.1_01234
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGAGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEATTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPA
+GTLERLEAADLWGEGHRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001073.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001073.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f089d60d63f9b25c9fbad40c129403aa1b8f2063
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001073.fa
@@ -0,0 +1,44 @@
+>GCF_002008305.4_01277
+MAARPRRPRPHPADLPPALAAAVTVAARRAGSRESRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAAYAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIAPYPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSALAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTAVRGWLRAVLSAPRPGGRGR
+>GCF_003691675.1_00996
+MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRGR
+>GCF_005280335.1_01610
+MRTGVKAASPLARWTPPVLSVLASSAFVLAGASSALAGVFARTVVTPVRRHTETTAVLAV
+VDTPTGPEVILKADEYTTVPGVYSLTFDGGAGCARIGRISSFDPRDGTVQRVVEEVYFGD
+LAAATRGRLTGFVYPTPADAGLDAEEVLVPVPGGHAPAWLVGPDPDDDGAARPAAGIWAI
+MVHGRGARRNEGIRTVPTAQRLGMTSLLISYRNDGDAPDAADSRYGLGTTEWEDVEAAIR
+YALDNGASDVVLFGWSMGGAVVLQAVDRSDLAPQVRGVVLTGPVVDWVDVLQHQARLNRI
+PEAVGVLGQWLLSNRAGRFITGLAAPVDLKSLDWVTRAEHVRVPTLIIHSEDDEYVPVGP
+SQDLAERNPGLVRFVRFHQARHTREQNVDPKRWDTTVRGWLRAVLNADRPGAAER
+>GCF_020097155.1_01505
+MACPRRHSPRLRARPDLRDALLGSLRGSAAVARPAARLAPAAASVAASAAFVLAGASAGL
+AGVFARTVVTPVRSRPEHTAVLAVLDTGDGMDVILPADEHTTVPGTYSLTFHGGEGCARI
+GAIRSYDPRDGTVQRVVEEVYSGDLRSAVRGRFTAFIWPGPAEAGLEAADVEVPVPGGAA
+PAWRIDPPPAEDGEERAGEGMWAVMVHGRGAVRNEGLRAVPTAARLGMTSLLVSYRNDGD
+APDAEDARYGLGTTEWEDVEAAVRYALDHGARDVVLFGWSMGGAVVLQTADRSDLTSRVR
+GIVLTGPVVDWMDVLRHQARLNRIPEGIGLLGQWLLSNRAGRLVTGLAAPVDLKALDWVT
+RADHVRVPTLILHSEDDEYVPVGPSQDLAERNPALVRFVRFHQARHTREQNVDPVKWDRS
+VRGFLRAVLTAPRPGAVSPPGAPQAPSGSSPRRRSSGSSSASRPRNAR
+>GCF_023573625.1_01235
+MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001074.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001074.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b66c0b9b31b11e1899458b43653310421433ad82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001074.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01278
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR
+>GCF_003691675.1_00997
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR
+>GCF_005280335.1_01609
+MTDTPQTPQDPDRTDAAQASPVVGHGAGAPRGARLTDEEWARRLTPEEFQVLRRAGTERA
+YTGEYWDSHVQGVYACRACGAELFRSDEKFDSHCGWPSFFAPLAEDRVEYLKDTTLGVER
+VEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADASGAGSDDDAAGRA
+>GCF_020097155.1_01504
+MSQNHATVPSGADDAARPAALTDEEWARRLTPEEFHVLRRAGTERPYTGEYWDSRVQGVY
+ACRACGVELFRSEEKFDSHCGWPSFFAPLAEDRVVYVKDATLGMERIEVRCAACGSHMGH
+VFAGEGYDTPTDLRYCINSISLRLTPADVAAIGTEADPAGDRA
+>GCF_023573625.1_01236
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001075.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001075.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e7cc713629128280cd9801a3ac80ad2d439fb0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001075.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01279
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERHHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP
+>GCF_003691675.1_00998
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP
+>GCF_005280335.1_01607
+MTVIGPRRLAPVTGPRGAVAPAPAPLPAAFRRALADLRTARPRPEVRLREIAAPAGQAPH
+AVALAAEVCGSPGADDVLATGRFVLLHDPSPAARWPGGFRAVTWIRASLEPDVALDQLAG
+AVAWTWLVEALERRHAEHTQAGGTATRSIAEGFGTLGTAPDATDIELRASWTPAPRDLGA
+HLEAWSDMIGAFAGLPPR
+>GCF_020097155.1_01502
+MTESGPRAPAPAAGGASGAFADALADLRAAHPRPEVRLRPIPDPPGLAPFAVTLAADVLD
+PHGAEADPLATGRFVLLHDPAGSPVWRGDFRVVTYIRASLEPDVATDHLAGAVAWDWLAE
+ALERRHAAHTEAGGTATRQLAEHFGTLALEPGWTDIELRASWTPGPRDLGAHLEAWSDMI
+CAFAGLPPLADDDVPAAVPLRP
+>GCF_023573625.1_01237
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001076.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001076.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ca4e8264b9f9a4d45b7e5a170bf52c3ef879eae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001076.fa
@@ -0,0 +1,42 @@
+>GCF_002008305.4_01280
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVAGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERGDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA
+>GCF_003691675.1_00999
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAIDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERDDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA
+>GCF_005280335.1_01606
+MTDVPEPAEPDATPRLIAEPADGVPRVTDTPAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLEPLQEALSGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVAGLPRVGLAAVLESMLGVTLAKEHSAADWSVRPLPEAMLAYAALDVELLV
+PLRAAMLELLEAEGKREWAEQEFEHVRTAPAPGPRADPWRRTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSLIAAAESQPRTVPALRQTSGFHGRAASREAPPLDHRD
+PRRRRGRRARRRPARPGARRGRPAPAPGVEGPRPARRPPPEDRQGARGPARRAAGPAHGE
+PAHPGHPAPALLGAAAAADARGRGRVPPRARGPALAGGPGGRGGHRGPAGPGPRRGLSRG
+GRRADAAVGRGPTHR
+>GCF_020097155.1_01501
+MTSPTSPAVATSPDPSDRPGGEQAAPTLVAEPAGGVPVVTDTPAGLAACAAALAAGTGPV
+AVDAERASGIRYGQRAFLVQLKRAGAGIWLVDPEAFEDLAPLDEALRGVEWVLHAASQDL
+PCLADCGMRPDLLFDTELAARLAGLPRVGLAAVLESQLGLTLAKEHSMADWSTRPLPVDW
+LNYAALDVELLVELRDALAVLLEEQGKLAWAEQEFEHVRTTPPAAPRQDPWRRTSGMAAL
+KRPVQLAVLRRLWQAREDLAQHRDLAPGRLLPDSALVAAASTLPRTVPELRATRGFHGRS
+AAREAPRWITAIRAGIEDAAAGQAPPRHGPGSDAPPPPRAWRDRDPLADRRLTTAKPRIA
+RAAEALGMPPENLLTPDTLRRVCWTPPETITPETVAAALAERGARPWQVEQTSAIITVAL
+LDPDPARDR
+>GCF_023573625.1_01238
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERGDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001077.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e5668d6f2e529954fb924c2ea31dcc6cd1bb4a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001077.fa
@@ -0,0 +1,69 @@
+>GCF_002008305.4_01281
+MTSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATL
+LGLGRVLDEQAARAAAGEIQALAVTGVEGTFAAGADLSLIASITDDVGRDLALLGHAVYD
+RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP
+HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVTGDESV
+AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEALFTGARTRTRAESAQA
+EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA
+LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGQALAGLITADTDKA
+VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLERPERLVG
+FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG
+EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA
+NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE
+DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA
+AQA
+>GCF_003691675.1_01000
+MTSVSLASFDHLPALAPDEVVTTVTVTDHALPDGAGTLALLTLDNGQGPRRPATLGPATL
+LGLGRVLDEQAARAAAGAIQALAVTGVEGTFAAGADLSLIAGLTDDVGRDLALLGHAVYD
+RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP
+HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAGDESV
+AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQA
+EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA
+LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGEALAGLITADTDKA
+VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPERLVG
+FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG
+EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA
+NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE
+DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA
+AQA
+>GCF_005280335.1_01605
+MTFTPAPLAPFESLLPLVPDEVLTHVAATDHVLPGGAGTLVLLTLDNGQGPRRPATLGPA
+SLLELGRAVDAQAERARAGEVQALALTGVEGTFAAGADLSLIAGIEDRTVGRDLARLGHA
+VHDRIDAFPAPTLALVNGTALGGGLELALAADHRVVAADARGFGLPEVRLGLIPGWSGVW
+RVPHLIGPEAAVEVVLKNPLDNNRMLDARTAHGLGLMDEVAEGDLLEAGLAFAARIVAGD
+DAALAAVRDHRDRDVSDAAWDRALEAMEALQAGRPGRDLPARRALQELFAGARTRTREES
+AEAEAEALHGLIGSDEFRRTVYAFLDLLQRRAKRPVGDPGKELAREVTKVGVVGAGLMAG
+QLALVFAQHLRVPVVMTDMDQERVDRGLAGVRGQVEKMVSRGRITAEQGEALAGLITAST
+DKSVYADADVVIEAVFEELEVKRTVFRELEPIVREDAVLMTNTSSLSVAAMAEVLEHPER
+LVGFHFFNPVAQMPLIEVVRVAETSDEAVATAFELSRRLRKTGVLVHDAAAFVVNRVLLR
+MMGEVQASFDEGTDAHTADHALDPLALPMTPFTLLAMVGIPVAQHVSESLQAAFGAERFP
+VSANLQRLIDAGKTAIWAKDVRRDKVEEEAAGATGETIPAGTAALIERGSSPQTAEELRR
+RVEDALAEEIGLLLAEGVVAAPEDVDLCMILGAGWPLHLGGITPYLDDCGAAERVNGTRF
+HG
+>GCF_020097155.1_01500
+MSHTPAPLDQFEHLSTIAPDEILTRATATDHALPDGAGTLALITLDNGQGPRRPATLGSA
+SLLELARAVDEQAARASAGEIQALGITGVEGVFAAGADLALVASLPADAETGRALGRLGH
+AVYDRIDAFPVPTVALVNGTALGGGLELALACDRRVIAPEVKALGLPEVRLGLIPGWSGV
+WRAPHLVGPEAAVALLLTNPLDNGRMIGAADAVRLGLMDSLAEGDLLAAGLTAAADAVAG
+RTVQRTADVSDAAWDRALQAFGAAQSARPGRDLPARRHLEELFAGARTRTRAESAEAEAD
+ALADLIGSAEFRRTVYAFLGLVQGRAKRPAGDPGVEQAHTVHRVGVVGAGLMAGQLALLF
+ATALRVPVVMTDLDQERVDRGLAYVRSQLERSVTKGRMKAEDAEAVAGLITGATDVSAHA
+EAEFVIEAVFEELEVKRTVFRQLEQVVSPTAILATNTSSLSVAGMAEVLEHPERLVGFHF
+FNPVAQMPLVEIVRVAETTDAAVATAFELARRLRKTAVLVNDAAAFVVNRVLLRMMGEIQ
+NSFDQGTDAHTADHALDPLAFPMTPFTLAAMVGLPVAQHVSESLQAAFGAERFPVSENLQ
+RLIEAKKTAIWAKDVKSPEEAGGATGETIPADTAALIEQGDTPQTADELRVRVEDALAEE
+IGLLLDEGVVAAPDDVDLCMILGAGWPLHLGGITPYLDDCGASERVRGARFHQA
+>GCF_023573625.1_01239
+MTSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATL
+LGLGRVLDEQAARAAAGEIQALAVTGVEGTFAAGADLSLIAGLTDDVGRDLALLGHAVYD
+RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP
+HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAGDESV
+AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQA
+EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA
+LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGEALAGLITADTDKA
+VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPERLVG
+FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG
+EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA
+NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE
+DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA
+AQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001078.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..56ee542b1cbd2b0c5cc9cb08ab0ca478fd8bdb13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001078.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01282
+MTDPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRTGFAPTTAQRAAR
+DGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA
+RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA
+VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA
+>GCF_003691675.1_01001
+MTHPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRMGFAPTPAQRAAR
+GGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA
+RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA
+VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA
+>GCF_005280335.1_01603
+MTDPAPVRPSLDLTPFERWEAVTLDGEHVGFLHRVLDGTLLTTRMGFAPTPAQRRARPEL
+PERYLAQSQVSFTADGTSWDWTSHEDSAGAQRVRIDRERAGLDADVLPSYAEYLLLAVAA
+ADGPVVVAARLEESSPLQGGLRMPRAELRPADAGDGDVSVTVVADGAALGAHLVRDGAVV
+ASDWGGGTASTPVAGRAEATEGLDEHVVTFSGMPLV
+>GCF_020097155.1_01499
+MSARYDLTPFETWEAVALDGVHAGFLHRRLADGILTTRMAFQPTGAQRRERADLPQRYLA
+QARVRFSADGSTWEVCDFEDSLTTQNVRIARERAGLGAEVVPSWAEHLLITAQRTPEHDG
+APYLRLEESSPLQGPVRMPPAVLRIGAREAVPAAGPAGSEAGQARPEGLRVEVVSEGHVL
+AVHWLGEPATEGRRPLVASDWGGGTVSVPVATAAEALEGLPADLHTFAQLPTD
+>GCF_023573625.1_01240
+MTHPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRMGFAPTPAQRAAR
+GGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA
+RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA
+VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001079.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa92aa42105e330458282fea91e85c339182ad65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001079.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_01283
+MTTQDSPLTPNSSRSACCGGHARPDTSRRTVLGRGAAVAAAGAGALALTGCTDQLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARQALMDYDAAVVDDRIVVKL
+>GCF_003691675.1_01002
+MTTQDSPLTPNSSRSGCCDDHARPDTSRRTVLGRGAAVAAAGAGTLALAGCTDRLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARKALMDYDAAVVDDRIVVKL
+>GCF_005280335.1_01602
+MTAQDSTPTPDPSAVAPPSAPAGCCGGRAAADAARPEASRRTVLGRGAAVAAAGAGALAL
+SGCTEQLREKENAQDHFAGADAVEALPAADLPVGAAREVEVEGRTLMMHRVDETTVTAFT
+NVCTHQGCLLQVVDRAEGPSFACPCHGSHFDVQTGKPFGGPARQPLMDYEAVVDGDRIVV
+KL
+>GCF_020097155.1_01498
+MTSQDPAPHTSASPCCSGCSAEPAGSSRRSVLGAGSLVALAGAGSVVLSGCTQQLKDEAA
+AGDHHVGSETTDAMALAELPVGGTTSVQVQGRTLLLHRADESTVTAFSNVCTHQGCLVQV
+VDRPEGTAYACPCHGSNFDVATGEPFGGPAKAPLTDYQAAIEGDRIVVKL
+>GCF_023573625.1_01241
+MTTQDSPLTPNSSRSGCCDDHARPDTSRRTVLGRGAAVAAAGAGTLALAGCTDRLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARKALMDYDAAVVDDRIVVKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001080.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001080.fa
new file mode 100644
index 0000000000000000000000000000000000000000..635ceed1d94aa48e58a41683324a5e410e2fe8d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001080.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_01284
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
+>GCF_003691675.1_01003
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
+>GCF_005280335.1_01601
+MGGAAAAALAAAANPLMPTPVEAVLGWGLSLAVGALWIAGFVSLSRGPLDARGRLPWAGA
+MLLLPVLGALIWFWWRHRYYPARRREQPGWDPNDRGAVVVPPRRGRPVPSGIGRPDPNAG
+VAAPKGLAPRRRYGAERD
+>GCF_020097155.1_01497
+MEPWLGWTLSAVVGTIWVAGLVSLLRGPLDERRRLPWALAMVVLPVIGAGAWFWWRHRHY
+PARKAAEPGWDPNRRDPVVLPPARSGRAAPTAIGRPDPWAGHAPHPDRLPTRRYGAPED
+>GCF_023573625.1_01242
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001081.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001081.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31227a0ee20c5a17f32fef0cdb49f65330be7c25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001081.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_01286
+MSIVRLYRESVGDDGARLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQAEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATAIERRTVERLRVEMTHQLAWRGLG
+EVEDVVEEVGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG
+>GCF_003691675.1_01005
+MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG
+EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG
+>GCF_005280335.1_01599
+MSIVRLYRETTNEDGSRLFEYREAWADVEGGEFVVHHGRVGHPGTVGEQPLADEAEGEEL
+LAAFLAQGAEEGFAEADPAGFALLPVAFRLRGREASDIERRNVEHLRVEVTHQLAWRGLG
+EVEDVTEEPGALVLAVRTPHARKAAAEIPVAARRADGVQPNKVEVRSAVQED
+>GCF_020097155.1_01495
+MSISRLYRDRTEEDGRRSFEYREAWIDPSGELFTVHHGRVGHPGTVGDQPLTSEAEGAEL
+MDAFLAQGEADGFAPADEDAFDVLEVAYRLRGRAITEIERRHGRTLREEVTHQLAWRGLG
+EVTDVVDGDGELVLVVRTPHAPKAAAEVPAAAKRAHGIQPNKVEVRRVDAPRTPAGAAPD
+ADGEG
+>GCF_023573625.1_01244
+MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG
+EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001083.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001083.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c38d2cc15717dc7b2a78e98fe47fb5ea9255c262
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001083.fa
@@ -0,0 +1,80 @@
+>GCF_002008305.4_01295
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMPDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+>GCF_003691675.1_01018
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMPDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+>GCF_005280335.1_01597
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAEKLPYSLKVLLENLLRTEDGANVTAEQIK
+ALASWNPDAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPAGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAMFPIDEVTLDYLRLTGRTAEQVDLVEAYTKEQGMWHDPSSEVKYSEYLE
+LDLSTVVPSISGPKRPQDRIELSDSKDQFRKDLHNYATQDEAGEGRPSKLVDVSMEDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDSEGNDVFLKDIWPDPTEVQKIID
+ESIDTEMFTSQYGTIFDGDERWQSLETPSGSTFEWDEQSTYVRKPPYFEGMTMQPDAVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGKYLLENGVERKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGGDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+>GCF_020097155.1_01493
+MTTVDSFGSKGVLDVNGSEYEIFRLNAVEGAQKLPYALKVLLENLLRTEDGANVTAEQIK
+ALASWDPTAEPDTEIQFTPARVIMQDFTGVPCIVDLATMREAIADLGGDPSRVNPLSPAE
+LVIDHSVQIDSFGNDAAVERNMDIEYQRNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARAVMVRDVDGVKRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGQIPAGATATDVVLTITEQLREHGVVGKFVEFYGEGVGAVPLANRATIG
+NMSPEFGSTAAMFPIDDVTLDYLRLTGRSEEQVALVEAYTKEQGLWHDPSAEVQYSEYLE
+LDLSTVVPSISGPKRPQDRIVLSDSKDQFRKDLHNYATQDEAGEGRPSKLVDVHMEDGRE
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLTAKPWVKTSVAPGSRVVTDY
+YEKSGLNASLDALGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDCDFENEALGTDQDGNDVFLKDIWPDPAEVQRIID
+ESIDTEMFTSQYGTIFDGDERWQSLETPTGKTFEWDEASTYVRKPPYFEGMPAQPEPVQD
+IAGARVLLKLGDSVTTDHISPAGSFKSDTPAGQYLLANGVERKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGTGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPAGESADSLGLTGTETFAIS
+GIAELNEGRTPKTVKVTATAEDGKVTEFDAVVRIDTPGEADYYRNGGILQYVLRQIAAKA
+>GCF_023573625.1_01253
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMADGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001084.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001084.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b33eaae5a9fafef90d4fcd5c9dfd1e37c253152
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001084.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01296
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
+>GCF_003691675.1_01019
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
+>GCF_005280335.1_01596
+MAVIDTSTGVTGIGGTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEEG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIAGLTVEPEVCFAGPEDEPTGQRWRTRNAFTVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEAKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKRHSPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+RHAPATLVDAVLEDARIEPGQTVADLYGGAGLFSAYLADAVGPEGRVFSVEAAGQASKDA
+RRNLHGQPQATVLNGPTDKALGSWIKYPERTVADGGLEGASLDTVVLDPPRAGAGRRAIE
+RLLALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPATQ
+LAAVPAIVEI
+>GCF_020097155.1_01492
+MDTSTEVVAPGGVIEVEAGAMAHGGHCVARHEGRVVFVRHAIPGEIVRVALTEAEPGARF
+WRGDVVEVVRPSEFRRIHQWKLADSLRAHASGRLPVGGAEYGHIVVHHQRRLKAQVFRDT
+VARIAGVTIEPEALHAGHEDEPTGQHWRTRTAFAVTPQGRIAMHAHRSAVLLPVRNMPLG
+VHALDALALWDWDFTGAARVDVATPADGTQPLVLATPTPQTLADEARLGKLRTRIRQAAN
+ACPVDVSTGFAVPGPKKFSPTGIQRITGRTWVHETVSSERGGERTFRVTGDGFWQVHQHA
+PATLVDAVLEDVDPQPGEVIADLYAGAGLFSAFLSDAVGEEGRVYSVEASRQASKDARRN
+LLSLPQAGVLNGPTDKVLGSWIKEPERTTRDGGLDGDRLDAVVLDPPRAGAGRRAIERIL
+ALAPGRICYVSCDPASFARDLAWLREGGYEVERARVFDLYPDTHHLESVTLLRPAGEVEQ
+TTL
+>GCF_023573625.1_01254
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001085.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bac2d83067b90eba327433f9e7d1aba1ebd62eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001085.fa
@@ -0,0 +1,61 @@
+>GCF_002008305.4_01297
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS
+>GCF_003691675.1_01020
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS
+>GCF_005280335.1_01595
+MATLSSLLRRGLLGRPVASHDVAEPRMSRWQALPVTSSNALSSLAYAPDEIVLTLVAAGT
+AALALGPLVGWGVVVVMLLIVASFRAAVAAVPQGGIYQMARTKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFAAALLPGLGLESRVLVACAALVGVLLTSLRSARLSRWALPVLVSAF
+VALTALLVAAGLWQEGQGLLGRAATSGWTQEGAGIGGTVGAVATALLALRAFSAGSVLLT
+GVEVPVSSSSAMARPAVATVRWVLAVMALTLGALTLGVMHLAQRTGVVVALDPARLRDAA
+GRPVAEADTPAPVIAQLADTVFGPGSVLSLATIAATALLLLFAARSAFRSFPALASRLAE
+DGYLPRQLRVRGDRLVHTWGVLALGAAALALVLLFRAQTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLAQTPGARARAAVRLRLTITAVAWVVTALAGVVVLVTRFAQGAWVALLAIVL
+GSLVMGRIRRHYEDVGRELAPDPEDDARALPSRVHVVVVVSTLNRPALRALAYARATRPS
+SLEAVVVDAERAVTEDVIDAWSRAGLPVPLTVVAAPYRDTVVPLVRHLRERRRRSPRDLT
+MVFIPEYVVRPGWRTLMHNRTATRQKRRLQREAGVMIGSVPWQIHEGQGDGQRSTTV
+>GCF_020097155.1_01491
+MSTPPSTLRRLLLGRPVASGARPAPRRGRWLALPATASNALSSLAYAPDEVILTLVASGT
+GALALGPLVGWAVVAVMVLIVLAFRAAVVAVPRGGIYRMARTKLGPRSGVVAAAALLLDF
+VFTAAVSVAAFAHHASALVPALRGHVGIVSAVALVLVLVSALRGERGSGALVTVLVAAFV
+GLLGTLVAVGLWQSGQGTLAAAPSAGLHVDGAGLGPVGDAATALLALRAFSAGSVLLSGV
+EVPLSATDRMARPAVRTARWVLTVLAVVVGTLTVGVMHLAQRTGVVVALHPDRLRTADGA
+PLAPDTAPAPVVAQLAETVFGAGSPGAVATVAVTSLLLLVAARGAFRSFPTLTARLAEDG
+WLPRQLRVRGDRMVHTGGTLALATATLLLLVLFRGRTALLVQLYVIGVLLAFALALVGML
+RLWRLKLAHTPGARARASVRVKLVVTAVGLGATALAGVVVLVTRFAQGAWVALLAIGVSA
+VVMGRIRRHYRAVEAELAPDPQDDARALPSRVHAVVVVSTLNRPALRALAYARATRPATL
+EAVVVDADRRQTERVVEDFARAGLPVPLTVIAAPYRDTVVPLVRHVRGRRLRSPRDLTMV
+FIPEHVVRGGWRRLLHNRTASRQKARLQREAGVMVGSVPWQIREGDPHRPVEGGIVACAA
+PGDVPEGVESS
+>GCF_023573625.1_01255
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001086.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001086.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a26e33fcafb293932db1382485facd3face1fd61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001086.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01298
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDRVEAALQGEARVPDGTDEDEEGRA
+>GCF_003691675.1_01021
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDQVEAALQGEARVPDGTDEDEEGRA
+>GCF_005280335.1_01594
+MAHYVIVGGGRVGTRLACALDAAGHSVALVDRDPRTVDGLVPGFSGELVAGVGFDRAALL
+AAGVDRAQGLAAVTAEDNTNIIAARVARETFHVEHVVARIYDADQAKVYQRLGIPTVASI
+QWTADQVLHRLLPAGTADVERRDASGRLLVTGLVPHPSWWGRRLTDVESGAGLRIAYLTR
+RGEGLLPRPGDRLQEGDLLHAVYPVDRRDQVEAALQGEAVRSDRDAEDEDEEGRA
+>GCF_020097155.1_01490
+MAHYVIVGAGRVGTRLAGALDTAGHSVAVIERSPELTAGLGPDFGGTVVAGIGFDRDALR
+RAGIEQAQGLAAVTTEDTTNVIAARVARETFGVQHVVARIYDAQRARVFQRLGIPTVASV
+EWTADQVLHRLLPAGTAEPSRRDASGRLAMGDYMPHRSWWGSPLHAVEAAVGARIAYLTR
+YGEGVLPSPDGVLQEGDVLHVAYPAARRDRVEAALQGEAGDVRAGEDEDQEEDA
+>GCF_023573625.1_01256
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDQVEAALQGEARVPDGTDEDEEGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001087.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001087.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ab71bb2369ed80589dd123ab2505faed753099f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001087.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01299
+MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC
+GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV
+RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS
+>GCF_003691675.1_01022
+MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC
+GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV
+RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS
+>GCF_005280335.1_01593
+MRAVIAGAGAVGASVARELHAHGHEVVVVEIRPDAAHKADVGGAKLVLGDACDLALLERC
+GAMEADVLVAATGDDRANLVCSLLGRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAVLSEFRVPAEHWLAGRRVGTVSWPQDAPLVAVV
+RDGVPRHATADEMLEAGDELFFLAAAAADAALRRLLVGEDRAQARPGAGSSSAAGRRPSS
+SPGAGALTDQASQSPRA
+>GCF_020097155.1_01489
+MRVVIAGAGAVGSSIARELHAHGHEVSVVESRADAAARSDLAGARTVLGDATDLGVLGRA
+GALGADVLVAATGDDRANLVASLLARSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVESGDLVRLLRLEAGGAALTEFRIPSGHWLRGRRVGTVSWPAAAPLVAIV
+RDGAPRSSTPDEVLEESDELFFLADAEAEGALRRLLVG
+>GCF_023573625.1_01257
+MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC
+GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV
+RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001088.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001088.fa
new file mode 100644
index 0000000000000000000000000000000000000000..250afbe2bbbd3ed6750c838fbb285abb857976b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001088.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01300
+MTEPRGPVTAAPDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMVGYVATQ
+QVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYYLWGFVT
+NAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVFALRLAV
+QVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVSSPGQDDGVPADSAASERP
+>GCF_003691675.1_01023
+MTEPRGPVTAAPDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMVGYVATQ
+QVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYYLWGFVT
+NAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVFALRLAV
+QVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVSSPGQDDGVPADSAASERP
+>GCF_005280335.1_01592
+MTEPRGPESPAPDVAGALPSRARVDEQGRLDALASVGGWRGIVEASLPTLVFMAGYVVSQ
+QVWPSGVAAVAVALVLGAVRLVQRQSPVQVLAGLAVVVLSVVVALTTGQARDYYLWGFVT
+NAAYGLAFALSVVVGWPAAGLVLGLVRGEGTHWRRSPRRRRAYATATWILVAVFTLRLAV
+QVPLYLADAVTALGVARLVMGLPLYALGLWLAWSVSAPAPGEDDGLRPAAEDEPAPGRA
+>GCF_020097155.1_01488
+MSAHPRPDHGPDAAPSAAEGLQALGARTRVDEDGRIDALATVGGVRGIVEASLPTLVFLV
+VFLLAGQVWTAGAAALGVAAVMTAARLAQRQSAAQALAGLLVVGVSVVLALTRGEARDFY
+LWGFVTNIAYGLALPLSAALGWPLAGLLFGMVRGEGLHWRADPARRRAYGIATLIVAAVS
+WLRLAVQAPLYLADAATALGVARVVMGLPLYALGLWLAWSVSTPRPGAPPLRRDPAAG
+>GCF_023573625.1_01258
+MTEPRGPVTAAPDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMVGYVATQ
+QVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYYLWGFVT
+NAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVFALRLAV
+QVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVSSPGQDDGVPADSAASERP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001090.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001090.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41a1e6a0bf112eba0260c7f787dae630e433352e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001090.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01302
+MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAADVGPHDVATRPDPAGMIDLGSLRLR
+AVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLSTTAH
+ATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAE
+PLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRPAPDEGRDVLADTATGPGDGA
+APEATALPERGPEITETR
+>GCF_003691675.1_01025
+MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAADVGPHDVATRPDPAGMIDLGSLRLR
+AVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLSTTAH
+ATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAE
+PLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRPAPDEGRDVLADTATGPGDGA
+APEATALPERGPEITETR
+>GCF_005280335.1_01590
+MIFGRNRKVRHEQVSLPEELLEERDHEVAALPEAAETGPHDVATRPDPAGAIDLGSLRMR
+AVQGMKLRLDVEDSTKRIVAATITLGRSALQVQAFSAPRRAGLWDEVREELRDSLDTTPN
+ATVQEQAGRFGTEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAA
+QLEQVFSDIVVVRGDEPMPPRELLPLRPPANARPVQRRRPGAARDAGRDVLADTERGPQE
+APALPERGPEITEIR
+>GCF_020097155.1_01486
+MIFGRNRNVRHEQVAVPEQLKDERDRLVEARPAPAAEGDRGPFDVEAAPSGRPSVDLGAL
+RVPAVQGMQLRLDVEDATQRIVAVTVTLERSALQIQAFSAPRAAGVWDDLRAEIKEALVG
+TPGAQVQEQSGGFGPEVLTRIPATLPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAYLPD
+AARALEDVFAGVVVVRGDAPLPPRELLPLRPPADAQPVRRRPRPHAGGEPDVHARRPDDA
+PETGAETLPERGPEITEIR
+>GCF_023573625.1_01260
+MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAADVGPHDVATRPDPAGMIDLGSLRLR
+AVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLSTTAH
+ATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAE
+PLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRPAPDEGRDVLADTATGPGDGA
+APEATALPERGPEITETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001092.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001092.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa1d6835fd25fbf97499f815f889f7cf4818c638
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001092.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01304
+MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG
+VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP
+LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR
+>GCF_003691675.1_01027
+MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG
+VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP
+LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR
+>GCF_005280335.1_01588
+MREPQQHPVSDAPVDRPQDPAQGSDRVLFEERLTPSAGVWVVALMLASLTILVFAPIDLW
+FGVAAAVVFFGLEALLLLTTTPRIVVRERTLQVGRASIERRHVGEVTGHRGEDARRQRGP
+LLHGLAYVVVRGWISPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMVQEDPADEDR
+>GCF_020097155.1_01484
+MQDASATPDHHAPRTVAASADPVQYEERLSPSVGVWLVALLLAGLCIFVLAPVALWAGFL
+AAAVFFVVEAVVLLASTPRIVVRERTLQVGRAQIERRHLGAVTGHRGEAARAQRGPLLHG
+LAYVCVRGWISPVVRIQIEDERDATPYWLASTRHPEDLVAALGGRMAGEG
+>GCF_023573625.1_01262
+MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG
+VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP
+LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001097.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001097.fa
new file mode 100644
index 0000000000000000000000000000000000000000..effceb0970016ace263b2d3096a3ae570d36e16f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001097.fa
@@ -0,0 +1,80 @@
+>GCF_002008305.4_01310
+MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY
+PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI
+VGLDGVRDAYATGRGTFRMRAAVDVEQVTARRTGLIVTELPYGVGPEKVIERIKAGVDAK
+KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ
+TLGLLPLLRVYVDHRLDVVRRRTAHRLQRRQDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+AAARTRLMGVFDLTQVQADHILELRLRQLTKFSRIELEAERDELQAAIAELEAILGSEAR
+LREVVSAELQAVADEFGDDRRTVLLEAETVAAPAASNAGGPTPAGAAQAGADLMVPDTAC
+WAVLTTSGRLLRTADRTPIASQGRRRKHDAFASVVATTARGEIGALTSTGALHRIQAVDL
+PAAPEPSAAPAMTGSVPAKELVPLGKGESLVALVPLDAVIALGTAQGVVKRVRPEWPLNR
+EVAEAIALKDGDAVVGAAPAVDDEDQLVFLTRAGQLLRYAASAVRPQGPAAGGVAGLRVA
+ADDAVLAFGVAPAASLTGPGDDAAAHPRPAVVVTVTDGEGDLLGSAGGSVKVTPLGEYPA
+KGRGTGGVRAHRLLKGETSLVLGWVGAGPALAASKAGVARALPVEYGRRDGSGVPVDQRI
+EAVGAGASPELLSAPPVADDPVTVSAD
+>GCF_003691675.1_01033
+MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY
+PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI
+VGLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYGVGPEKVIERIKAGVDAK
+KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ
+TLGLLPLLRVYVDHRLDVVRRRTGHRLGKHRDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+TAARTRLMGVFDLTQVQADHILELRLRQLTRFSRIELEAERDELQAAIAELEAILASDAR
+LREVVSAELQAVADEHGDDRRTVLLEAETAAAPAAGPAPSGPTPAGAAEAGADLMVPDTA
+CWALLSTSGRLLRTADRTPIAPQGRRRKHDAFASVVPTTARGEIGALTSAGALHRLQAVD
+LPVAGEPSAAPAMTAAVPAAELVPLAKGETLVALVPLDAVLALGTAHGVVKRVRPEWPLN
+RQVVDAVALKDGDAVVGAAPAPDEADQLVFLTRTGQLLRYAASAVRPQGPAGGGVAGIRL
+AAGDTVLAFGVAPAASLTETGADAAAHPRPAVVVTVTDGEADVLGSAPGSVKVTPLGEYP
+AKGRGTGGVRAHRLLKGESGLELGWIGAAPALAASRAGVARALPIEYGRRDGSGVPVDQR
+IEAVGAGASPDLVSAPPAEDDAVAVSAD
+>GCF_005280335.1_01582
+MSRSSRSRPSEQDVARPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLKP
+VQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPVV
+DGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEDTVDFVPNYDNQFQQPAVLPAAYP
+NLLVNGTTGIAVGMATNMAPHNLREVVAAARHLLADPEADLEAIMAHIPGPDLPSGGRIV
+GLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYAVGPEKVIERIKAGVDAKK
+LSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQT
+LGLLPLLRVYVDHRLDVVRRRTAHRLQRRQDRLHLVEGLLLALVDIDEVIEIIRSSDDTA
+AARTRLMGVFDLTQVQADHILELRLRQLTKFSRIELEAERDELQAAIAELEAILGSEARL
+REVVSAELQAVADEFGDDRRTVLLEAETVAAPAASTVGGPTPAGAAQAGADLMVPDTACW
+AVLTTSGRLLRTADRTPIASQGRRRKHDAFASVVATTARGEIGALTSTGALHRIQAVDLP
+AAPEPSAAPAMTGSVPAKELVPLGKGESLVALVPLDAVIALGTAQGVVKRVRPEWPLNRE
+VAEAIALKDGDAVVGAAPAVDDEDQLVFLTRAGQLLRYAASAVRPQGPAAGGVAGLRVAA
+DDAVLAFGVAPAASLTGPGDDAAAHPRPAVVVTVTDGEGDLLGSAGGSVKVTPLGEYPAK
+GRGTGGVRAHRLLKGETSLVLGWVGAGPALAASKAGVARALPVEYGRRDGSGVPVDQRIE
+AVGAGASPELLSAPPVADDPVTVSAD
+>GCF_020097155.1_01478
+MTTRSSRSRTAEADAPAPLPVEQENIVDVDVSQEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILFMMSQMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEDTVDFVPNYDNQFQQPAVLPAAY
+PNLLVNGAAGIAVGMATNMAPHNLREVVAAARHLLAHPDADLEALMAHVPGPDLPSGGRI
+VGLDGIRDAYATGRGTFRMRATASIEQVSSRRTGIVVTELPYAVGPEKVIEKIKDGVRGG
+RLQGISDVVDLTDRKHGLRLVVELKSGFNAQAVLAALYRHTPMEESFGINNVALVDGRPR
+TLGLRELLQVYVDHRMDVVRRRTVHRLGERRDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+AAARTRLMQVFDLSQVQAEHILELRLRQLTKFSRIELEAERDELAAAIAELEAILASDAR
+LREVVSAELQAVADEFGDDRRTELVTADAAASVVSAPGEPALPAGTGPSDGGELMIPDTA
+CWALLTTTGRLLRTVDRTPLAPQGRRRKHDAFVSVVPTTARGEVGALTSTGRVLRLQAVE
+LPAAEESSPAPALTAARPAKDLVPLAKGESLVALVPLDAVLALGTAHGVVKRVRPEWPLN
+RDELTAIALKDGDSVVGAAPAPDDGDHLVFVTRAGQLLHFAASQVRPQGPAGGGVAGLRV
+GAEDAVIAFGVAPAASMTAEGEDPAAHPRPAVVVTVTDGDADLLGSAGGSVKVTPLGEYP
+VKGRGTGGVRAHRLLKGETHLTLAWVGASPALAASKAGVARALPVEYGRRDGSGVPVDQR
+VEAVGAGASPELVAAAPVDDSGVEVSAD
+>GCF_023573625.1_01268
+MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY
+PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI
+VGLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYGVGPEKVIERIKAGVDAK
+KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ
+TLGLLPLLRVYVDHRLDVVRRRTGHRLGKHRDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+TAARTRLMGVFDLTQVQADHILELRLRQLTRFSRIELEAERDELQAAIAELEAILASDAR
+LREVVSAELQAVADEHGDDRRTVLLEAETAAAPAAGPAPSGPTPAGAAEAGADLMVPDTA
+CWALLSTSGRLLRTADRTPIAPQGRRRKHDAFASVVPTTARGEIGALTSAGALHRLQAVD
+LPVAGEPSAAPAMTAAVPAAELVPLAKGETLVALVPLDAVLALGTAHGVVKRVRPEWPLN
+RQVVDAVALKDGDAVVGAAPAPDEADQLVFLTRTGQLLRYAASAVRPQGPAGGGVAGIRL
+AAGDTVLAFGVAPAASLTETGADAAAHPRPAVVVTVTDGEADVLGSAPGSVKVTPLGEYP
+AKGRGTGGVRAHRLLKGESGLELGWIGAAPALAASRAGVARALPIEYGRRDGSGVPVDQR
+IEAVGAGASPDLVSAPPAEDDAVAVSAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001100.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001100.fa
new file mode 100644
index 0000000000000000000000000000000000000000..299b8480932add1e599b02c3071b75035ad56df3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001100.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01313
+MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLI
+NFIMGVATGIVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRV
+PRRLHLAAIWCAVIGAHLSAYFIMTANAFMQHPVGYEVVDGRPVLNDIGAVLANPIVLTH
+FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTGSKARDRLDHRVWI
+TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAG
+DRTTCTDVTTVIELPGLLSYLAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGA
+PIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGTVPDSRGWTATAVASIGAPFA
+ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL
+LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY
+>GCF_003691675.1_01036
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLI
+NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRI
+PRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVDGRPVLNDLGAVLTNPIVLTH
+YPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL
+TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSG
+GATTCEDVQGVIEVPGLLSYLAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGS
+EISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGTVPASRGWMRLAVASIGAPFA
+ANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL
+LGVEVFLLTRFVRGGVPAAMPELTAAEHSDEQKRDRDDVLAFAY
+>GCF_005280335.1_01579
+MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLI
+NFIMGVATGIVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRV
+PRRLHLAAIWCAVIGAHLSAYFILTANAFMQHPVGYEVVDGRPVLNDIGAVLANPIVLTH
+FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTDSKARDRLDHRVWI
+TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAG
+DRTTCTDVTTVIELPGLLSYLAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGA
+PIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGTVPDSRGWTATAVASIGAPFA
+ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL
+LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY
+>GCF_020097155.1_01475
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVRTGREHYLRMTKFWGKLFLI
+NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGMWIFGWDRL
+PRRLHLAAIWCAVIGAHLSAYFIMAANAFMQHPVGYEVVDGRPVLNDIVAVLTNPIVLTH
+FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDAEGRVVVGTTGSKARDALDHRVWI
+TSLRAGAAVVIVGFLGTAFTGHAQAQQMIHYQPTKMASAEAACHDGTAFSVLTLGDVNTP
+GATTCDDVTGVIEIPGLLSFLAYSDFTTPVPGITTLLPQFEARYGTQLPDDPMYGERAGQ
+EISYLPLMEVTYWGFRLMITFGGLAALAGALTLWMTRKGTVPDSKPWMITAVASIGASFA
+ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSGEEVLTSLIVFVVLYAVL
+LVVEVALLARYVRGGVPAGMPELTADEHRDPDDDRHDRDDVLAFAY
+>GCF_023573625.1_01271
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLI
+NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRI
+PRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVDGRPVLNDLGAVLTNPIVLTH
+YPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL
+TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSG
+GATTCEDVQGVIEVPGLLSYLAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGS
+EISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGTVPASRGWMRLAVASIGAPFA
+ANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL
+LGVEVFLLTRFVRGGVPAAMPELTAAEHSDEQKRDRDDVLAFAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001103.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001103.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4126df487d7c1a925446d0881779459e185e267e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001103.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01318
+MSGFGYDVGLDEAGMPELVERLESRRVLVTGASGLLGAGVARVLADAGNDVVTLQRRPSG
+VAGARDVQGSVTDPAAVEEALTGADTVVHVAAKVSVSGPEHEYEAVNVEGTRILLHAAQR
+HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAAVSAADVH
+HGEALVVTNGEPRPVGELIRQIALAGGAAEPERRVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLSWTPTVSIDEGLHRVAAYYRDR
+>GCF_003691675.1_01039
+MSGFGYDVGLDAAGMPDLVERLESRRVLVTGASGLLGAGVARVLADAGNDVTTLQRRPSG
+VPGARDVRGSVTDPAAVEEALTGADTVVHVAAKVSVSGPEHEYEAVNVEGTRILLHAAQR
+HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAALSAADVH
+HGEALVVTNGEPRPVGELIRQIALAGGAAEPERRVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLAWTPTVSIDEGLHRVAAYYRDR
+>GCF_005280335.1_01574
+MSGFGYDVGLDEAGMPELVERLESRRVLVTGASGLLGAGVARVLADAGNDVVTLQRRPSG
+VAGARDVQGSVTDPAAVERAVAGVDTVVHVAAKVSVSGPEHEFEAVNVEGTRILLHAAQR
+HGARRFVHISSPSVAHAGDSIVGEGAGPASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDMQLTDRIVQRARAGRMPVLGTGAPLIDTLYTGNAVEAVVAAVSAADHH
+HGEALVVTNGEPRPVGELVRQIALAGGAEEPERHVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLDWTPSVSIGEGLHRLAAYYRAR
+>GCF_020097155.1_01470
+MGFEVHLGDDGLLQLAERVEHRRVLVTGASGLLGSGVARVLAEAGNPVTTLQRRPSGVPG
+AVDVLGSVTDPAAVERALEGVDTVVHVAAKVSVSGPEEEFAAVNVEGTRILVHAARRRGV
+HRFVHVSSPSVAHAGASIVGEGAGPADPEHARGPYARTKAAGELIALGADADDFRVLALR
+PHLMWGPGDLQLTDRIVQRAREGRMPVLGSGAALVDTLYTGNAVEAVVAAVSAVDHTHGE
+ALVVTNGEPRPVGELIRRIALAGGAPEPERTVPAGVARRAGALIERAWERDLFGVRSSGR
+GSADGEPPLTEFLAEQLSTSHWFDQRRTREVLDWTPSVSMDEGLLRLAAYYRDR
+>GCF_023573625.1_01274
+MSGFGYDVGLDAAGMPDLVERLESRRVLVTGASGLLGAGVARVLADADNDVTTLQRRPSG
+VPGARDVRGSVTDPAAVEEALTGADTVVHVAAKVSVSGPKHEYEAVNVEGTRILLHAAQR
+HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAAVSAADVH
+HGEALVVTNGEPRPVGELIRQIALAGGATEPERRVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLAWTPTVSIDEGLHRVAAYYRDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001104.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001104.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aafe1abaf655b23a42992e7bf04c9acadfcefb81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001104.fa
@@ -0,0 +1,66 @@
+>GCF_002008305.4_01319
+MSGPRSRLDRPLSSTERPAPVPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHC
+LWEIIDNSVDEALAGFGQSIEITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLH
+AGGKFGGGSYAASGGLHGVGASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRP
+SPDAPFEPSTDASPLDVVGKAKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYL
+IPGLRITVKDLRRRPGTPGADGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFK
+ERVPVLGEDGRTSMQDVQRTCEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAAL
+LKVFRAQVEANARRLKAGSDKVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRI
+VSQVVEKQLTARLTSTARAQKQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMP
+AKLADCRSNDVASSELFIVEGDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILAN
+AECAALIQVVGGGAGRSFDLDAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAG
+RVYAAVPPLHRIEAVTRGVKEREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEM
+DADQLAETTMDPRHRMLRRVNIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRARID
+A
+>GCF_003691675.1_01040
+MPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI
+EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPAAPFEPSTDASPLDVVGK
+AKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYLIPGLRITVKDLRRRPGTPGA
+DGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT
+CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKVFRAQVEANARRLKAGSD
+KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVSQVVEKQLTARLTSTARAQ
+KQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL
+DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVK
+EREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV
+NIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRERIDA
+>GCF_005280335.1_01572
+MPANSEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGYGQSI
+EITLHPDGSVEVEDSGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGK
+AKRGQTGTRVRYWADEQIFIKDAAFSADDLHARARQTAYLIPGLRITVKDLRRRPGTPGA
+EGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGSFKERVPVLGEDGRTAMQDVQRT
+CEVDLALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKAFRTQVESNARRLKAGSD
+KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVAQVVEKELTARLTATARAQ
+KQQVHVLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL
+DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVFAAVPPLHRIEAVTKGVK
+EREVIYTYSEQELYATLARLEKEGRSYKEPIQRYKGLGEMDADQLAETTMDPRHRTLRRV
+NIAEVEAAERVFDLLMGSSVAPRKDFIVSHADELDRERIDA
+>GCF_020097155.1_01468
+MPANTEYSARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI
+DVTLHPDGSVEVADNGRGIPVDVEPRTGLTGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVVRGGKVHQLSFRRGEPGRFQDGSRPTPDAPFEPAADAAPLDVVGK
+AKRGQTGTRVRYWADEQIFTPDATFSMEDLQARARQTAYLIPGLRIAVTDLRRLTGTAGE
+AGPVQEVYQYDGGIAEFVDHLTPAKPVTDVWRIQGSGTFTERVPVLGEDGRTQMQDVQRT
+CEVDVALRWDVGYETVFRSFVNIIATPKGGTHQSGFESALLKVFRAQVEAGARRLKAGSD
+RPDKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTPAVRRIVARVVEKELTALLTSTARGQ
+KQQVGALLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVAASELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILSNAECAALIQVVGGGAGRGFDL
+DAARYGKVILMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGKK
+EREVIYTYSEAELHEVLARLEAEGRTYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV
+TISEVEAAERVFELLMGSSVAPRKAFIVSNADELDRERIDA
+>GCF_023573625.1_01275
+MPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI
+EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGK
+AKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYLIPGLRITVKDLRRRPGTPGA
+DGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT
+CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKAFRAQVEANARRLKAGSD
+KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVSQVVEKQLTARFTSTARAQ
+KQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL
+DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVK
+EREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV
+NIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRERIDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001105.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001105.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c0648056837aa850c8df4108ee19ad8ad80bb62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001105.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01320
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD
+ETDRLTAGA
+>GCF_003691675.1_01041
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD
+ETDRLTAGA
+>GCF_005280335.1_01571
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLPSGGALQFCGHHARAVEDALRPQAAHWQD
+ETDRLTAGA
+>GCF_020097155.1_01467
+MSITAVAEPAALTRADRCDRCGAQAYVRAVLPSGGELLFCGHHARGVEASLRPQAALWQD
+QTEELDGSTAA
+>GCF_023573625.1_01276
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQTALWQD
+ETDRLTAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001106.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001106.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfa170d092ce6c7377248426db7d6487b537ca9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001106.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01321
+MDCKDPRVAADETERPRVTTSTTSGVQDGKETTASEATTTRTRSTAAKKSAATKSATTKG
+ATTKGATTRTTATKSAATKTAATPTAKKKATRKPTAAKTTATAKTTAAAKTTAAVKTTAT
+KKTATTRGKKATASAASAEQAEDDEEFVEARERTEAADAVEEDVVEDETATEDSDDEDAD
+GSDAPERPAMDAEAVTGTKAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDY
+LKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHL
+LEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAI
+TRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQK
+YGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVV
+AMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
+>GCF_003691675.1_01042
+MDCKDPRVAADETERPRVTTSTTSGVQDGKETTASEATTTRTRSTAAKKSAAKKSAATKS
+ATTKGATTRTTATKSAATKTAATPTAKKKATRKPTAAKTTATAKTTAAKKTATTGGKKAT
+ASAASAEQAEDDEELVQARERTEAADAVEEDVVADETATEDSDDEDADGSDAPERPAMDA
+EAVTGTTAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNA
+EQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHLLEANLRLVVSLA
+KRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIR
+IPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPL
+GEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPK
+TLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
+>GCF_005280335.1_01570
+MTTSTTNGAQDAPETTDSGAATTRSRSTAAKKTTAAKSTTAKGTAARKTASSTTAAKSTA
+KSAAAKGAATKAAAKTAAADGEAPAKTTTRRTAASKTTAAKSTPTKPAAKTTTRKKAAPA
+ATAKGKKATASAAAQAEQDEELADAVERTDAADAVDPDVADVVDGEAKAATEDSDDEDAD
+GSDAPDAPAMDQEAVTGTKAGSGQAVAQTKGAFVMDDSEDDAPVQQVVVAGATADPVKDY
+LKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQAEASDDYRERRDIQLIIADGRKAKNHL
+LEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAI
+TRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQK
+YGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADVVSFTLLQEQLHSVLDTLSEREAGVV
+AMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
+>GCF_020097155.1_01466
+MTAGTPTERPRVTTSTTSGKQDGKETAASTTTAAAAKKTTTAAKKKTTAAAAKKPAAAKT
+ASGASTAAKKTTAKSTAAQATTTRGATTKKAAADAETEAAPAAAPRKRTSTATSTAKAAP
+KKTTRAPKKTASKAVAEEELVEEEDLELDADDVAEQASQDGDDADADGSDAPAAEDLVAT
+TEKPAETAAKGAFVMDNSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNAEQEVDLAM
+RIEAGLYAEHHFAENPPEDYRLRRDVELIIADGRRAKNHLLEANLRLVVSLAKRYTGRGM
+LFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEV
+INKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEF
+GDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKV
+YGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
+>GCF_023573625.1_01277
+MDCKDPRVAADETERPRVTTSTTSGAQDGKETTASGATTTRTRSTAAKKSTATKSATTKG
+ATTRTTATKSAATKTAATPTAKKKAARKPAAAKTTATAKTTATKKTATTRGKKATASAGS
+AEQAEDDEEFVEARERTEAADAVEEDVVEDETATEDSDDADADGSDAPERPAMDAEAVTG
+TKAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNAEQEVD
+LAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHLLEANLRLVVSLAKRYTG
+RGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHM
+VEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGD
+SEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEI
+GKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001110.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001110.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33312e3ea4053977cd364ad75d37b97cae70663f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001110.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01325
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEEFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
+>GCF_003691675.1_01046
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGINATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGSI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
+>GCF_005280335.1_01566
+MADSATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKLGGTCLHWGCIPTKAYLH
+AAEVADETRNSAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLTGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYKAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVEVTIIEGLETLVPNEDPAIIKVLAREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGITMDRGFVITDERLHTGVGSI
+YAVGDIVPGLQLAHRGYQQGIFVAEEIAGNSPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVVEYNLAGNGKSSILGTGGIIKMVRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHG
+>GCF_020097155.1_01462
+MADSATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKVGVNATLESVDMAKVRDYKDGIVSGKHKGLAGLLKMRKVQVIEGAGK
+LVSKNEVEVDGTRYTAENIVLASGSVSKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKVFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMVRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
+>GCF_023573625.1_01281
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001111.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001111.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb7c454104d78161a2fe128647b259c444e1fb80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001111.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01326
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDGAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGSSGQDEASAEEIEDK
+ATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSAQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLRTLRQRLEGGEFANELGL
+>GCF_003691675.1_01047
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDGAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGSSGQDEASAEEIEDK
+ATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSAQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLTTLRQRLEGGEFANELGL
+>GCF_005280335.1_01565
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLQEIL
+ADEDETVEVGAPLATIGDGDGGGSSESDDDAQAEESEEPAAEEAQEDEEQQEPEGEPAPE
+ERSSTQDSEEKSSGGASGGDASEVTLPALGESVTEGTVTRWLKAVGDEVEVDEPLLEVST
+DKVDTEIPSPVAGTLLEIRAEEDETVEVGAVLALVGSGSAGGSSDSSDDSAKDDSAPDEA
+SAEEIEDKATEAETGEETEEAAQDAGEEKEEKAPEASASENASREESAEQEKAAAADAPE
+ATSPGQGYVTPLVRRLAHQNDVDLSTVRGTGVGGRIRKQDVLAAALAQQAGSAESAPAQE
+QGSKEQAAAASSAPAVASSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDV
+TRIVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASED
+IAIAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGS
+VGALFDTPIINQPQVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGAD
+AGRFLTTLRQRLEGGEFANELGL
+>GCF_020097155.1_01461
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDEAPSAGGEDSEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLVEILANEDDTVEVGAVLARVGSGAAPAASQDPAPAADTASPEEIEDKAT
+EAPTGEQTEEAAEQAGDVKQEQAPAASPAETASAAPAASAPAAETSASEPGPGYVTPLVR
+RLAKQNGVDLSTVRGTGVGGRIRKQDVLAASLANQASSGSASPAAAEEQQTPAAASAPAP
+AAVRGETEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDMTRIVQLRGKAKASFQEKNGVK
+LTYLPFITQAVTEALKQHPKLNASFSEDNKEITYHASEDIAIAVDTDRGLLVPVVKDAGT
+LNLAGLAQKIADVAERTRTNKINPDELSGGTFSITNIGSVGALFDTPIINQPQVAILGTG
+AIVKRPMVVADADGNDTIAIRHMMYLSLTYDHRLVDGADAGRFLQTLKARLEGGEFAAEL
+GL
+>GCF_023573625.1_01282
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDEAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAILALVGSGSAGGGSAPSEGSSGQDEASADEIEDK
+ATEAEAPEETEEAAEAAGAEKSEETPEASPSEEASRRESAERDSAQGESAEAPAATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLTTLRQRLEGGQFADELGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001113.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001113.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de520bfef263fdd724c90f1cdeb24c5eb5e93c2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001113.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01328
+MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWEPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVEGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRGRRAAPRRRALARRRGAAPRRGVLVAAGLATALAVGGGTAGL
+WWPASLGDATEGAPEPAGAVPAGTSVDAARPADGTPESGTPARVPDAGAPGEDAAGEDAV
+DVGEALAAVGHARTAALIDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTV
+EQAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGR
+DGGAAGRTWRVETVDPR
+>GCF_003691675.1_01049
+MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWEPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVEGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRRRAAPRRRALALRRGAAPRRGVLVAAGLATALAVGGGTAGLW
+WPASLGDATEGAPEPAGAVPAGTSVDAARPADGTPESGTPARVPDAGAPGEDAAGEDAVD
+VGEALAAVGHARTAALIDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVE
+QAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRD
+GGAAGRTWRVETVDPR
+>GCF_005280335.1_01563
+MRDWDEADDGAVGRVGGGPETEPERTSELGTAAPRAPGWAPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGHAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVQGAGAEPEASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRRRAGPGRRALVGRRGAAPRRGVLLAAGLATALAVGGGTAGLW
+WPAAPGSAAEGAPAEGAPEPAGTEPTGTPVDAARPADGTPESGTPARATDTGAPGEDAAG
+ADAVDVGEALAAVGQARTAALTDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGL
+EVTVEQAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGED
+PEARDGGAAGRTWRVETVDPR
+>GCF_020097155.1_01459
+MEAEDAERSGGVPPVGRPATDDWFADGGRDVSAWADPPRGGEGPAAVEPGVGDVGSPAEL
+GPADRPPQAPGLRVVSRIGMGGQAEAWLVRREDGTECVLKVPRADGDPDAVAKEAAVYGH
+LRHPHLLRVLGTVDTDRGTGVLSERLPAGSLASMVHDAGPLRPGQAVTVLVPVAQALAHL
+HEHGVVHGDVSPGNVLFGVDGRPALADLGVARVVGGPRGRGGTPGFTAPEDEAGVGEGGA
+AADVYAWGALGWFALTGRAPGPREHRAPLPVLVPDVPVELALLLSAALDPDPAGRPGAAE
+AAVAAYDAAPPEPVPLHESAPAEVAHLLPTVVPPARPGGSGDARRSRPRAGGRRDAGRGR
+GGRKRRNRSPRSRGWHPVMLVGAAVLAGTVVSAAVGGLTDRPEDQGEGAGSRAVAAPPTS
+PTAAPANPRASVTPTGAADPKDAITPTRDGGVPSAAGTGPAAVLPAEDAAAALAAVAEGR
+TAALTDPDPARVDAYAVPDGPAWRRDRAIQDQLREGGSAFSGLVVTLEAVGRPRPAEAGG
+SGGAEAGWVVVPAVLRMSAHTVLDDAGSVVGEVPASEEDVSVTLVPGGEGRWRAAAVDPR
+>GCF_023573625.1_01284
+MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWAPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVQGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRRRAGPGRRALARRRGAAPRRGVLVAAGLATALAVGGGTAGLW
+WPASLGDATEGAPEPAGAVPAGTSVDAARPADGTRESGAPARVPDTGAPGEDAAGEDAVD
+VGETLAAVGHARTAALTDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVE
+QAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRD
+GGAAGRTWRVETVDPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001114.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001114.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a344e4b26bea23affc2ef4bd8a7b9f6933ccc50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001114.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01329
+MPETLLPPLRLLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
+>GCF_003691675.1_01050
+MPETPLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
+>GCF_005280335.1_01562
+MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
+>GCF_020097155.1_01458
+MPHALLPPVRVLGLAPDLIDYEEGWALQRTLHADVVAGRSDGEILLLEHEAVYTAGRRTE
+DADRPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEEVLIRTAAEF
+GVTAVRVDGRAGIWITAREGDPRPDRKLGAIGLSIHDGVSMHGFSFNCSNSLTPYETIIA
+CGIADASTTTLSVETGREVTPVDVLPVLVRHLEDLGPEHIALTPTEGTPA
+>GCF_023573625.1_01285
+MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001116.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8badd1314949a3618d6396233377e42e9f3c0840
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001116.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01331
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALVVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPSRRAMRGR
+>GCF_003691675.1_01052
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALVVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPGRRAMRGR
+>GCF_005280335.1_01560
+MTKNSQPPASSSGSTSADLKQVKAMQRDRRRRVKEETRAQRRDKRANRGPGIISQLKQAY
+AMTKANDPKVGLWMLLAFVGVLVLGLVIGLLLNNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVPEQPVAVNPKTQDVVYRAVGRPGVVLVTEGPSNR
+IAALVGKEEKAMRRFLPGVPVTVVEAGNGQGQVPLHELPRTLKSMKKALTAQEVQAVDKR
+VNALNVNRLPIPKGVDPMKARPSRRAMRGR
+>GCF_020097155.1_01456
+MAKNPSTSPSSSGSSSLKEVKAMQRDRRAQLKADAKAERAQKRANAGPGIISQLKQVFAI
+TRQQNPRLVLWMVLAFASVLVLGLVVGLLLHNWITWLLLAIPFGVLAAVIVMNRLGERAM
+FDRLEGQTGAAGATLSSLGRGWIVGEQPSAVNPKTHDLVYRAIGKPGVVLVTEGPASRVG
+KLVSKEQKAMERFLPGVPVHVVETGRGEGQIPLREVPKTLKALPKKLTAQEVSAVDKRLS
+ALGTQKPPIPKGVDPMRARPDRRGMRGR
+>GCF_023573625.1_01287
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALIVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPSRRAMRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001117.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001117.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9161f676bf7f1539d8a8064bfc39e24f9c398106
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001117.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_01332
+MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT
+AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR
+LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM
+>GCF_003691675.1_01053
+MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT
+AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR
+LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM
+>GCF_005280335.1_01559
+MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT
+AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR
+LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM
+>GCF_020097155.1_01455
+MSCVFPACNASSGPDYPGGVAHRASDPAPRDRSERDAAGRAEPLISRADLAGWIDGPGGG
+RAGGRWPGDLLGLPEHGPASMATAARRAGALMIDWALALVVSNLAFGGDAIATLLVFAAM
+HVVGLTLLATTVGKALCRIQVVREGTGGTAPVHRVLIRTALLCLVLPAVVVGPDGRGMHD
+RVAGTVELHM
+>GCF_023573625.1_01288
+MVAHYAGGVARRAPDPQDRTETTGRAEPLITRRDLAGWVDGPGGGRAGGRWPGDLLGLPE
+RGPASMATAARRMGALVLDWFIALGISWLAFDADAIATLLVFAAMHVIGLTLLATTVGKA
+VCRIQVVRVGGRPAGLLRILLRTALLCLVLPAVVVGPDGRGMHDKLADTVEIRM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001118.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001118.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02480ecb43b9c33373f9af818797d18c386351f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001118.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01333
+MFTSPADVLAYIKDEGIEFVDVRFTDLPGMQHHFNVPASSVDEDFFVTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVGAAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
+>GCF_003691675.1_01054
+MFTSPADVLAYIKDEGIEFVDVRFTDLPGMQHHFNVPASSVDEDFFVTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVGAAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
+>GCF_005280335.1_01558
+MFTSPADVLAYIKEEGIEFVDIRFTDLPGMQHHFNVPASTVDEDFFTTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVAAAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
+>GCF_020097155.1_01454
+MFTSVEDVLAYIKDEGVEFVDIRFTDLPGMQHHFNVPASTVDEDFFVTGQLFDGSSIRGF
+AGLAESDMQLIPDVTTAFVDPFRVRKTLAMNFSIVNPRTGEDYRRDPRGVAQRAEAYLAS
+TGIADTAFFAPEAEFYVFDDVRYESSARSSFYRVDSTEAHWNTSRDEEGGNLGHKTPRQG
+GYFPVTPVDKQADLRDEICAVLAEVGLEVERSHHEVGSAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVAEMFGKSVTFMPKPVFGEAGSGMHCHQSLWLGGEPLFYDEKGYANLSDTARW
+YIGGLLQHASAVLAFTNPTVNSYRRLVPGFEAPVSMVYSQGNRSAGVRIPVTGSNPKAKR
+LEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPPEEAADIQKAPTSLE
+EALNALEEDHEFLLAGDVFTEELIRTWIDYKREMELTPLAARPNPYEFELYYSC
+>GCF_023573625.1_01289
+MFTSPQEVLTYIREEGVEFVDVRFTDLPGLQHHFNVPASSVDEDFFVTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICAVLAEVGLTVERSHHEVGAPGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001119.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001119.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94c944dcf95120abab4159b5cbaf3f393f530c54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001119.fa
@@ -0,0 +1,95 @@
+>GCF_002008305.4_01335
+MSSLSTTGALPAVPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRA
+LLLWVRLAEREPRVHHALRDPETTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAAT
+APALAQPDPADGEPWGDASATLRRLLLDSVGADPDTDRPVAAVTGKDAAVALRRAYRRQL
+AAIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIG
+MGKCGAGELNYVSDVDVVFAHAVREAADGADPDAEVPDGPRAAALAAELAAGIGRVIQGA
+APEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGER
+YIAEIWPRVWESSSRDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQ
+LVHGRADESLRVRGTLDAVRALHAASYITTRDARAFDEHYRWLRTLEHRIQLVHLRRTHL
+MPVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALS
+AEDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGAD
+PDGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVG
+DDRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLE
+AVTGALSDIDQVTVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVH
+RPRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLD
+SYREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTADAREIRRIKA
+RVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTLPALRAIARH
+GLLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGGELE
+ERYLRVTRLARQVFETRFYGL
+>GCF_003691675.1_01056
+MSALPDAATADAPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRAL
+LLWVRLAEREPRVHHALRDPGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATA
+PALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPLAAVTGKDAAVALRRAYRRQLA
+AIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIGM
+GKCGAGELNYVSDVDVVFAHAVREAADGADPDAQVPDGPRAAALAAELAAGIGRVIQGAA
+PEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERY
+IAEIWPRVWESSARDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQL
+VHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRIQLVHLRRTHLM
+PVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSA
+EDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADP
+DGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVGD
+DRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLEA
+VTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHR
+PRPGVDEGRAREQAEEVVRTLMALLQKPVAPPLPGERRLEVDADLRPEGRQGPLVRTLDS
+YREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAQDLSAADAREIRRIKAR
+VEAERLPRGADPARHVKLGRGGLSDVEWLVQSMQLKHAGQIEDLRVTGTLPALRAIARHD
+LLPESEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTTGGELEE
+RYLRVTRLARQVFETRFYGL
+>GCF_005280335.1_01556
+MSALPDAATADAPDRRALAQAGVADARRVQSLLASPEFEGADVAPLVKRLGHAADPDRAL
+LLWVRLAEREPRVHRALRDPETTARLLRLLGASEALGEFLIRRPEHLDLVLEPESAAATA
+PALAQPDPADGEEWADEPAALRRLLLEAVEADPDADRPRAGLTGADAAVALRRAYRRQLA
+AIALRDLDSADPAAVMPSVGRWLADLAGAAVDAALAVSRATLAEREGPAVDRVDLAVIGM
+GKCGARELNYISDVDVVFVHELLDPGPDAAGEAGADGADGEASDAVDGTRAAVLAAELAA
+GIGRVIQAAAPEPGLWEVDANLRPEGKDGALSRTLDSHAEYYRRWAHGWEFQALLKARPI
+AGSADLGARYLERIWPRVWESSAREGFVDSVRAMRSRVLETIAPAEREREIKLGSGGLRD
+VEFTAQLLQLVHGRADESIRVRGTLDAVRALHEASYISTRDAAAFDEHYRWLRTLEHRIQ
+LVHLRRTHLMPVKDEALRIVARSLRGAQETGPATGEDLQAAFTRVRRAVRGLHETVFYRP
+LLSTTAALSDDEVRLSAEAVRERLAALGYRDPKGALRHIEALTQGVSRRAAIQRQLLPAM
+LGWFAEGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLAASRFVGDLLEH
+SPEAVAWVGDDRELEPRGTVQLWRQADARLDRRIEAQETPAAVRHVRQVRRSETLRVALA
+DISGLLDLEAVTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYG
+SDLDALFVHRPRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGR
+QGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTAD
+AREIRRIKARVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTL
+PALRAIARHGLLPEAEVAVLEEAWLLASRIRAAVLLWTGKVGDVLPTNMRDLEAIARLSG
+VGTAGGELEERYLRVTRLARQVFEARFYGL
+>GCF_020097155.1_01452
+MAPTPDSHVPGPRRALVHAGVADLTRAERLLSSPELAEQDADAALAALAHAADPDSALLL
+YIRLAERDPQVHRVLAEADRARDLLRLLGASEALGEFLIRRPEHLDLVLDPARAAATAPA
+LAQQDPTDGGDWHDEPAALRALLLEAVGADPAADQPVAGLTGADASVALRRAYRRQLTAI
+ALADLASREPTLVMPAVGRWLADLAGAALEAALAVSRAELRAREGAAVDCVELAVIGMGK
+CGARELNYVSDVDVVFVHDVLEPGAPDAPSAQEAARLAAELAAGISRVLSGPAPEPGLWE
+VDANLRPEGRDGALSRTLDSHVEYYRRWAHGWEFQALLKARPVAGSPALGERYVAAVWPR
+VWESSAREGFVENVRAMRTRVLDTIARDERDREIKLGAGGLRDVEFTAQLVQLVHGRADE
+SVRVRGTLDALRVLHAASYISSRDMRAFDAAYRWLRLLEHRIQLVHLRRTHLMPVKEGPR
+RVVARSMRGAGDVHPVAGDDLQDRFSRVRREVRALHETVFYRPLLSTTAALSDEDVRLSA
+DAVQARLSALGYRDPRRALAHIEALTRGVSRRAAVQRQLLPAMLGWFADGADPDAGLLAF
+RRLSESLGSSPWFLRMLRDSTDAARRLCLVLAGSRRVGDLLEHAPESVAWIGETRELAPR
+GLSALTSEVTARLDRRSPEESAAQVIRHVRQIRQREILRTALADITGVVGLEEVGHALAD
+VDQAAVQGALRVAGQAVLDGADPLTEVVVVAMGRQGGREIAYGSDLDAMFVHRPLAGADE
+TAAAAQAEAVARQLMALLQQPAAPPLPSEQPLDVDADLRPEGRQGPLVRTLDSYREYYAR
+WAEVWERQALLRARVVAGPAGLAEEFTAWADGVRYGDELSAGDAREIRRIKARVEAERLP
+RGADPARHVKLGRGGLSDVEWLVQSLQLRHAHDEPELRVTGTLPALRALARLDLLPPSEA
+ALLEEAWLLATRVRSALVLWTGKGSDVLPTNARDLGALARLAGDACGGGVAFEERYLRVT
+RQARQVFEQRFYGL
+>GCF_023573625.1_01291
+MSALPDAATADAPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRAL
+LLWVRLAEREPRVHHALRDPGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATA
+PALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPLAAVTGKDAAVALRRAYRRQLA
+AIALRDLDSAEPTAAMPSVGRWLADLAGAAVDAALAVSRAVLTEREGPVVDRVDLAVIGM
+GKCGAGELNYVSDVDVVFAHAVREAADGADPDAQVPDGPRAAALAAELAAGIGRVIQGAA
+PEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERY
+IAEIWPRVWESSARDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQL
+VHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRIQLVHLRRTHLM
+PVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSA
+EDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADP
+DGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVGD
+DRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLEA
+VTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHR
+PRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLDS
+YREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTADAREIRRIKAR
+VEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTLPALRAIARHG
+LLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGGELEE
+RYLRVTRLARQVFETRFYGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001120.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9138eafc449a40e8d75f807df3db3e9f64528f4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001120.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01336
+MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPSTFQILPWRGDQGQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD
+RGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSHHPG
+SGMHTHFSLFEGDANAFYDPADEFRLSVTGRRFIAGLLRHSVEITAVTHQFVNSYKRLWG
+GGEAPSYTSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLIAAGLKGI
+EEGYEVPEAAAEDISALTTHERRVLGHVPLPGTLHDALRTAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
+>GCF_003691675.1_01057
+MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPSTFQILPWRGDQGQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD
+QGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSEHPG
+SGMHTHISLFEGDSNAFYDPADEFRLSVTGRRFIAGLLRHSVEISAVTHQFVNSYKRLWG
+GGEAPSYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLIAAGLKGI
+EEGYELPESAAEDVSALTTHERRVLGHVPLPGTLHDALRAAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
+>GCF_005280335.1_01555
+MDRQQDYVLRTIEDRDVRFVRLWFTDVVGTLKSVALSPAEVENAFAEGLGFDGSSIDGYT
+RISESDMLLQPDPATFQILPWRGDGGQSSRMFCDVLTPDGRPAPADPRHVLRRVLEKASD
+MGFSCFMHPEIEFYLLTSDQPGPDGRPVPVDRAGYFDNVPGSDAADFRRDAVTLLESMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSEHPG
+SGMHTHISLFEGDSNAFYDPADEFRLSVTGRRFIAGLLRHSVEISAVTHQFVNSYKRLWG
+GGEAPSYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLLAAGLKGI
+EEGYELPESAAEDVSALTTHERRVLGHDPLPGTLHDALRAAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
+>GCF_020097155.1_01451
+MDRQQDFVLRTIEDRDVRFVRLWFTDVIGTLKSVALAPAEVEAAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPATFQILPWRGEAGQTSRMFCDVLTPDGRPAPADPRNVLRRVLDKASD
+MGFSCYTHPEIEFYLLASDRPGPDGRPVPVDSAGYFDHVPGGAAQDFRRDAVTLLEDMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVQTFRTIMKEVAARQGHYATFMPKPFGDQPG
+SGMHTHFSLFEGDSNAFYDPADEFRLSVTGRRFIAGLLKHSVEISLVTHQFVNSYKRLWG
+ADEAPAYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGLDASANPYLAYALLLAAGLKGV
+EENYDLPEPASEDVGALTPQERRVLGHVSLPGTLHDAVRAAEESEFVADVLGEHVYEALL
+RNKRQEWDDYRVEITPYELRRYMTGL
+>GCF_023573625.1_01292
+MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPSTFQILPWRGDQEQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD
+RGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSHHPG
+SGMHTHFSLFEGDANAFYDPADEFRLSVTGRRFIAGLLRHSVEITAVTHQFVNSYKRLWG
+GGEAPSYTSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLLAAGLKGI
+EEGYELPESAAEDVSALTTHERRVLGHVPLPGTLHDALRAAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001121.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001121.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72dfd8a134a9914e561e9e0cadcd80f95ba6ba02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001121.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01338
+MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV
+LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES
+AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG
+AVERMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM
+LGLREGRVPRFVRQYARLHEVVGDAVRAYRADVLDGAFPAPEHGFQG
+>GCF_003691675.1_01058
+MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV
+LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES
+AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG
+AAERMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM
+LGLREGRVPRFVRQYARLHEVVGEAVRAYRADVLDGAFPAPEHGFEG
+>GCF_005280335.1_01554
+MLTAYDAMTAALFDEAGIEVLLVGDSVGNTVLGHSSTLPVTLDQMILFSQAVVRGAQRAL
+VVADLPFGSYEASPQQAVESAVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVIAHIG
+FTPQSEHVIGGYRVQGRGEGAVEAMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVP
+TVGIGAGPGTTGQVLVWQDMLGLREGRTPRFVRQYARLHEVIGAGVRAYRRDVLDGAFPA
+PEHGFEA
+>GCF_020097155.1_01450
+MDSRTVTPPASSPAASEAAAPYGGAATAAAAAPVEAPARYRTVHLQRAKDEGRRFAMLTT
+YDAMTAALFDEAGVEVLLVGDSLGNTVLGHGSTLPVTLEDMIVFSAAVARGARRAFVLAD
+LPFGSYEASPEQAVRAGVRLMKEAGVHGVKVEGDERFAPHIAAMVAAGVPVMGHIGFTPQ
+SEHVLGGYRVQGRGEGAAERLIASARALEDAGAFAVLMEMVPSDVAAAVDAALRVPTVGI
+GAGPKTTGQVLVWQDMLGLGAGRTPRFVKRYADLRAVMGDAVRAYRADVLSGAFPDPAHA
+FES
+>GCF_023573625.1_01293
+MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV
+LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES
+AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG
+AAERMTVSARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM
+LGLREGRVPRFVRQYARLHEVVGEAVRAYRADVLDGAFPAPEHGFEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001122.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001122.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49578f24720d38047ab32de9a6301202a9aef4d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001122.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01339
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNETADAWDERDDD
+WDSRPVDDAS
+>GCF_003691675.1_01059
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNEAADAEDARDDD
+WDSRPVDDAS
+>GCF_005280335.1_01553
+MSEKSEYWYNVRTQQVEEGAQSDWSQLLGPFGTREEAQGAMSRVQANNEAADAADERDDN
+WDNNPFNDAD
+>GCF_020097155.1_01449
+MTDTHEPGSGYWFNVRTHQIEEGPQSDWKELLGPYQTRQDAENALARVQARNEAADAEDA
+HDDAWDASPLNDAS
+>GCF_023573625.1_01294
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNEAADAEDARDDD
+WDSRPVDDAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001123.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001123.fa
new file mode 100644
index 0000000000000000000000000000000000000000..912e772a7f03e79188bfd1231a2227213f1c379b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001123.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01340
+MSQRQNPVAPSSHNGPRPAGPTAPEPGSFAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGKASDVYDAAGVERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
+>GCF_003691675.1_01060
+MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGNASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
+>GCF_005280335.1_01552
+MSHRQSTASPSSHNGPRPEGPAAPQPGSLAPVGTLTPGAPSPAPPVPASIPRPEYVGRAT
+ADEGNASDVYDAAGIERIRAAGRLAARAMEHTAAYIRPGVTTDELDRIAHAYLVEHGAYP
+SCLGYRGFPRSICTSMNEVICHGIPDSTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLEPGMVFTIEPMLTLGTIDWDQWDDGWTVVTRDRRRTAQFEHT
+LVVTDDGAEILTLP
+>GCF_020097155.1_01448
+MSTTARPTSQPSHNGPRPEGPPAPEPGSRAPLGTLTPGAPSPAPAVPASIVRPEYVGRAT
+ADEGNASDVYDTEGIGRIREAGRIAAQAMEHTAEHIRPGITTDELDRIAHEFIVAAGAYP
+SCLGYRGFPRSICTSVNEVICHGIPDGTVLEDGDIVNLDITAYKDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIKAVKPGREINVIGRAIESYARRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHNRLMVPGMVFTIEPMITLGGIDWEQWDDGWTVVTKDRRRTAQFEHT
+LVVTEDGAEILTLP
+>GCF_023573625.1_01295
+MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGKASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001124.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001124.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4327e4641749b8d65e2a1654cdb88dc834fe13b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001124.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01342
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
+>GCF_003691675.1_01062
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
+>GCF_005280335.1_01550
+MHCPFCRHEDSRVVDSRSLEDGSAIRRRRQCQSCGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRASGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFADAIAELRAGTDERGRPAVQPRLFSR
+>GCF_020097155.1_01446
+MHCPYCRHEDSRVVDSRSLEDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVSSDDLAVLAQEVEEAVRASGNAEVDAHEVGLAILGPLRRLDQVA
+YLRFASVYRDFESLSDFEDAIAELRAQEGEAPGRPAVQPRLFSR
+>GCF_023573625.1_01297
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001125.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001125.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0d36c83fe62e1902f253e7bf23b5b7e8205f8a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001125.fa
@@ -0,0 +1,105 @@
+>GCF_002008305.4_01343
+MTVSADARPDAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG
+AYDFWSKAKAAGVKPIIGLEAYVAPGQQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ
+YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSVPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREEKGSYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD
+LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD
+VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV
+MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG
+>GCF_003691675.1_01063
+MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG
+AYDFWSKAKAAGVKPIIGLEAYVAPGHQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ
+YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVVTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSAPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGRENEGSYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD
+LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD
+VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV
+MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG
+>GCF_005280335.1_01549
+MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAERLGMDSLAITDHGYLFG
+AYDFWSQAKSAGIRPIIGLEAYVTPGHQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SENTAGMHNLFRMSSIASLDSVYAKWPRLDRELLSQYSSGLIATTGCPSGEVQTRLRLGQ
+YDEAVAAAAEFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCDVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRPEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSLGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSEPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDAIENVKANQGVELDLETLDVDDAASYDLLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREDKGAYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVSQKRKEDHGEFTFD
+LFALGGPQEDESDAADGVAVPDLPEWAKKEKLAYEREMLGLYVSDHPLQGLDGVLAQHAD
+TQITRVLDDDGPADGSQVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRISMPSFKATEQV
+VGQLADVLRTHEGSSEVRLSLVGQRGTQEFQLGPQFRVNPNPALFGDLKILLGPACLS
+>GCF_020097155.1_01445
+MSVQQETTAEATRDGGFVHLHTHTEYSMLDGAAKLDELFAEANRLGMDSLAITDHGYLFG
+AFDFWKKATDAGIKPIIGLEAYLTPGQQHRSDKEKIRWGEPHQRGDDVSGGGAYTHMTML
+AESTQGMHNLFRMGSIASLDSVYAKWPRIDRELLSQYSSGLIATTGCPSGEVQTRLRLGQ
+YKEAVEAAAEFRDIFGRDNFYCEVMQHGLDIEKRVVEDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLAIQSGSKLNEPTYDQGGSRFAFSGTDYYLKSPRQMRELFAELPEACDNT
+LLIAERCETSFDTSANYMPRFPTPEGEDETSWLIKEVAKGLAYRYPEGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLRHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPEAKRYAEAGEFRELVAADPVAKQVFETA
+KGIEGLKRQWGVHAAGVIMSSHPVIDVIPIMRRLQDGQVITQFDYPTAEGLGLIKMDFLG
+LRNLTIISDAIENIRANRGVDLDLEHLDVDDAESYALLARGDTLGVFQLDGGPMRALLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGLQEITPIHPELAEPLKDILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEGAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESFLNFTPVGDDIRFGMGAVRNVGGNVVKGMVQAREEKGLYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVQQKRKEDHGEFTFD
+LFALGGAADAADDSDASDGVAVPDLPEWPKKERLAFEREMLGLYVSDHPLQGLDGVLSQF
+ADTQITRILDDDGPADGAHVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSLDVMFFGQ
+VYAPIAMMLAEDLVVAVKGRVQRRDDGSVVLSAMELAIPELTDATGGPVRITMPAFKATE
+RVVGQLGDVLRTHEGSTEVRLSLTGQRGVQEFQLGPQYRVTPNPALFGDLKILLGPSCLG
+>GCF_023573625.1_01298
+MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG
+AYDFWSKATAAGVKPIIGLEAYVAPGQQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ
+YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSVPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREEKGSYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD
+LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD
+VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV
+MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001126.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001126.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14b59d1583f7039a435639774346052e95bd494d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001126.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01344
+MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLEDGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDED
+>GCF_003691675.1_01064
+MGMRPGLTERLQVAEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYATLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDED
+>GCF_005280335.1_01548
+MEPIPGATARIEVTPDRAGRRADAVLAEVLGLSRSALADWFSRGLVRAESRTGRRDRVLA
+KSAKAVAGEVLAVDVPDDPDPLEVRAERVDALRILHEDEHLIAVDKPTGVAAHPSPGWAG
+PTVVGALAALGHDISTSGAPERQGIVHRLDVGTTGVMVVAKTEQAYAALKDQFRRRVPEK
+VYHALVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDGGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLSFPHPVTGEPVSV
+TSEHPDDLAHALARLRRDGS
+>GCF_020097155.1_01444
+MGLRPGLTERLAVTEDDAGRRADAVLADAFGVSRASLADLFSRGLVRAESRTGRRDRVLA
+KSAKAVAGETLAVDVPVDPDPLEVRAERVDAMTVLYEDDDLLAVDKPTGVAAHPSPGWFG
+PTVVGGLAGLGRRISTSGAPERQGIVHRLDVGTTGVMVVAKSERAYTALKDQFRERVPEK
+VYHAVVQGMPDPLEGTIDAPIGRDPNHHWRFAVLEGGRPSVTHYETVEAFGRATLLEIHL
+ETGRTHQIRVHTSALRHPCAGDLTYGADPRLAAELGLTRQWLHAHRLALPHPATGERLEI
+VSPYPDDLAHALRVLRGEDRGAAPDA
+>GCF_023573625.1_01299
+MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGRDISTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRMAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001128.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001128.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d37984f6b59235ba391f5ad7618736f8ab7147b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001128.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01346
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APAAGPAADTPEAAATPASAEESAPAAAPESADAAATSAAGVLAMAQRLHDEHVAAGEQR
+STELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQLRSFETDYRSRLTSYIE
+GQLREIRAQKRVEPPTPTA
+>GCF_003691675.1_01066
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APVADTPEAAETPSPVEEPAPAAAPEAADAAATSAAGVLAMAQRLHDEHVAAGEQRSTEL
+VAEAEATAARLVSDAEEQKARTLEALAEERAGLEGEVEQLRSFETDYRSRLTSYIEGQLR
+EIRAQKRVEPPTPTA
+>GCF_005280335.1_01546
+MALSWEDVVNKQFQPTKFREGYDQGEVDDFLDEIVGELKRLQGLNEQLTAENEALRAGGA
+VPDADAAVDAPVADADAAAVVDAGQSPAPAALADAEPGLEVEPTPSSADPASASAAGVLA
+MAQRVHDEHVAAGEQRRDELISEAEARAEALVAEAEETRTRTLEELAADKAGLEAEVEQL
+RGFETDYRSRLTAYIEGQLREIRSQERVEPAQRPA
+>GCF_020097155.1_01442
+MVLSWEDVVNKEFQLTKFREGYDREEVEDFLDEVVEELKRLTEENDRLRSDLDACREGAP
+AQAEASAPAAGEAAPALQAPAPVAPVEPSAPGEPVAPTDSATSAAGVLAMAQRLHDEYVA
+EGEQRRDRIIADAEAEATTVVRQAEETRTRTLSDLESRRKGLEADVERLRAFETDYRSRL
+TAYIEGQLREITAQERLEPAKGTV
+>GCF_023573625.1_01301
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APAAAPAADTPEAAATPASVEEAAPAAAPESADAAATSAAGVLAMAQRLHDEHVAAGEQR
+STELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQLRSFETDYRSRLTSYIE
+GQLREIRAQKRVEPPTPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001130.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001130.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e486d444fa9f70af565ef2c192b3b958dcde8c1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001130.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01348
+MAGALKKTMIYLGLADGDEYDEQPRAAERETAPRHEVVEARRPAEPDTDPHMEAVRPAAV
+RDPEPAERPEPVTPSGSTAADPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT
+LSTVHPRSYNDAKAIGEAFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS
+KVFLLTPATVDVVGAEQGESGAADSPFDGD
+>GCF_003691675.1_01068
+MAGALKKTMIYLGLADGDEYDEQPRAAEREAAPRHEVVEARRPAEPDTDPHMEAVRPAAV
+RDPEPAERPEPVTPSGSTAAEPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT
+LSTVHPRSYNDAKAIGESFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS
+KVFLLTPATVDVVGAEQGESGVADSPFDGD
+>GCF_005280335.1_01544
+MAGALKKTMIYLGLADGEEYDEQQRAAERDAAERRDVVEARRAAEPDTDPSMEPVRSATV
+VRPESIERAESPAPSGSTAAAPAEPAELRRSSRPEPVDPGYRAPVTPIKRAAASSAEGAP
+VSTLSTVHPRSYNDAKAIGEAFRSGMPVIMNVTELGENEAKRLVDFAAGLVFGLHGSISR
+ITSKVFLLTPANVDVVGAEQGDAEESGDPYDGD
+>GCF_020097155.1_01440
+MAGGLKKTMIYLGLADGDEYDDDPRHEAVDAAPRREPVEARRVAEPAPRLEPEDEEFDEP
+STPSHAGSTAAAAAEPAPRRAASRPETADPGHRAPVTPIKRAAAPSAEGDAVRTLSTVHP
+RSYNDAKRIGEAFRTGTPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITSKVFLLT
+PSSVEVVGEEPPAGRDGDAPYDND
+>GCF_023573625.1_01303
+MAGALKKTMIYLGLADGDEYDEQPRATEREAAPRHEVVEARRPAEPDTDPHMEAVRPAAV
+RDPEPAERPEPVTPSGSTAADPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT
+LSTVHPRSYNDAKAIGEAFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS
+KVFLLTPATVDVVGAEQGESGAADSPFDGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001132.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001132.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19fc39f598d3a82e0be29dab358aedf6ad90291f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001132.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01350
+MTAAEGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGLARVS
+AARRALERVMGVPEGATLYLDQVHSADVVWADGPGRGGASAPVADAAVSRDGSRPLAVMV
+ADCLPVVVVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPEADRTGPGLRAWIGPGV
+CGRCYEVPAAMRDEAAARLPATAATTSWGTPALDLPAGAAEVLRARGVATATIDVCTRED
+ERLFSHRRAPGEGRFAGLVWRADPDATVPRGDA
+>GCF_003691675.1_01070
+MTAAGGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGPARVS
+AARRALERMMGVPEGATLYLDQVHSADVVWADGPGRGGAPAPVADAAVSRDGSRPLAVMV
+ADCLPVVVVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPETDRTGPGLRAWIGPGV
+CGRCYEVPAAMRAEAAARLPATAATTSWGTPALDLPAGAAQVLRARGVATATIDVCTRED
+ERLFSHRRAPGEGRFAGLVWRADPDATTPRGEA
+>GCF_005280335.1_01542
+MTAAEGPVGTVPVPAGPFVHREAVATAGGTVHVAWSGVAAGNLGLHVVADEDAAGRRAVG
+EARRGLERAMGVPVGSTLYLDQVHSADAVWADGPGWGEEAGPTADAAVSRDGGRALAVMV
+ADCLPVVLVDEATGATAVAHAGRRGLVDGVLEGTVDRLLSLRPADRRDAPGLRAWIGPGV
+CGRCYEVPEQMRAEAAERVPATAATTAWGTPGLDLPAGAVAILRGRGADVAVVQACTLED
+ERLFSHRRAPGQGRFAGLVWRADEDASTPTRAA
+>GCF_020097155.1_01438
+MSLAGGPVGTQPVPSGPFVHREDLRADARGRVAHVAWTSAEAGSLAFHILGAEQEQARAD
+VVAARHRVEDAMGVPRGSVFYLEQVHSVDVVTAGPGWEEGFAPTADASVSPDGHTPLAVM
+VADCLPVVFVDGLTGATAVAHAGRRGLLDGVLENTVDALLALRPEGSAGAFGLKAWIGPG
+ISGESYEVPQAMQDEAVARIPELEATTSWGTPALALASGAQAVLRARGVAVERIALDTFT
+DERVFSHRRAPGRGRFAGLVWTTPADVDQDHDAGDARG
+>GCF_023573625.1_01305
+MTAAEGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGLARVS
+AARRALERAMGVPEDATLYLDQVHSADVVWADGPGRGGAPAPVADAAVSRDGSRPLAVMV
+ADCLPVVFVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPETDRTGPGLRAWIGPGV
+CGRCYEVPAAMRTEAAARLPATAATTSWGTPALDLSAGAAQVLRARGVTTATIDVCTRED
+ERLFSHRRAPGEGRFAGLVWRTDLDATTPRGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001133.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001133.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c3fe2d7743f85ddf394ad0f0e44196c2a773b7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001133.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_01351
+MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR
+ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS
+LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF
+RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL
+AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG
+DEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPAQPQPAAQPQPAAPAQPQQAE
+RPAVRGTVPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK
+>GCF_003691675.1_01071
+MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR
+ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS
+LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF
+RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL
+AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG
+DEVRVTVIAAGFDKVDVTSAPAAPQAAQQQAAPQRAAAPAQPQPVPAQPQQAERPAVRGT
+VPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK
+>GCF_005280335.1_01541
+MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDATSAPASPQAGQFQQAPQRPAQQAQPQQQAPAPQQHQAQPA
+QQEQPQQVQPQSVRGTVPLAPQQPQQTEQRRQQDLPTVVEPDLGAGSSDLDVPDFLK
+>GCF_020097155.1_01437
+MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAENGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDATSAPAAPFQQQAAPQRAAAPQQPAQQAQQAPVSQQAAPQR
+PSVPGTMPLNSSSAFGGAPAQPAATQQPAAPQQPAAPQRAQQDLPTVVEPEFGSSDLDVP
+DFLK
+>GCF_023573625.1_01306
+MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR
+ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS
+LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF
+RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL
+AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG
+DEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPTQPHPVPAQPQPAPAQPQPAP
+AQPQQAERPAVRGTVPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001134.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001134.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15f9f8f22e4a715a126617f526c1e15e4ce05e00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001134.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01352
+MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLGALGWVVFFSPVLA
+VDRVEVTGTRHVSAAEVQERLEPVYGVPLSRVGAGRVGELVGGLPGVAEVQTVPRLPTGL
+EVVVREHETRARRDGDDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELAQRAQEERAEV
+AEVLAALPEAVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGPVAEAFLADERH
+GSAEGGVAEIDVSVPTRPITR
+>GCF_003691675.1_01072
+MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLTALGWVVFFSPVLA
+VDRVEVTGTRHVSATDVQERLAPVYGVPLSRVGAGRVGELAGGLPGVAEVQTVPRLPTGL
+EVVVREHEARARRDGGDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELAQRVQEERAEV
+AEVLAALPESVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGSVAEAFLADERH
+GSAEAGVAEIDISVPTRPITR
+>GCF_005280335.1_01540
+MTPGRGGRPPRPAGPAQPPAGSTVVPFPGRSVRRRRAVRWAVAGAVAALLGALAWVLLFS
+PVLAVDEVDVTGTRHVSAEAVQERLAPLHGVPLPRVGSSAVRELVGDLPGVAEVRVVAHP
+PTRVEAAVREHEARARRGGEAGVDLLLDDGTVLAGVPAERVEGESLPEFSEELSAGPRRD
+REEVAAVLAGLPAPVAERVESVDSSRAGQVRLGLRDGVVLVWGDAEDAELKGTVATAFLE
+GDQHGSRAGGVREVDVSVPTRPITR
+>GCF_020097155.1_01436
+MVAFPGRSARERRRRRAGMLAAVFAALALAAWAVFASPLLAVDRIDVTGTRLVDRAAVEE
+RVAPLRGVPLPRIGSSSAGDLLSGMPGVASARTVAVPPTALEVRIEELAPVARSAGGDRA
+QVLLEDGSVLGSVPVSALPGEGEEGGALPSAPEALLTAGPDVRASAATVLRALPDGVRDR
+VRGVDAGSPEQVRLDLGGGRTLVWGDASEPERKAAVAQALLDGLEDARGVREVDVSVPDR
+PVTR
+>GCF_023573625.1_01307
+MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLTVLGWVVFFSPVLA
+VDRVEVTGTRHVSATDVQERLEPVYGVPLSRVGAGRVGELVGGLPGVAEVQTVPRLPTGL
+EVAVREHEARARRDGDDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELPQRAQEERAEV
+AEVLAALPESVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGSVAEAFLADERH
+GSAEGGVAEIDVSVPTRPITR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001137.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001137.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0aec465f1b4b827f723b90e8f5812ab30bfb501
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001137.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01355
+MSPIELRPVRPRAADDAPEHRERILRRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVLKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLVLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR
+>GCF_003691675.1_01075
+MSPIELRPVRPRADDDAPEHRERLLHRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLGLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQASVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR
+>GCF_005280335.1_01537
+MSPTELHPVRTPADEEETEARSRPLQRLWRLVEGRRALDLSVLLIGGSTFLLTALGLVMV
+LSSSSVEAIGTGGGSYGLFLRQTMWAVAGLAALLLFSRLPIGWIKALAWPAFGLAVVLLS
+LVAFTPLGVTVGGNTNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALVPV
+LPGGLLLIGLVMAGSDLGTAIILALVLAAVLFVAGTHHGVFIAFSAVTVVGAIALTLLAP
+HRMVRVQAWLGDCSDASDPCFQPDHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLGVLLAYLALAVGMYRVAAGTTSPFIRLATWGIMAWLVGQAFVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLTAVGIVLAFARHERRRAEEPDARPDADDPDTDPLPV
+IPAPASQES
+>GCF_020097155.1_01433
+MPSTATRPEASSRASARTAVRPRLAGFWGALEGRRALDWAALLIGLCTAVLTVLGLVMVL
+SASSVEAISSSGGSYGLFLRQGGWALGGAVLLAVLRRLPVDLYRRLAWAAYLFAFLLLAL
+VAFTPLGKEVNGNTNWLQLGPVTFQPSEAAKLAMALWAAAVLQRKERLVHLVSHALVPVL
+PFGVALILLVLKGRDLGTALILAFILAVILFVAGTPGRVFAVLAGIGVVAALGMTVFAAN
+RMERVQAWLFGCEGLQGDPCMQPDHGIYALASGGWWGVGLGQSRQKWNYIPEAENDFIFT
+ILGEELGLVGTLLVLACFVGLAVGMYRVAAGASSTFVRLATWGILAWIVGQAAMNIAMVT
+GLLPVVGVPLPFISYGGSALTLSLAAVGVVLSFARHERDLLPAAEASAADPASSASPQES
+R
+>GCF_023573625.1_01310
+MSPIELRPVRPRADDDAPEHRERLLPRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLILVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSMLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001140.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001140.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6799dc151ebf3dc4d8100b0bd4d97a3dfd8562bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001140.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01359
+MTTPSDPPAPLTPAQQDAAFRPSHTPAAAWPALAQALAEAGIAAHVHGAAPADGVTGVSL
+DSRVVRPGDLYVAVPGARAHGAAFAATALEAGAVGVLTDAAGRALLAEQGLADVPVLEVD
+AVRTAAGTVAARVYGGGGDTGPRLLGVTGTNGKTTTSFLAAALLEALGRRSGIVGTILIR
+AGEREVPSTLTTPEATQLHALMALMREEEVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL
+TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG
+PAAPTPGALAEHDPGLRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA
+ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM
+VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVLIVTDDTPHSED
+PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRATAIRRAVELAGPQDGILLAGRGHE
+TTMDYDGELVPLDDRVALREALAARVAAASASGSGPAREGKVIES
+>GCF_003691675.1_01079
+MTTPSDPPAPLTPAQQDAAFRPSHTPATPWPALAQSLAGAGIAAHVHGAAPADGVTGVSL
+DSRVVRPGDLYVAVPGAHAHGAAFAARALEAGAVGVLTDAAGRALLAEQDLADAPVLEAD
+AVRTAAGTVAARVYGGGGDAGPRLVGVTGTNGKTTTSFLAAALLEALGHRSGIVGTILIR
+AGEREVPSTLTTPEATQLHALMALMREEQVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL
+TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG
+PAAPTPGALAEHDPGVRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA
+ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM
+VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVVIVTDDTPHSED
+PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRAAAIRRAVELAGPQDGILLAGRGHE
+TTMDYDGELVPLDDRVALREALAAGAAVASASVSGPVREGKVIES
+>GCF_005280335.1_01534
+MSSQPAQPQPLTPAQQDDAFRPSRTPATPWDELTRALQAAGVAARTHGRGPAAGVTGACL
+DSRVVRPGDLYVALPGARSHGADFARAAVDAGAAGVLTDAEGRARLAEQGLDGSAVIEVD
+SVRTAAGVVAARVYGGGQDAGPRLIGITGTNGKTTTSFLAAALLEALDRRSGVIGTILIR
+AGGREVPSTLTTPESTQLHALMALMREEQVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL
+TRDHLDMHGSMEEYFEAKAGLFDPERTARAVITVDGGEGPRWGLSMARAVRTPVTTLALG
+PAAPHPGALAEEDPDFRADWEIAELVPDGLGHRFTLRHGATGRALRASVGLPGRFNAANA
+ALAVLLVLYAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGRAPDAVVDFAHNPDGM
+VQALRSLADAREAAGRSGRTLIVFGSAGDRDREKRPIMGEIAARAADVVIVTDDTPHTED
+PAPIRAQILEGARAEAARLLQAEGRTVLVEEVADRAVAIRRAAELAAPQDGILVAGRGHE
+TTMDYDGELVPLDDRQALREALAARAAAASPRASDPGSGAPRGGKVDES
+>GCF_020097155.1_01429
+MTDDAPQTTAPLTPAEQDAAFRPAAVTPVAWAEVAAALRAAGQDVRERSAAAAPAVTGAA
+LDSRVVRPGDLYVALPGARAHGAAFAAAAREAGAAGVLTDGDGVALLAEQGLDDLPVLEV
+ESVRAAAGVAAARIYGGGPDAGPRLLGVTGTNGKTTTSFLAASIVEALGERSGIIGTILT
+RAGDRQVPSTLTTPESAQLHALMALMRQEGVDTAVMEVSSHAVEYRRIAGLHYAVAGFTN
+LTQDHLDQHGTMEGYFRAKLGLFEADRTDRAVVVLDGGEGPRWGVKTARRAGAPVTTLAL
+GAASPTPGALAEEHPDVVPDWQVTDLVADGLGHRFALVHAATGRRLPASVGLPGLFNVAN
+AALAALMVLESIGEDRLDELAAVLDVPAGTGPLAAAVPGRMEVVGREPDAVVDFAHNPDG
+MVQALRALGDARAAAGRAGRTLIVFGAAGDRDATKRPLMGRIAAEHADVVIVTDDTPHTE
+DPAPIRAQLLEGAREEAARAAAAGREVRVEEFADRAAAIRRAAELAAPEDGILVAGRGHE
+TEMDYDGTLVPLDDRVALRDALAARRPGDAQEPGVAGGKVAGK
+>GCF_023573625.1_01314
+MTTPSDPPAPLTPAQQDAAFRPSHTPATPWPALAHALAEAGIAAHVHGAAPADGVTGVSL
+DSRVVRPGDLYVAVPGARAHGAAFAATALEAGAVGVLTDAAGRALLAEQGLVDVPVLEVD
+AVRTAAGTVAARVYGGGGDAGPRLVGVTGTNGKTTTSFLAAALLEALGRRSGIVGTILIR
+AGEREVPSTLTTPEATQLHALMALMREEEVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL
+TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG
+PAAPTPGALAEHDPGLRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA
+ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM
+VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVLIVTDDTPHSED
+PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRATAIRRAVELAGPQDGILLAGRGHE
+TTMDYDGELVPLDDRVALREALAARVAAASASGSGPAREGKVIES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001141.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001141.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1c8889566ace8f6a6a3f65160fc35a113c155bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001141.fa
@@ -0,0 +1,57 @@
+>GCF_002008305.4_01360
+MRTRILLLLVFVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV
+LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS
+RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE
+LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL
+AAEYEAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA
+LPIAAAVDAGKVTATDGFTVPGSQDFDGQTIRDFSPHPTFDMTVAGIYARSYNTGTVQIA
+EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEQWDGRQRLTTAFGQGYTQTTLHT
+AQMYQALANGGVLIPARLIDATVDGDGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ
+GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNLGFTAVAPLDDPRFVVSVSMHRPPSKQ
+GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW
+>GCF_003691675.1_01080
+MRTRILLLLVLVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV
+LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS
+RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE
+LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL
+AAEYDAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA
+LPIAAAVDAGKVTATDGFTVPSSQDFDGQTIKDFSPHPTFDMTVAGIYARSYNTGTVQIA
+EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEKWDGRQRLTTAFGQGYTQTTLHT
+AQMYQALANGGVLIPARLIDATVDGEGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ
+GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNFGFTAVAPLDDPRFVVSVSMHRPPSKQ
+GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW
+>GCF_005280335.1_01533
+MTDRPAFSSPRGGSTVGPAPGLPDARIRGLLLLVLVLLGGLALRLVYVQGVDPTGQAAAA
+MDKRLTHQETLPERGSILDRDGDVLASSVRRYDMVVDQRLVKDFNEWDREARKTVLVDVD
+SRLASLAEVLELPEEQVREATIGSRPYNVVKRSVTPEMRDAAMALKVPGLLAEPVDRRVY
+PNGSVAGSIVGFMGGDGTPLEGLELSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAV
+DGADLRLTLDKDAQWFAQETMGALAAEHDAEWANAVVLDAKTGDVLVMADSTTVDPADPE
+GTEPYFRSSTVMSTPYEPGSTGKALPIAAALDAGAVTATDGYTVPSSQEFDGQTIRDFAP
+HETYDMTVAGIFARSYNTGTVQVAEEISDELRYEYMRSFGVGKPIDLGLPRTAGGVLVPP
+GEWDGRQRLTTAFGQGYTQTTLHTAQMYQAMANGGVMEPARLIDATVDGDGAEKRWEPAA
+EPHRVVSEATAADMLRMMETVVTQGTSKAAAIPGYRVGGKSSTAEAASDTGRYDGYNFGF
+TAVAPLDDPRFVVSVSMHRPPSQLGSRAVTSAAAQIMEHMLRQADVPADGAAPQDYDVFV
+DDPQDRPW
+>GCF_020097155.1_01428
+MPVSRSRVSGAGSRTAPPIGTARVRSRTVLLLLLALVTVLGLRLVWVQGIDASGAAATAM
+SERLKTQEIRPERGAITDRDGAVLASTVRRYDIVVDQRLVKDFKEWDAEKRQSVLVSIDS
+RLSSLAEALGMSEDEVRAAAIGDRPWAVLKRSVTPEVRDRVLALKVPGVLADAVDRRTYP
+SGAVAGSLVGFMSSDGTPLEGLEKSQDAVLSGTPGTRTFEVGATGIRIPNAPEDVTPAVD
+GATLRLTLDKDAQWYAQEAMARLADTYSAQWANAVVMDAKTGEVLALADSATVDPGDPQA
+ADARARTPGVVYTPYEPGSTGKTATMAAALDMGLVTPETGLEVPDRLELKGQPPIRDASP
+HETYTMTVAGVYARSYNTGTVMVAEKMSDEQRYEYMRSFGIGRPIDLGLPQPARSVLAAP
+GDWDGRQRLVTAFGQGYTVTTLHTAQMFQAIANGGVLEPARLIAATVGADGTEHRWDPGV
+ASRRVVSEQTAEEMLRMMETVVTQGTSTVAQLPGYRVGGKSSTAQVAGETGTYDGYNYGF
+TAVAPLDDPRYVVSVSMNRPSAGGSSKVVAAAAADVMQHMLRQGGVPPGGAEPDDYRVFV
+DDPQERPW
+>GCF_023573625.1_01315
+MRTRILLLLVFVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV
+LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS
+RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE
+LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL
+AAEYEAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA
+LPIAAAVDAGKVTATDGFTVPGSQDFDGQTIRDFSPHPTFDMTVAGIYARSYNTGTVQIA
+EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEQWDGRQRLTTAFGQGYTQTTLHT
+AQMYQALANGGVLIPARLIDATVDGDGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ
+GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNLGFTAVAPLDDPRFVVSVSLHRPPSKQ
+GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001142.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001142.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55eb74d20365bf85143aaa7d04c891c36093b765
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001142.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01361
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAEQVGHLEAPQNLAARADALG
+MVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDGQDEIEGPRT
+LGGEDASAAPDQDAADR
+>GCF_003691675.1_01081
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPAPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVIETNERLAEQVGNLEAPQNLAARADALG
+MVAPAGTASVDAGTGEFGGEAQAAQDGDVSATYVAPPADADVVRQGASAEGQDEIEGPRT
+LGGEDASAAADQDAADR
+>GCF_005280335.1_01532
+MTLHEEMSMAAHARIAEPLRHTGAPARPAPQERTPLSVVPAPLPRSRSGMTVLCVVVLLA
+ALAAVLVMNITMSNRQYALLDLRQEQQAVTEVNERLAEQVGYLEAPQNVAARADALGMVA
+PAGTASVDAATGEFRGEAQPAREGEISATFVAPPVNADAVRQGSAGSADADRGDIEGPRT
+LGAPAAAPGAAASDDRDASDR
+>GCF_020097155.1_01427
+MTAYEETGMSAQAWRDEARTAWPRTGATPEREHRQRTPLSVVPTPLPRSGSGVAVLCGLV
+LLVALGLVLVMNITMSNRQFTLLDLRAQQTTLTETNERLAEQAGYLDAPQNLAARAGAMG
+MVSPGATSTVDVASGAVAGPSTGAGSTTLPEGRIAPPADADLARQGEAQGQIPGPRTVDP
+AAPTAAPSGETAPTPAPTDAPAGR
+>GCF_023573625.1_01316
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAERVGHLEAPQNLAARADALG
+MVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDGQDEIEGPRT
+LGGEDASAAPDQDAADR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001144.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001144.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5a095bbda83b2c8e29112ceb0fe45d481a66b63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001144.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01363
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCIYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
+>GCF_003691675.1_01083
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCVYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
+>GCF_005280335.1_01530
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCVYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NAYLAEQEAAFSETDEDVLPGVF
+>GCF_020097155.1_01425
+MFLGTYTPRLDEKWRLILPAKFREELADGLVLTRGQERCVYVFSAAEFERVHEQLRSAPL
+SSRQARDYIRVFLSGASDETPDKQGRITVPSPLRQYAGLDRDVTVIGAGTRAEIWDTAAW
+AAYLAEQEAAFSETDEDVLGGIL
+>GCF_023573625.1_01318
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCIYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001145.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001145.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00eebc607bfa0b249c7ee20e86d9ce4d6355ba11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001145.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01364
+MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV
+ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW
+DERRAGGD
+>GCF_003691675.1_01084
+MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV
+ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW
+DERRAGGD
+>GCF_005280335.1_01529
+MPLSEHEQRMLDQLEHQLRTEDPRLATQMADTRRDPVPVKRVVLGAVLAVVGLLVIVMGV
+ANQLVPVGVLGALVVGAGIFLVTTRPRGGRAAGADRPGPGRGGRPGGGRPEGGRPGGDFM
+GRLERRWDARREQGD
+>GCF_020097155.1_01424
+MPLSDHEQRVLDELERQLHADDPSLASQLSTPRGPAPVRRIVLGAAMMLAGLAVVLVGVS
+THLVVVGVLGAVLLGGGILVLTSRRVSASRAPGAPVAGDGGPHAGRRRGGLMDRLDREWD
+SRGRADT
+>GCF_023573625.1_01319
+MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV
+ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW
+DERRAGGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001146.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001146.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d8c64315d526fe6192821514b8394244310495e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001146.fa
@@ -0,0 +1,44 @@
+>GCF_002008305.4_01365
+MSETAPAAPRDEATILHVDMDAFFLSVELRERPDLEGRPAAVAAPSGRSVVLSASYAARA
+YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA
+GARRRLGPPEHIGHLIRERVRSALGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPERTL
+DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID
+PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEQATAGAVTVRLKA
+PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPVRLVGVRAERLGDEADQPPA
+QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA
+PRPGPGGPDRE
+>GCF_003691675.1_01085
+MSESAPAAPRDEATILHVDMDAFFLSVELREQPDLEGRPAAVAAPSGRSVVLSASYAARA
+YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA
+GARRRLGPPEHIGHLIRERVRSALGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPQRTL
+DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID
+PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEQVTAGAVTVRLKA
+PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPVRLVGVRAERLGDEADQPPA
+QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA
+PRPGPGGPDRE
+>GCF_005280335.1_01528
+MSDTAAAQARPEASILHVDMDAFFLSVELRERPDLTGRPAAVAAPSGRSVVLSASYEARA
+YGVRSAMPLAHARALCPPLVVVPPRQDVYRSVSADVMALLGQVTPVLEQLSVDEAFLDVA
+GARRRLGPPARIGGLIRRRVREELGLPCTVGAAGVKFVAKMASTAAKPDGLLVVPPERTL
+EFLHPLPVGRLWGVGPKAAEALRRRGMATIRDLAAADPEQLERAFGAAGRSWAQLSRGID
+PRPVAPRPAARSIGADHTFDVDPLDVAGVDLEVLRLCHRVAARLRAEEVAAGAVTVRLKD
+PDGRVRSRTARLARPTTTAHGLLGPARRLVAELHAQRPHPVRLVGVRAERLTDADEPAPE
+QEALFGGSGFGDDDAAEGGAGDWAGAEAAADAVARRFPTAAVRPASLLRRAAGRPDTRRD
+VPGP
+>GCF_020097155.1_01423
+MSAPDPGPAPSSPPPPRREPSILHVDMDAFFLSVERRERPELRGVPAAVAHPEGRSVVLS
+ASYEARAYGVRSAMPLAQARALCPPLRVTPPRQELYRSTSARVMDLFGRVTPVVEQLSVD
+EAFLDVAGARRLLGPPERIAALIRERVRAELGLPCTVGGAGVKFVAKMASTAAKPDGMLL
+VPPQCTLAFLHPRPVGALWGVGPQAARRLRERGVETIGDLAARDPRWLREAFGAAGAAWA
+ELAAGRDPRPVAPREPARSVGADHTFDVDARDPAALDREVLSLCHRVAARLRSGGHTAAA
+VTVRVKDPALATRARTVRLPAPTASGRVLHAHAGPAVAGLLTERPHPVRLVGVRAERLSD
+AEAHGAVQEALFAPEGHEGPTDDAGWRRAEEAADAVARRFPGAGVRPASLLGPPEGS
+>GCF_023573625.1_01320
+MSETAPAAPRDEATILHVDMDAFFLSVELREQPDLEGRPAAVAAPSGRSVVLSASYAARA
+YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA
+GARRRLGPPEHIGHLIRERVRSELGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPERTL
+DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID
+PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEGVTAGAVTVRLKA
+PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPIRLVGVRAERLGGEADQPPA
+QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA
+PRPGPGGPDRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001147.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001147.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea94843b2cc06d9335b7c9394cb36b5341a3cc8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001147.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01366
+MPADVAVPRPRPADQDRFRAAVADALDRLLAEHRDLARDVHPLTAPLVDAIADLTAGGKR
+LRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFE
+SLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFGVM
+AGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTAFA
+RVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEAAALDA
+DLGDPDLGADRVAHWQGVLEACGARRAVEERVAALSHEAAGAVAGLLAHGVPEDVSAELT
+QLIDAYTSRRH
+>GCF_003691675.1_01086
+MPADVAVPRPRPRPADQDRFRAAVADALDRLLAEHRELARDIHPLTAPLVDAIADLTAGG
+KRLRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRR
+FESLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFG
+VMAGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTA
+FARVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEAAAL
+DADLGDPDLGADRVAHWQAVLEACGARRAVEERVAALSHEAAGAVAGLLAHGVPEDVSTE
+LTRLIDAYTPRRH
+>GCF_005280335.1_01527
+MPVDAAVTRPRPADQDRFRAAVAEELTRTLDEHRERARAVHPLTVPLVDAVGDLAAGGKR
+LRAVLGWLGWRAAGGDPENPRIARTGAALELFQAAALIHDDILDRSDTRRGMPSVHRRFE
+AEHRASGWRHDAGHFGVSAAILAGDVALGMSETAFAAALEGAGRPARARDEFERMRFGVM
+VGQYLDVAAEMAPPATDPAEAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDALVAAFA
+EVSLPFGLAFQYQDDLLGVFGDPAATGKPAGDDLREGKRTVLIARAVALLSPADAAALDA
+DLGDPGLSAERIAHWQRALEECGARQAVTDRVAALSARAAEAVGALEAHGVPADVRAELT
+ALIEAATTRRH
+>GCF_020097155.1_01422
+MPTPETASVSDFRAAVAERLTAVLDGHARGAARIHPDADPVVEAVSVLTSGGKRLRAVLC
+WLGWRAAGGSPTDPRAAVAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFEARHREH
+GWRHEAEHFGVSAAILAGDVALALSDSMFSRAIEGTPRAERARREMERMRFEVMVGQYLD
+VAAEMAPPAADPAAAERAARAVVEHKSARYSAVHPLALGALLAGADDDLVAAFEAVSLPF
+GMAFQLQDDLLGVFGDPAHTGKPAGDDLREGKRTVLVARAEALLPRGEAAALDAELGDPA
+LSAERVAHWQRRLEEVGARTAVADEVDRLSAEARRGLERLAALGVGTDVRGELAELIDAY
+TVRTA
+>GCF_023573625.1_01321
+MPADVAVPRPRPADQDRFRAAVADALDRLLAEHRERARDVHPLTAPLVDAIADLTAGGKR
+LRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFE
+SLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFGVM
+AGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTAFA
+RVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEVAALDA
+DLGDPDLGADRVAHWQAVLEACGARQAVEERVAVLSHEAAGAVAGLLAHGVPEDVSAELT
+RLIDAYTSRRH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001150.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001150.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30f7196698d9b83a527162524ef58d31d0c3adcc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001150.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01370
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTTVADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA
+>GCF_003691675.1_01090
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTTTADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA
+>GCF_005280335.1_01522
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPVAQAPSWADEAEHRAAVAELSQVPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEEARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTSAADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRALGTRPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERVAPRR
+>GCF_020097155.1_01418
+MHEDPRDQIMAFGTAISEGAAPDPALDAWRELPIKQAPTWADEDDFRAAVAELSQVPPLV
+FAGEVDVLRTRLADVARGQAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQYAKPRSSDTETRDGVTLPSFRGEIVNGFEFTEEARRHDARRMVTAYHTA
+SSTLNLVRAFTQGGFADLRSVHQWNRGFMENPAYAQYEQIAAEIDRAVRFMDAAGADFEA
+MRRTEFYAAHEALLLDYERALTRLDSRTGLPYATSAHFLWIGERTRDVDGAHVDFLSRVR
+NPIGVKLGPTTTVDDVRALADRLDPEREPGRLTFITRMGADKVRDVLPGIVAGVRDEGLQ
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDELTGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPVDEADFDEHYETLCDPRLNHQQSLELAFKVTDALAHPHQD
+>GCF_023573625.1_01325
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTTVADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001151.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001151.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96054a22ee4b6668a12a330980f7e1e666364194
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001151.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01371
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKHEYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDRVQPIGHVLPRIRRLGMIFGEPL
+DFSDRAEAVGDPRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRTAAPPRARD
+>GCF_003691675.1_01091
+MSTFYWSAKTFAVAPATRLLFRPWVKGLANVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKHEYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLAALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGVPVVPIAMIGTDRVQPIGHVLPRIRRLGMIFGEPL
+DFSGRAAAADDRRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRVAAPPRAGD
+>GCF_005280335.1_01521
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGAAILASNHLSVSDSVFMPAMLERQV
+HFLAKKDYFTGAGPKGWITRKFFEATNQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDQAQPIGRTLPRIRRIGMIFGEPL
+DFSDRAEGVTDARVLRAVTDEIMEAIRRLSGQEYVDAYAADVKSGRVPAPPRARD
+>GCF_020097155.1_01417
+MSAFYWSAKTFVVAPATRLLFRPWVKGLSHVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKQEYFTGRGAKGWATKKFFEATNQLPMDRSGGAASLRSLEAGLECLREGKLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDRVQPIGRILPTLRRLGMIFGEPL
+DFSHLQGREGDHRALRQVTDEIVEAIRRLSGQDYVDVYAADVKSGRVAVPPRAGRD
+>GCF_023573625.1_01326
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKREYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDQVQPIGHVLPRIRRLGMIFGEPL
+DFSDRAEAVGDPRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRTAAPPRARD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001152.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001152.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21382b8243e3990518019233b518488978c56039
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001152.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01372
+MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL
+PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV
+LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAALGRIQR
+AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDYDLP
+LLIDHGRSAVAAMTTH
+>GCF_003691675.1_01092
+MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL
+PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV
+LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAAVGRIQR
+AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDHDLP
+LLIDHGRSAVAAMTTH
+>GCF_005280335.1_01520
+MDRPVPPVEPAPPAVPAPAVDPVHLPLRLAPGSGAGADRCVVVLHGFTSGPDSVRAWAEG
+IAAGGSHVSVPLLPGHGTRWQDLAATGADEIRGAVRETVDRELSRHRHVVVAGISMGGAL
+ALDAAAHRPVSAAIVVNPALRFASPLAPLAPALAPFVPSVAPIANDIADPDARELAYPRT
+PVAGVAAVGRIQRAARRALPRITAPVTVFRSARDAVVPAASHRTLLRGLRRAPVDVVPLP
+RSRHVATLDYDLPLLIERSRAAVEAATRA
+>GCF_020097155.1_01416
+MTRLRPAAPDRRPAPGVDPAQRPFRLPATSLPGVAVVMLHGFTSGPDSVRAWAEGVAAGG
+AAVHVPLLPGHGTRWEDLGTTDADELRAAVRDAVDAALATHRRVVVAGISMGGALALDAA
+AHRDVAGVLVVNPALRFGSPLAVAAPLLRHVVPSVPSIAGDIADPDARELAYERAPVAGV
+AQVGRIQTAARRGLGRITAPVTVFRSAEDAVVPERSHHTLLRGLTAAPVEVVRLLHSRHV
+ATLDRDLPLLVARSRDAVAAAAR
+>GCF_023573625.1_01327
+MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL
+PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV
+LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAALGRIQR
+AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDYDLP
+LLIDHGRSAVAAMTTH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001154.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001154.fa
new file mode 100644
index 0000000000000000000000000000000000000000..576d7d3b55684ced9895836f60d4f6abccae9a70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001154.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01374
+MSPPPAGRPTGPDATASGPVPILGGMATTAEHHDLLIIGSGSGNSLVSEHWKGRSVVIAD
+SGPFGGTCLNVGCIPTKMYAYPASLAALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGI
+SRDGLRHRRDDLDYTSVIQEEVRFVGPRRVRTASGREITADQVVVAAGSRPTLPEIPGLD
+LPSVHTSDTVMRLDRLPRRLLVVGGGFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSV
+STTFTKIAARRWDLRTGWTPAGIEPVEDAERAADGWVRVRLDRAEGQEQTGIVEEAIEAD
+AVLIAVGRTPNTDRLDPAAAGLDVTDDGILASDEHQRALSDGAPVEGVYVLGDVANTWQL
+KHVANHEARVVAHNLEHPDDLRANTLGPVPAAVFTHPQAASVGLTVEQALADYGADAITV
+KTQPFGDVAYGWAMEDTEGVCTVVAEKATGRILGGHILGHEAANLIQPLVTGMAFGIDAH
+RLARGQYWPHPALTEVVENALLGLDVPDSGLL
+>GCF_003691675.1_01094
+MATSAEHHDLLIIGSGSGNSLISEHWKGRSVVIADSGTFGGTCLNVGCIPTKMYAYPAGL
+AALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGISRDGLRYRRDDLDYTSVIQEEVRFV
+GPRRVRTASGREITADQVVVAAGSRPTLPEIPGLDLPSVHTSDTVMRLDRLPRRLLVVGG
+GFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSVSTTFTKIAARRWDLRTGWTPAGIEP
+VEDAERAADGWVRVRLDRAGGQEQTGIVEEAIEADTVLIAVGRTPNTDRLDPAAAGLDVT
+DDGVLASDEHQRALSDGAPVEGVYVLGDVANTWQLKHVANHEARVVAHNLEHPDDLRANT
+LGPVPAAVFTHPQVASVGLTVEQALADYGADAITVKTQSFGDVAYGWAMEDTEGVCTVVA
+EKATGRILGGHILGHEAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGLD
+VPDSGLL
+>GCF_005280335.1_01518
+MATSTEHHDLLIIGSGSGNSLVTEHWEGRSVAIADSGVFGGTCLNVGCIPTKMYAYPAGL
+AASAGAESERLGVGLEFTGADFPAIRDRIFQRIDAISEGGLRYRRDELEHTSVIQEEVRF
+VGPRRVRTASGREVTADQVVIAAGSRPTLPRIPGVDLPSVHTSDTVMRLPRLPRRLLVIG
+GGFIACEFASIFAALGSEVIHVNRGHRLLKAHDLSVSTAFTEIAARQWDVRTGWTPAGVE
+PVADPDRAAQGWVRVRLDRAEGQEQTGTVEEVVEADAVLMAIGRTPNTDRLDVDAAGLDV
+TEDGVLATDRHQRVLSGGAPVEGVYALGDVANTWQLKHVANHEARVVAHNLEHPEDLRSA
+VLAPVAAAVFTRPQVAAVGLTVEQALAEHGADAITVKTQAFGDVAYGWAMEDSEGLCTVV
+AEKATGRILGGHILGHDAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGL
+DVPDSGLL
+>GCF_020097155.1_01413
+MSPDPAASSAGDEVDGPDDPHVRAVSYADAMATTERFDLIILGSGSGNSLVTDHWEGRRV
+AIVDAGVFGGTCLNVGCIPTKMYAYPAQLAASGAEAERLGVGLDFTGADFEGIRDRIFGR
+IDAISEGGLRYRRDQLEHTEVVAEEAWFSGPKELTTASGRVLAGEQVVVAAGSRPTVPDV
+PGVGLPSVHTSDTIMRLPRQPKRLVILGGGYIASEFAAIFSGLGTEVVQVNRGARLLKAH
+DSSISTRFTALAARQWDVRTGWTLAGVEPVGDQRRADEGWVRVRLDAVEGQEQMVEREET
+LEADAVLLAVGRTPNTDRLRPEAAGFDVTAAGVLAVDEHQRVLSSGVPVEGVYALGDVAN
+AWQLKHVANHEARVVAHNLEHPEDLRANTLGPVPAAVFTRPQIASVGLTQDEARELLGED
+AVTVKEQAFGDVAYGWAMEDAEGVCTIVAERATGRILGAHLMGHDAANLIQPLVTAMSFG
+IDAHRLARGQYWPHPALTEVVENALLGLDVPDSGLL
+>GCF_023573625.1_01329
+MATSAEHHDLLIIGSGSGNSLISEHWKGRSVVIADSGTFGGTCLNVGCIPTKMYAYPAGL
+AALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGISRDGLRYRRDDLDYTSVIQEEVRFV
+GPRRVRTASGREITADQVVVAAGSRPTLPEIPGLDLPSVHTSDTVMRLDRLPRRLLVVGG
+GFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSVSTTFTKIAARRWDLRTGWTPAGIEP
+VEDAERAADGWVRVRLDRAGGQEQTGIVEEAIEADTVLIAVGRTPNTDRLDPAAAGLDVT
+DDGVLASDEHQRALSDAAPVEGVYVLGDVANTWQLKHVANHEARVVAHNLEHPDDLRANT
+LGPVPAAVFTHPQVASVGLTVEQALADYGADAITVKTQSFGDVAYGWAMEDTEGVCTVVA
+EKATGRILGGHILGHEAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGLD
+VPDSGLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001158.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001158.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f207e4f2b1234b0ab336b94e6499b8ba7d2ff89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001158.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01378
+MIDPRPLPDAVPTARPAGRLGIGEVVAALEAEFPGVTASKVRFLEDRGLVLPERTPAGYR
+RFRPEDVDRLRFVLALQRDHFLPLKVIADHLAALDRGERPTGLPGTAAVPASSDAARLGR
+EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG
+LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV
+GLEQWDD
+>GCF_003691675.1_01098
+MTDPRPRPDAVPTARPAGRLGIGEVVASLEVEFPGVTASKVRFLEDRGLVLPERTSAGYR
+RFRPEDVDRLRFVLALQRDHFLPLKVIADHLAALDRGERPTGLPGTAAAPASSDAERLGR
+EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG
+LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV
+GLEQWDD
+>GCF_005280335.1_01514
+MTEPQHADAGPRTRPAGRLGIGEVVAALKSDFPGVSASKVRFLEDRGLVLPERTPAGYRR
+YRPEDVDRLRFVLTVQRDHFLPLKVIAAQLAALDRGEVPADLPGGVVAPGASDASRLGRE
+VAAGRRGWTRSELAEESGAGEELLAELDQYSLLPADEDGAYSSHAMEVARAAVVLAGHGL
+EPRHLRPFRAAADRELGLVERAVAPLQARRDANMRPRVARSAQEIAQASLRLHSALVAEG
+LEQWDDGAVG
+>GCF_020097155.1_01409
+MSAPHEPSAAPPPAGAALGIGDLVAALEPSFPGVSASKVRFLEDRGLVRPERTAAGYRRY
+RPADVDRIRLVLTLQRDRFLPLKVIREHLDALDRGERPEDLGEAPAAAQEAVRLGHGIAD
+PDRRWTRAELAREAEVPAPLVDELDQYALLPRAEDGLHPPAALGVVRAAGRLAAHGIEPR
+HLRPFRAAADRELGLVQSAVAPLATRRDAGTRERAARTAEEIATACLALHAALVRAGLES
+LDG
+>GCF_023573625.1_01333
+MTDPRPRPDAVPTARPAGRLGIGEVVASLEVEFPGVTASKVRFLEERGLVLPERTSAGYR
+RFRPEDVDRLRFVLALQRDHFLPLKVIAEHLAALDRGERPTGLPGTAAAPASSDAERLGR
+EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG
+LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV
+GLEQWDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001159.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001159.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e548c563782576e1d1417e3ae9b277aac0b7435f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001159.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01379
+MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL
+DKDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR
+SGMHVQIGKYRLTYYAAPARG
+>GCF_003691675.1_01099
+MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL
+DEDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR
+SGMHVQIGKYRLTYYAGPARG
+>GCF_005280335.1_01513
+MNQPGREPDLSTSSINLTELAPLVAADLSAEESDAIRALPAGSALLLADGGPEKAARFLL
+DQDVVTVGRHPDADIFLDDVTVSRRHAEFRAEAGGHRLVDMNSLNGTFVNHDRVDDVLLR
+SGTHVQIGKYRLTYFTSTQRG
+>GCF_020097155.1_01408
+MTQQEPSLHTSSISLTDLAPVAETGLSPEETAAVRALPAGAALLVAHEGPDAGARFLLDT
+PVVTVGRHPESDILLDDVTVSRRHAEFRAVDGGHELVDLSSLNGTYVNNDRVDQVRLRTG
+MQLQIGRYRLSYHAAEPA
+>GCF_023573625.1_01334
+MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL
+DEDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR
+SGMHVQIGKYRLTYYAGPARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001160.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001160.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c15dfc13205a3d8d451281db784beaad02a82cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001160.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01380
+MSSIPEGLKYSAEHEWIAEAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS
+>GCF_003691675.1_01100
+MSSIPEGLKYSAEHEWIAKAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS
+>GCF_005280335.1_01512
+MSSIPEGLKYSAEHEWIAEAGQAGTVRIGITDFAQDALGDVVYVDLPEVGSEVTAGTAVG
+EVESTKSVSDIYAPVTGTVAAVNEDLDGEPGLVNSAPYEGGWLFEVTLADEAQLEGLLDA
+EGYASHTS
+>GCF_020097155.1_01407
+MSSIPEGLKYSTDHEWAQDAAEPGVVRVGITDFAQDALGDVVYVDLPSVGDEVTAGAAIG
+EVESTKSVSDIMAPVSGTVTAVNEELDGEPALVNSAPYEGGWLVEIKLSDPAEVDGLLDA
+AGYAAHVG
+>GCF_023573625.1_01335
+MSSIPEGLKYSAEHEWIAEAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001164.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90124d08455ec45acc1fbcb2cb7f7e9ac71b863e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001164.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01406
+MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD
+IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA
+GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA
+AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD
+TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG
+NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG
+MVEISVLPGRRDELVAALTAAGWKVV
+>GCF_003691675.1_01136
+MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD
+IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA
+GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA
+AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD
+TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG
+NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG
+MVEISVPPGRRDELVAALTAAGWKVV
+>GCF_005280335.1_01490
+MSAAAETAAAVPGALPAGIPQPVLVRGTGLLGASIGIGLSAAGADVLLHDLSPAALAVAA
+DIGAGRPMRIDDDGADAGPAPALVVVAAPPDVTADVVVDSLRRWPEALVLDIASVKEAIA
+AGVRAAVDDGRLGPSDPDRHLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTLPAAV
+QAGRALALALRATPYRMDARAHDESVAMISHLPQIAASLVAARLQDTPDQALALAGNGLR
+DTTRIAASDPQLWVQILSGNAERIVPALHGLRDDLDRLIRTLEAPGAPGSRLDMARLIAE
+GNAGRARVPGKHGAPPQAFAVVTVIVDDTPGQIAAVLDEVGRTDVNVEDLRLEHASGHRA
+GMVDISVLPGRRDELVAALSAAGWKVV
+>GCF_020097155.1_01401
+MIPAEGGAGPAGLSGPVLVRGTGLLGASIGLGLRAAGADVLLDDPSPTALAVARDIGAGA
+VVDLDDPALAPGLVVVGAPPDVTPAVVVDSLRRWPHAVVTDIASIKGAILAEVREAATRG
+DIAPGDVARYLPGHPMAGSERSGPVAARGTLFTASPWVLCPAAETDPAALAAGEALARTL
+QATVHRMSAADHDASVALISHLPQIAASLVASRLQDAPDPSLALAGNGLRDTTRIAASDP
+HLWVQILAGNAPQIVPTLHGLREDLDRLIGTLEAPSAPGARLDVARLIAEGNAGRARIPG
+KHGAPPQAFALVTVIVDDTPGQLAALFEEIGRAGVNVEDIRLDHASGYRVGMVDVSVLPG
+RKDELVSALTDAGWKVV
+>GCF_023573625.1_01356
+MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD
+IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA
+GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA
+AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD
+TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG
+NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG
+MVEISVLPGRRDELVAALTAAGWKVV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001165.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001165.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8a4fc4eb0b5e52f6a002d1f9a57c89a336e71bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001165.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01407
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL
+>GCF_003691675.1_01137
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL
+>GCF_005280335.1_01489
+MNSRKPRGSGRTPSVGRRGGPFQERDFQRQLGARRGPAGPRDEAPFDEDAVPRTRGRRGR
+GAGAARAKAANLDRIHDESGERLQKVLASAGVASRRVSEDLIAEGRVEVDGVIVTEPGVR
+VDPARAVIRVDGISVQTDVTKQYYVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+KVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGS
+VRALSAQELGHLKALVGL
+>GCF_020097155.1_01400
+MNSRKPRGSGRTPAAGKRGGPFSERDFQRNLGARRGPARPKDEPAFDEDAAERRVRSRRG
+KGAGAARAKAQHLEEIHVEDGERLQKVLASAGVASRRVCEDLIAEGRVEVDGVVVTEPGV
+RVDPVRSRIQVDGISVQTDVTKQYFVFNKPRGVISTMLDPEGRPSIATYLKPGQENLFHV
+GRLDNETEGLLILTNDGELANRLTHPSWEVPKTYLVQTRGPLAKGVSNRLREGVELEDGL
+AKVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQG
+SVRAMTAQEQGHLKALVDL
+>GCF_023573625.1_01357
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001169.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001169.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b292da6eb730a9a605548c259dac4d600c2a9c3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001169.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01415
+MLYSTKTAEQKRIDLRETLKQGGAQQFPGAFTPLSAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVELDTAVKRIAAAVHARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRRQLADAGVAMVI
+YPVTLLRSAMGAAERVLNAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL
+>GCF_003691675.1_01146
+MLYSTKTAEQKRIDLRQTLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVELDTAVKRIAAAVHARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRRQLADAGVAMVI
+YPVTLLRSAMGAAERVLHAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL
+>GCF_005280335.1_01484
+MLYSTKTAEQKRVDLRAALAEGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVALRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELAPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIKDEGTQASQVDQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIDENNANL
+>GCF_020097155.1_01391
+MLYSKKTAAQKRIDLRETLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFEDAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELAPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIREEGTQQSQVDQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIDSNNANL
+>GCF_023573625.1_01365
+MLYSTKTAEQKRIDLRQTLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001170.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001170.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17ddc1bdc8e7eae9d428e2c322108f9d5491fefc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001170.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01416
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT
+DEELAAFEHFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESRQDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
+>GCF_003691675.1_01147
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWTGELPT
+DEELTAFERFERTHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQEVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
+>GCF_005280335.1_01483
+MTETEIKKGLAGVVVDTTAISKVNPDTNSLLYRGYPVQDLAAKLPFESVALLLWNGELPT
+DEELAEFQRFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAKALFAAFPAAVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA
+NALIRPLSSYDGPEQRELPAG
+>GCF_020097155.1_01390
+MTETEIKKGLAGVVVDTTAVSKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWNGELPT
+DAELEEFQRFERAHRALDPEVKAAVDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAKALFAAFPAVVAYDQRRRRGQEVVEPRADLDYAQNFLWMSFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPIFIAARITGWTAHIMEQRAA
+NALIRPLSAYNGPEQRELPGK
+>GCF_023573625.1_01366
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT
+DEELAAFERFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001171.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3eb7af82881f6cba22c80de3cbbfb4be23ab65eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001171.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01418
+MSADPAPRGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERYRRWLEAQG
+VRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEGLTPADPAL
+DVHPPKPGARLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVVGLDVD
+DVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMAGAARSTPA
+LFVNACGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVVQELLG
+HASVTTTQVYTLVTVDSLREVYSAAHPRAR
+>GCF_003691675.1_01149
+MSTDPAARGSGEAEARGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERYRRW
+LEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEGLTP
+ADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVV
+GLDVDDVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMTGVT
+RSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVV
+QELLGHASVTTTQVYTLVTVDSLREVYSAAHPRAR
+>GCF_005280335.1_01481
+MSTDPAARGSGEAEARGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERY
+RRWLEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPFAVRSAARVLAAVRGLHRFWALEG
+LTPADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARIS
+EVVGLDVDDVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMT
+GAARSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADV
+RVVQELLGHASVTTTQVYTLVTVDSLREVYAAAHPRAR
+>GCF_020097155.1_01389
+MSASPELHRALDRHLDHLAVERGLASATLAAYRRDLGRYLAWLEASRVDRPADVDPGHVA
+GFLSALGTGDDGGRPLGARSAARVLSAVRGMHRFWALEGLTPTDPAADVAPPRPPERLPK
+ALPVETVTRILEAVPTAEPADLRDRALLEFLYGTGARVSEAVGLDVDDVVGVAGDRGAGR
+GDDDRLPVVRLFGKGSKERLVPVGSHAADALAAWLVRGRPALAAAATRPVPALFLNLRGG
+RLSRQSAWSILKAAAERAGVAQDVSPHTLRHSFATHLMQGGADVRVVQELLGHASVTTTQ
+VYTRVTAEALREVYASAHPRARWTT
+>GCF_023573625.1_01368
+MSPHAPQTSALAAPFRRHLDHLAVERGLAENTLAAYRCDLARYRRWLEAAGVRAPGDVDP
+GHVAGFLQALATGDDGGRPLAVRSAARVLAAVRGLHRFWALEGLTPADPARDVHPPKPGD
+RLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVVGLDVDDVVGLAQTG
+DDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMTGVTRSTPALFVNARGGR
+LSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVVQELLGHASVTTTQV
+YTLVTVDSLREVYSAAHPRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001173.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77d17738d1d3a28093a4b7a79872b9ec2c169877
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001173.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01420
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRVTADHAALRLAQEAGAVVDEGDNGTHDLVLSRSVTASGDGTRSRATAGGRS
+VPVGLLSEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPREGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPDLAAAAARLAEAAVVLTDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG
+>GCF_003691675.1_01151
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDTMDETPGAVSLVEAAQQAVLAAPGDDPELAAAAARLAEAAVVLTDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG
+>GCF_005280335.1_01479
+MIEHLRISGLGVIGEATVDLDPGLTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGAA
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADDGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGAEAQRRALDAFGGAELAASLRAYRADHAAVSAA
+RRERDELTAHRQERAREAEALQRSLEEIDLAEPLAGEDAELRELIRRLEDVEELRAASGE
+AHARLAGAEMDALEETPGAVSLVEGARQAVLAAPGDDPALAAAAERLAEAAVVLTDIAAD
+LARYTADLDTDAASDLDAAQSRLAELTRLQRLYGPELEDVIGWAETQRPRLDELQGDSGR
+LEELEGELERLESALRERAAALTALRTAAAGRLEEAVTQELHALFMPDASFHVDLAPVGG
+DGLGPHGAEDVALALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLSAEERVEELARMLAGHGDSAAAREHARELLEASARERG
+>GCF_020097155.1_01387
+MIDWMQITGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGRRADAGAVRRGSR
+RAAVDAGVRLPADHPALSLAVEAGAVLDDAGDGSADLVLSRSVTASGDGTRSRAGLGGRA
+VPVGVLAEVGSALVAVHGQNDQVRLQSAAAQRHALDAFGGPQLVAAAAAYRADHTAYVAA
+RRERDLLVERQQERAREAEALQRGLEEIDRAEPEAGEDETLRALIRRLEDVEELRAAADG
+GHAHLAGPDIESGDDLPGAITLVESARAAVQAAPGDDPELAAAAGRLAEASVILGDIAAD
+LARFSADLDGDAVSDLDAAQTRLAELSRLQRLYGPELTDVLAWAEAQRPRLEELQGDSGR
+IDELEADLARLDASRRERAAELTTLRTAAAGRLEQAVTAELHALFMPDASFHVSLVPLDD
+GDPGPHGAEDVALALRPHAGAEPRPLGRGASGGELSRVMLALEVVLAETDPVPTFVFDEV
+DAGVGGEAAVSIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPEAGVTTSDVV
+TLGQQERVDELARMLAGHGDSAAARAHARELLEASAAERA
+>GCF_023573625.1_01370
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPELAAAAARLAEAAVVLSDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTEAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001174.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001174.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea118bd9275d203acbc026c188f5035fcce86dd3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001174.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01421
+MPYTPGRRILVLTHTGREDAISAALQATRMFAEEGLVTVMLEQDVAAIRAAAGDPPEFAP
+ETLGVDCELEDITLGLVLGGDGSVLRAADFVRGYNVPLLAVNLGHVGFLAESERTDLHRT
+VQAIASESYVVIERMALDVVVHVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT
+SFGCDGVVLATPTGSTAYAFSAGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARVEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQERAGVLHEVETVEPRHAGPRPDVVEPATMPLSVPSPADIQRHRDRGARHPGE
+DA
+>GCF_003691675.1_01152
+MPYTPGRRVLVLTHTGREDAISAALQATRMFAEEGLVSVMLEQDVAAIRAAAGDPPEFAP
+EALGVDCELEDITLGLVLGGDGSVLRAADFVRGHNVPLLAVNLGHVGFLAESERTDLHRT
+VQAIASESYVVIERMALDVVVLVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT
+AFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQERAGVLHAVETVEPRHAGPRPDVVEPATMPLSVLSPADIQRHRDRGARHPGE
+DA
+>GCF_005280335.1_01478
+MPHNPGRRVLVLAHTGREDAISAALQATRILEEEGLVSVMLEQDVAAIRENADAPAGFAP
+QTLGVDCGLEDIVLGLVLGGDGSVLRAADFVRGYDVPLLAVNLGHVGFLAESERTDLQRT
+VQAIASEAYVVIERMALDVVVRVEDREVARTWALNEASVEKSNRERMLEVVISVDNAPIS
+SFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQEREAVLREVETVEPRHAGPRPDVVEPATMPLSVLSAADIQRYRDRGARYPGE
+DA
+>GCF_020097155.1_01386
+MSETPSRRVLVLAHTGRADAIAAALQATAMLAEEGLDTVMLAEDVAAILESGTDAVGFRP
+LTLGRDCTLDDVQLGLVLGGDGSVLRAADFVRGHGIPLVAVNLGHVGFLAESERTDLHRT
+VKAIADGAYVVIERMALDVTVRVEGREVARTWALNEASVEKSNRERMLEVVVSVDDSPLT
+SFGCDGVVLASPTGSTAYAFSAGGPVVWPGVEALLCVPISAHALFSRPLVVGPHSTVAVD
+VLTRTRETGVLWCDGRRTVELPPRARIEVTRSAEPVRLARLRPTPFAERLVRKFRLPTEG
+WRGPVTEADRRTGPLAEVETVEPRHAAPRPDVVPPPSEPLTVLSPEALARYRGRDGREGD
+RTS
+>GCF_023573625.1_01371
+MPYTPGRRVLVLTHTGREDAISAALQATRMFAEEGLVSVMLEQDVAAIRAAAGDPPEFAP
+EALGVDCELEDITLGLVLGGDGSVLRAADFVRGHNVPLLAVNLGHVGFLAESERTDLHRT
+VQAIASESYVVIERMALDVVVLVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT
+AFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQERAGVLHAVETVEPRHAGPRPDVVEPATMPLSVLSPADIQRHRDRGARHPGE
+DA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001175.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001175.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ae442e50a2b174fa57b6724d005ecd7fc5130da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001175.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01422
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPADRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVGVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHNQLAP
+PVRADPRVLVREGLNIRDLTAEDIDGPVDLVVSDLSFISLRLVLAPLASVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRHAVVGVTAAALGAGLAPRGLARSGLAGQDGNAEFF
+LRLRRPDATAADNPAGGTSPAPPAGERAAGWVRGAHIDWS
+>GCF_003691675.1_01153
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVAVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP
+PVQADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSGLAGQDGNAEFF
+LRLHRPDATAADDPAGRTSPATPADERAAGWVRGAHIDWS
+>GCF_005280335.1_01477
+MAEAVRADVALAARGLARSRTEASALIRAGQVLVDGRPVRRASERVAPTASLTLADDGPR
+WVSRAAHKLVSALEAFPDVAVRGRRALDAGASTGGFTQVLLEGGAARVAAVDVGHGQLVD
+LVRTDPRVLVREGLNVRDLTVQDVEGEVDLVVSDLSFISLRLVMDALAGVCRPGADLLLM
+VKPQFEVGRAALPRTGVVTDPAARRDVVAAVAAAALDSGLELRGLARSGLPGQDGNVEFF
+LRLRRPAADAAGAPGTGLDDDAPAAEAVAAAWTAAAEVDWA
+>GCF_020097155.1_01385
+MGEARRADVALAADGLARSRTEAAALVKEGVVLVDGTPVRRPSQPVASGAVLSLLDQGPR
+WVSRAAHKLVSALEAFPVPVAGRRALDAGASTGGFTQVLLERGAARVAAVDVGHGQLVQE
+LRADPRVLVREGLNVRDLTATDVEGSVDLVVSDLSFISLRLVLDALAGVCRPDADLLLMV
+KPQFEVGRAALPRTGVVTDPRARRSAVEGVVAAALGTGLAARGVARSGLPGQDGNVEFFL
+HLRAPAAPRDGGAVAGDADEDERRRRAAALVAAADVDWS
+>GCF_023573625.1_01372
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVAVAGRQALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP
+PVRADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSDLAGQDGNAEFF
+LRLHRPDATAADDPAGRTSPATPADERAAGWVRGAHIDWS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001176.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001176.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90738acb7a3a9572dcfdce794d30d69a1bf1c5c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001176.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01423
+MSTTFFDGHDGLLCDLDGVVYAGDGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE
+HLRTLGVPAEAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA
+QCPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR
+ATGTAPVAAGKPEPRLFRTAADALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR
+ETAAAAPGPDRPTWVRAHLPALLAGGAEASADPRRG
+>GCF_003691675.1_01154
+MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE
+HLRTLGVPAQAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA
+QRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR
+ATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR
+ETAAAAPGPDRPTWVRAHLPALLAGGAEAFADPRRG
+>GCF_005280335.1_01476
+MSPTLPRGHDGLLCDLDGVVYAGGGAVPGAVETLTALAERGVPVGFVTNNASRAPESVAE
+HLRSLGVPARPEQVFGSAPAGVDLLEETLGARTGRVLVVGSDYLRQVVRDRGFEVVAASQ
+DRPDAVIQGFDPGVGWAELAQAAYAVNAGAAWVATNLDASIPRAEGIAPGNGALVGAVGQ
+ATGTAPAAAGKPEPLLFRTAARALGLTRPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR
+ENAGSAPEADRPTWIVEDLPALLSEPDGQAGTADGRRG
+>GCF_020097155.1_01384
+MTDPAASTFFGGHDGLLCDLDGVVYAGGEAIPGAVETVSALAERGVPVGFVTNNASRPPE
+AVAEQLRRFGLEVSPSHVFGSAPVGVDLLEERLTAAGHEGPARVLVVGSVHLADLVAARG
+HHVVETAAERPDAVLQGFDPRVDWSRLAEAAYAVNAGAAWVATNLDLSIPRAEGVAPGNG
+ALALAVTQATGVIPVAAGKPEPRLFHTAAAALGLQAPLMVGDRLDTDIRGGNAAGMETVL
+VLTGVGSRHAAGEAPEEDRPTWIVDDMTALLGEPAEAARG
+>GCF_023573625.1_01373
+MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE
+HLRTLGVPAQAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA
+QRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR
+ATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR
+ETAAAAPGPDRPTWVRAHLPALLAGGAEAFADPRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001177.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89b89295bf6c3083425cfc89f68b123134375bfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001177.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01424
+MTGKELDRGTLKEINGLDERAASWVAKHLVMAGRYLDVDPTLAFQHALAASRKGGRLSRV
+REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS
+RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG
+RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRNRRPSPRERRHERYAAEAG
+AEPTADGSPAEEPEAAAEPTLVPRQEAVAQPPAAVDTPDEVDPNQLSLFDALEAPEADER
+>GCF_003691675.1_01155
+MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALAFQHALAASRKGGRLSRV
+REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS
+RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG
+RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRDRRPSPRERRHERYAAEAG
+AEPTADGSPAEEPEAATEPTEAPRPEAAAEPPAAVDAPDEVDPNQLSLFDALEAPEADER
+>GCF_005280335.1_01475
+MAEDTPRGRRDDRRSPGDGAGRSRGGSGDARRFGGPRDGRRSGGSGEGRSGQDRRDRSSE
+GFRGGRSGDGPRRERSSDGPRRERSSDGFRRDRSSDGPRGERSGDGPRGPRAGGDRRQSG
+AGSARGGFEGRRGGERREGAGGERRDRRSASSSPRWEGRGQDRTERTERRERPAHNPRDL
+RAANRVDQERSPDIDADVTGQELDRGTLKEVNGLDERPASWVAKHLVMAGRYIDVDPALA
+FQHALAASRKGGRLSRVREAVALTAYAAGEYADALREFRTYRRMTGDDTHVAAQVDSERA
+LGRPAKALQLAAEIDTARLDRAARVELAMVVSGIREDAGDLQGAHDALQIPELDRRRGYP
+FSPRLFQRQADVLLLLGRADEARLWARAVRVAEKALGIGGFAEPEIVDVDTEPVDDRRER
+GPSPRERRYAENAAPAAEEVPDTPEADDEVAADADTEAPASTESELDAPPAAVAQADEVD
+PNQMSLFDELDGGEGEGR
+>GCF_020097155.1_01383
+MAERSAREPRDDRRGDGHDGTRSGTPRGRRDGDGGRRQGEGRPFRPHRDGEGVGRSRNVG
+GRDGAAPRPGRPERAQRERPAHSPSDLRAANRVDQQRSPDIDGDVTGKELDRGTLKEIGG
+LDERPATWVAKHLVMAGRYIDEDPELAFQHALAASRKGGRLARVREAVALTAYAAGEYHE
+ALREFRTYRRMTGDDTHIAAQVDSERALGRHEKALQLAGEVDTSRLDRAARVELAMVVSG
+VREDLGDLEGALAALKIPELDRRRGYPFSPRLFQRQADVLTALGRTQEAAVWQRSVHVAE
+RALGIGGFAEPEIVDVEVEPAEDDRPVRGHRERHTGPRVSDASQSSAESAPVGEGSAEEH
+GQAAPAERES
+>GCF_023573625.1_01374
+MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALAFQHALAASRKGGRLSRV
+REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS
+RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG
+RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRDRRPSPRERRHERYAAEAG
+AEPTADGSPAEEPEAATEPTEAPRPEAAAEPPAAVDAPDEVDPNQLSLFDALEAPEADER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001178.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001178.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54e5d9355995e9ae2c7eda76e4ef69b7e17ff3c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001178.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01428
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDALAGRHLLVRRGKKNMAGADLGEA
+>GCF_003691675.1_01159
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAKMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQKRLAWEVTALAHGEETTTKVIEASHAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDALAGRHLLVRRGKKSMAGADLGEG
+>GCF_005280335.1_01471
+MAPDNEERAARLRAQANDPSFENVWQELLWRGLVHVSTDEAALEEALAGEPISYYCGFDP
+TAASLHLGHLVQLLTLRRLQLAGHRPMALVGGATGLIGDPRQTSERVLNSQETVAGWVES
+LREQIQPYLSFEGENAATMVNNLDWTAGMSALDFLREVGKNFRVGTMMKKEIVAKRLNSE
+EGISYTEFSYQVLQGNDFLELYRRHGVSLQTGGSDQWGNLTAGTELIRKVEGVPAHALGT
+PLITNADGTKFGKSEGNAIWLDAAMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQKRLAWEVTSLAHGEEATTKVIEASQAVFGGGDLGEVDAETLGAIL
+SELPQADRTQWEGEPGTVTAVELLVSTGLVGSKSEARRTVKEGGASVNNERVSDADRVYT
+REDALAGRHLLVRRGKKNMAGADFGSQDADRG
+>GCF_020097155.1_01378
+MAETTVTRAERLRQQANDPSFENVWQELTWRGLVHVSTDEAALEEALAGEPISYYCGFDP
+TAPSLHLGHLVQLLLMRRLQLAGHRPVALVGGATGLIGDPRQTSERVLNTREVVQEWVES
+LRAQIEPYLAFEGDNGARMVNNLDWTASMSALDFLREVGKNFRVGTMVKKEIVAKRLHSE
+EGISYTEFSYQVLQGNDFLELYRQHGVTLQSGGSDQWGNLTSGTELIRKVEGAHVHALGT
+PLITNSDGTKFGKSEGNAIWLDADMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAAKVDAEPFRREAQKRLAWEVTALAHGEEAARTVIDASAAVFGGGDLSEVDVDVLSAVL
+AELPQADAAQWGAAGKPTAVELLVSTGLVSSNSEARRTIKEGGASVNNVKVADAEQVFGA
+DEALAGRYLLVRRGKKNMAAADLRSGE
+>GCF_023573625.1_01378
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDAFAGRHLLVRRGKKNMAGADLGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001179.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001179.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f34bb80b4da1eed8f95f7002d1b78ed9d01acd83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001179.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_01429
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDAEVGALLRPADAPWTEADVPLLDEAAELLGRLDTPGRGGESAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALDAVEAERDRVPEAL
+TAVIAPAERTGELLTALRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVLPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE
+>GCF_003691675.1_01161
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDVEVGALLRPADAPWTEADVPLLDEAAELLGRLETPGRGGESAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANETRGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALEAVEVERDRVPEAL
+TAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE
+>GCF_005280335.1_01470
+MTDAVSVRQSELELERARVAERYARLDALREEKERQLAAVRRTGLEGSLQNHSERDAFAS
+LYEDRLAQLLAVDDRLVFGRLDLDPERAGDPDEERYIGRIGLTTEEHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDVLDPDLLGQEGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLAGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPERDLDAAAVKGRLEMAQV
+IAHAVAQRQRLLAQPRRLMIEGTAVKLKPAAVRRARDRARATGKPHNEARVTFVKILVRE
+LAEKLSKKLEKSSGAPVQRDLLLEDVRTSRDVRVALNLCWMPLTPQKLVGDLLTREHLLR
+AAAPWLSDGEVGALLRPADAPWTEADVPLLDEAAELLGRLEAPAKGGESAAQHERNLENA
+RASLENMHQTLADMGVDGVVDAEQLAAANEARAVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLEPEFGDRWRLEELTVNYRSP
+ARVMRWASQVAQAAGLEVSRPRAVREGEHAPRLTVRPGADLVALTLDAVAGERDRVPEGL
+VAVITAAAHAPELLAALRERWGRARVDTAPLPGVEIVVATPWETKGLEFDAVVLAAPERL
+VDDARGVVGDLYVAMTRATQSLSVVSTAAVAALPAGLADPPA
+>GCF_020097155.1_01377
+MTDTVSSRQAELELERERVAVRYARLDALRAEKEEQLARVRRSGLQGSVQNHSERDAFAS
+LYEDRLAQLYAVDERLVFGRLDLDADDAGDVEQRYIGRIGLTDEGQERLLVDWRAQEAGA
+FYQATAARRLGVGRRRHLLLRGREVRDFEDDVLDPSLIAEGAAGAQSQGALLAAVTARRT
+GRMGDIVATIQAEQDEVIRADTSGALVVQGGPGTGKTAVALHRAAYLLYTHRDRLAKSGV
+LVVGPSNAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPDRSARAAELKGRLEMADVV
+AAAVAQRQRLIPETRRLEIEGTVVKLKPAMVRRARDRARATGKPHNEARTTFVKILVREL
+AEKLRKKLEKSSGVPVQRDLLLEDVRTARDVRVALNLCWMPLTPQKLVGDLLTKEHLLRA
+AAPGLSDGDVAALLRTDPDAWVESDVPLLDEAAELLGELEEPHRPGESEAQHRRNVENAQ
+ASLENMHQTLAELGVDGVVDAEQLAAANEVRAVRRTTAEQAAHDRTWTFGHVVVDEAQEL
+SPMQWRLLARRCPLKSFTVVGDIAQASRRGGARSWKDVLGPEFGDRMRLEELTVNYRSPA
+RITRWAAQVAQAAGLEISSPEAVREGEHEPLLTVEPGADPTRLAQRVVEAERGRVGDGLV
+AVIVPADDAAEHLTHLQDRWGSLVDRAPAPGVEVVVVTARETKGLEFDAVVLVSPERIVA
+DADGVVGDLYVAMTRCTQSISVVSGAAEEELPAGLMPVPA
+>GCF_023573625.1_01379
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDAEVGTLLRPADAPWTEADVPLLDEAAELLGRLETPGRGGEFAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALDAVEVERDRVPEAL
+TAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001180.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001180.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76adfd48a032fc2fca6da4164bff81e66ebaee8b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001180.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01430
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPHAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALEPLRRWADTPG
+SVVDAR
+>GCF_003691675.1_01162
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVAAELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVRLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVMAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG
+SVVDAR
+>GCF_005280335.1_01469
+MTENPEARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHAA
+GLLGAEDLEGMIAALDRLETDVRSGAYAPADSDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGLVATVDALLSQVQAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARTAVSPYGSGALAGSSLGLDPEAVAAELGFDSAVWNSID
+GTASRDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVKLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLAGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFETERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+EEYAAISPALTPQVREVLSTEGSLNSRDAQGGTAPAAVAAQVEALERTLEPLRRWAQTPG
+SVVDAR
+>GCF_020097155.1_01376
+MSENSTPRHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLTADELAGMIDALDRLEADVRSGAYAPAESDEDVHGSLERGLIERAGAELGGKLRAGR
+SRNDQVATLGRMFLRDHARVVARGVLATVDALVEQAEAHPFAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFTRDLQRLVDWDARAAVSPYGSGALAGSTLGLDPNAVAAELGFDSAVWNSID
+GTAARDVYAEFAWVAGMIGVDLSRISEEVIFWATKEAGFVRLHDSYSTGSSIMPQKKNPD
+VAELARGKAGRLIGDLAGLMATLKGLPLAYNRDLQEDKEPVFDAVDTLELLLPAVSGMIA
+TLSFNTERMAALAPQGFALATDIAEWLVRQGVPFRVAHELSGEAVQVAESRGVELWDLTD
+EEYAGISAHLTPAVREVLSTEGSLNARRGQGGTAPEAVAEQLAALKAALEPLRAFAASAG
+SVVDAR
+>GCF_023573625.1_01380
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG
+SVVDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001181.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001181.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea49c9ea274ab8e8020d1113ef6ea1672fa420b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001181.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01431
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAQRNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+HVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGSDDLQDVARLSND
+>GCF_003691675.1_01163
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADAREEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+QVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGGDDLQDVARLSND
+>GCF_005280335.1_01468
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTRDKAIDYAERNELPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFSPAPDVVTIAFERGVPTALDGRALSSLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+TVDQRWTELVYDGQWFSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASERDQRLRGGDDLKDVARLANS
+>GCF_020097155.1_01375
+MKDRIVLAYSGGLDTSVAIGWIGEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNELPIATTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFEQGVPTALDGRALSALEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+QVDQRWTELVYDGQWFSPLKKSLDTFIDDTQKHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIYGLSAKTASEREQRLGGAADLADVARLSND
+>GCF_023573625.1_01381
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+HVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGGDDLQDVARLSND
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001182.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001182.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d671ff9ab133bc259ac62f5ea4c484561ad526c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001182.fa
@@ -0,0 +1,33 @@
+>GCF_002008305.4_01432
+MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESSGTWD
+INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL
+TQADADAGDVDAAPVAVERTATVQRQSAADETAADQAAAEQAAADQAAAEQAAADQAAAE
+RWAAKQAAADQAAAERWAAKQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAEKAAAQKAA
+AAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWTALYEANKG
+AVSDAAVIYVGQELVLPQA
+>GCF_003691675.1_01164
+MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESNGTWD
+INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL
+TQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAEQAAADQAAAERWAAEQA
+AADQAAAERWAAEQAAAEQAAAERWAAKQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAE
+KPAAQKAAAAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWT
+ALYEANKGAVSDAAVIYVGQELVLPQA
+>GCF_005280335.1_01467
+MDTMTLFTSTRTRRTTASVAAGMTLMGAAAVGFSAPAQAATEETWDAIAFCESTNRWDIN
+TGNGFYGGLQFTLSSWQGVGGQGYPHQASKAEQIKRAEMLQDLQGWGAWPKCAAGLTQAD
+ADATDAAPVAVERTSSVQRQAAAEQAAAEEAAAEQAAAEEAAAEQAAAEQWAAEQAAAEQ
+AAAERAEAKRAAAAEKAAAKKAAAAERAAAHQAAAEQAVVAEAETIVVKAGDSLWKLAAE
+HEVEGGWTALYEANKDTVSDAAMIYVGQELVLPQA
+>GCF_020097155.1_01374
+MTFFTTSSRRATATALTGMTLVGAAAAFAAPAQAASVETWDKIAACESNGNWAINTGNGY
+YGGLQFSLTSWRGVGGTGYPHEASKAEQIKRAEILQDMQGWRAWPVCSVKAGLSGADTAP
+DAYSTTPVQRQSTQASASAAQDWAAEQSAAEQRAAEKAAAQRAAAAAHTPKSVLKAAEKA
+NTENATELAAAEDTVFVKPGDSLWKIAKTHKVAGGWKALHEANKDIIEDASVIYVGQELV
+LPTA
+>GCF_023573625.1_01382
+MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSALAQAATVDTWDRLAECESNGTWD
+INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL
+TQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAEQAAADQAAAERWAAEQA
+AADQAAAERWAAEQAAADQAAAERWAAEQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAE
+KAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWTALYEANKGAVS
+DAAVIYVGQELVLPQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001184.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b445adba7c9e079de95b1860fc910ceb1d178b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001184.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01434
+MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV
+SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS
+SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRTLTYLGDAANNMAHSYLLGCATAGMH
+VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAAEALAGADVVVTDTWVSMGQEEEK
+EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA
+QKALIAWLLYRSGLAEEPR
+>GCF_003691675.1_01166
+MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV
+SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS
+SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGCATAGMH
+VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSMGQEEEK
+EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA
+QKALIAWLLYRSGLAEEPR
+>GCF_005280335.1_01464
+MTPAPTPAPAAVRHFLVDTDLTPGEQAEVLDLAAQMKTDRFAHRPLAGPRTGVVFFDKTS
+TRTRVSFAAGIAELGGSPLIVNPGESQLGHKESVADTARVLERMVGIIVWRTFAQSGLEE
+MAAHSRVPVVNALSDDYHPCQILADLLTVREHLGGTQGRVLAYLGDAANNMAHSYLLGCA
+TAGMHVRIAGPAGHLPAEHVVAAARERAAETGGSVLVTTDAAEALDGADVVVTDTWVSMG
+QEDEKEARLALFRDYQVDAAAMARAGSDAIFLHCLPAYRGYEVSAEVIDGPQSVVFDEAE
+NRLHAQKALMAWLLYRSGLAEDPR
+>GCF_020097155.1_01372
+MTAAPGTDVPVRHFLVDTDLSPAEQAEVLDLALEMKADRFRHRPLAGPQTGIVFFDKTST
+RTRVSFAAGIADLGGTPLIVNPGESQLGHKESIADTARVLERMVGVIVWRTYAQSGLEEM
+AAHSRVPVVNALSDDYHPCQLLADLLTVREHKGRTRGLTMAYLGDAANNMANSYLLGGVT
+AGMHVRVAGPEGFLPDPAVVRAAEERAGETGGSVLVTTDAAAALDGADVVVTDTWVSMGQ
+EDEKEERLRLFADYRVDAAAMARAASDAVFLHCLPAYRGYEVTEDVIDGPQSVVFDEAEN
+RLHAQKALMAWLLYRSGLAQDPR
+>GCF_023573625.1_01384
+MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV
+SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS
+SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGCATAGMH
+VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSMGQEEEK
+EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA
+QKALIAWLLYRSGLAEEPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001187.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001187.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa900f915174612a215c9e320032a4f757a2338b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001187.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01437
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNQGPRDAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLEDARRTAEHAAAALGTAADDVLVCSTGLIGERLPMDT
+LTAGVAEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPAAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLTAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>GCF_003691675.1_01169
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNEGPRDAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLEDARRPAEHAAAALGTSADDVLVCSTGLIGERLPMDT
+LTAGVAEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPEAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLSAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>GCF_005280335.1_01461
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNDGPRRAAAAVFTANRVAAAPVLWSRQAVS
+DGRADAVVLNSGGANAATGAPGFQDAHATAEHAAEALGVSSGDVLVCSTGLIGERLDRER
+LFAGVAAAAGALSADGGEDAAVAIKTTDTVAKTAQARGEGFIVGGMAKGAGMLAPGMATM
+LCVITTDADVPAAVLDAALKDAVRTTFNRVDSDGCMSTNDTVILLASGAAGVAPDPEAFA
+ATLHEVCADLSRQLVADAEGAAHDVAVRVHGAQTEDAAEAVARAVTRSNLFKAAIFGQDP
+NWGRVIAAVGTVPEEVAAFDPYALDVSFNGVQVCRGSGVGEDRALVDLSAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>GCF_020097155.1_01369
+MSVTAAQGFRAAGVTAGLKPSGKPDVAVVVNDGPSHTAAGVFTTNRVAAAPVRWSRQVLT
+DGRADAVVLNSGGANAATGHAGFQDAHRTAEHAAEALGVSAGDVVVCSTGLIGERLPLDT
+LLAGVDAAAAGLAEDGGADAALAIMTTDTVPKEAQASGEGWTVGGMAKGAGMLAPGMATM
+LCVVTTDADLPAAALRAALEEAVRTTFNRVDSDGCMSTNDTVVLLASGASGVAPEPTQFG
+AALHAVCADLARQLVGDAEGAGHDVLIRVVNASDEDAGEAVARAVSRSNLLKTAIFGQDP
+NWGRVISAVGTVPEEVAPFDADALDVSFNGVQVCRAAGVGDSRAGVDLSGREVVIEIDLH
+AGDAVVELWTNDLTHDYVHENSAYST
+>GCF_023573625.1_01387
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNEGPRRAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLADARRTAEHAAAALATAADDVLVCSTGLIGERLPMDT
+LTAGVSEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPEAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLTAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001188.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001188.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6bcb7227f1a752b414fda359228b3d789bbc90a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001188.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01438
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMPR
+GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAVLDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
+>GCF_003691675.1_01170
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTADVLAGHDVVILALPHEASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR
+GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
+>GCF_005280335.1_01460
+MTHTVAVSGASGYAGGEALRLLAGHPDVAVGAITAHSNAGERLGALQPHLHSLADRVLEE
+TTADVLAGHDVVILALPHGASGALAAQIAERSPETLVIDAGADHRLESAADWEAFYGSEH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLSQAAGERVQISFTPTLAPMAR
+GILATATARLRPGADPAAVRGAWERAYADERFVHLLPEGLWPATKSVLGSNHVQMQLAVD
+ERAGRVIVTAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
+>GCF_020097155.1_01368
+MTFTVAVSGASGYAGGEVLRLLAGHPEVQIGAISAHSNAGERLGSLQPHLHALADRVLDD
+TTADVLAGHDVVVLALPHGASAAVAAELAERSPRTLVIDAGADHRLESAADWERFYGTDH
+AGTWPYGLPELPGQRERLAGATRIAVPGCYPTTSILALAPGFAAGLLETRDVVIVAASGT
+SGAGRAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVQISFTPTLAPMPR
+GILATATARLKEGVTADRVRAAWEDAYGPERFVHLLPEGQWPTTKAVVGSNHVVMQLAVD
+PHAGRVIVTAALDNLTKGTAGGALQSMNIALGLPEQLGLEIQGVAP
+>GCF_023573625.1_01388
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR
+GILATATARLRPGVAAADVRDAWAEAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001189.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001189.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10de9118566bf38c67a080d71551f401f920646a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001189.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01439
+MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS
+GVYTMDLPFTPGTEGSGEVVALGEGVDAGLLGARVATATATGAYAEHFTAPADRLLTVPE
+GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT
+ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHVVYDGVGKDTFDTSLEVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD
+VRIGERFPLADAAAAHAALESRSTTGKVLLTLS
+>GCF_003691675.1_01171
+MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS
+GTYAMDLPFTPGTEGSGEVVALGEGVDAALLGARVATATATGAYAEHFTAPADRLLAVPE
+GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT
+ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHVVYDGVGKDTFDTSLEVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD
+VRIGERFPLADAAAAHAALESRSTTGKVLLTLS
+>GCF_005280335.1_01459
+MPHASSPAVPRTHHAVVVAETGGPEVLRWTQADVPAPGPGRVLVRTAAVGLNYIETYQRA
+GVYPMDLPFVPGTEASGTVVGLGEGVDPTLLGARVATATAQGAYAEHFTAPADRLLTVPE
+GVDLADAAALPLQGMTAHYLCRSTFPVEEGQTVVVTAGAGGVGLLLTQLAAARGARVITT
+ASTEAKRELSRAAGAAAAVDYPELAATVDRLTDGHGAHAVFDGVGKDTFETSLRVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGGLYVTRPSLVHYTRTEEETRGRSDELFAAWAAGELD
+VRIGERIPLAEAAAAHAALESRATTGKVLLTLG
+>GCF_020097155.1_01367
+MSTHAEIPARHHAIIAEEVGGPEVLRWTETAVPTPGAGEVLVRTAAAGLNFIETYQRSGV
+YAVPHPFTPGSEGSGVVVALGPGVDEALRGARVATAAGRGTYAEHFTAPADQLLHVPAGV
+DLADAAALPLQGMTAHYLCRSTFPVEPGHVVALTAGAGGVGLLLTQLAAARGATVITAAS
+TEDKRALSAAAGASAAVPYAELRQTVLDATGGEGAHAVFDGVGADTFEDSLASLRVRGTL
+VLFGGASGQVPPFDLQRLNSGGGLYVTRPSLAHYTRTAEETAWRGRELFDAWSAGALDVR
+IGARVPLAEAGRAHTLLASRATTGKVLLPLS
+>GCF_023573625.1_01389
+MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS
+GVYTMDLPFTPGTEGSGEVVALGEGVDAGLLGARVATATATGAYAEHFTAPADRLLTVPE
+GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT
+ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHAVYDGVGKDTFDTSLEVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD
+VRIGERFPLADAAAAHAALESRSTTGKVLLTLS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001190.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d510df962951a013ae3ba0408c397144fa58b14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001190.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01441
+MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS
+RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLHQRVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM
+MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW
+FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG
+PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH
+AGVSRAQVDELFDAWTLRPELPPFPG
+>GCF_003691675.1_01173
+MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS
+RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLDQPVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM
+MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW
+FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG
+PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH
+AGVSRAQVDELFDAWTLRPELPPFPG
+>GCF_005280335.1_01457
+MSTDPYVPGVGTDAAVIEHVVLDLDVRLAANRVSGTAVLSVRLTRQSRRIELDLHRLRVS
+KVGAAVDGRALPASFSQPRRWPSRLVVDLGESRPEGTLVELTVAYAGTPTPRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPVSRSTADITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLTQPVPAYLLTVQIGRYRLVDAAAPADGLPPLRLVASTRTEQRARAALATQPAM
+MAAFIAAYGPYPFEEYTAVVADDVLEIPLEAAGMSLFGTNHLDGSWESERLIAHEMAHQW
+FGNAVTLGRWADLWLHEGFACWSEWLWAEASGRSSIASMARRAWQRLAEDPVEHVLTEPG
+AAEMFEDWVYKRGALTVEALRVLLGREVFGSMLRAWVDEHRFGTVDTAGLRAHVHAWAPR
+AQVTPEQVDELFEAWTRRPELPPFPG
+>GCF_020097155.1_01365
+MSTDPYIPGVGSDTATIEHLRVELDVRLASNRVAGVAELHVRLCRQSDTVELDLHRLAVD
+GAAGTHDGRPLKVRATTPRNRPHRVVVHLGASLPEGSLVVLRLSYSGHPRPRRSPWGTIG
+WEELTDGVLVAGQPHGASTWVPCIDSPAVRQTADITVTCDAGYLPVANGRGTRLRSRGSR
+ETWRWVMDRPVPAYLLTLQIGRYRQVTAPGSGTPESAAAGGVPPLRLVVSPRLQARAEAA
+MAGQGRMMEAFTAAYGPYPFDDYAAVVADDVLEIPLEAAGLSLFGVNHLDGSWESERLIA
+HEMAHQWFGNAVTLGRWSDLWLHEGFACYSEWLWAEASGRAALRHEAKQAWHGLKRQGED
+LVLAAPGAADMFDDRVYKRGALTVLAVRTLLGDAVFGEMLRDWVARHRFATVDTPGFRAH
+VLAWAPRADVAPEDVDALFDAWTLRPELPAFPG
+>GCF_023573625.1_01391
+MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS
+RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLDQPVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM
+MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW
+FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG
+PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH
+AGVSRAQVDELFDAWTLRPELPPFPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001191.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001191.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c2fa5aa0e0ce64c678f4c28eef0586c304dc8e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001191.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_01442
+MSVATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACPRCGSAAH
+GVPALTGLPPGRVALVSFTRVRMPGTEDRARIGAWWAPARPADGLGLGVDVERADAAAFA
+DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV
+PADVVLVDLTDRLPGGLLGALALRGR
+>GCF_003691675.1_01174
+MSVATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACPRCGSAAH
+GVPALTGLPPGRVALVSFTRVRMPGTEDRARIGAWWAPARPADGLGLGVDVERADAAAFA
+DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV
+PADVVLVDLTDRLPGGLLGALALRGR
+>GCF_005280335.1_01456
+MPGGDGDGAEDAAGPDDGPAAAPGLGLDVERVDAPAFADRDALGEVGFSTAERAWVAALP
+RSERPAARARLWTRKEALVKAAGTGFTGDPADVAALHPPPGVVLLDVAAGLPDGIVGSVA
+LRRA
+>GCF_020097155.1_01364
+MTTAPTSPTRGIEVGAVGVSRTEGTAQVLAALGTRLGLGPRALALAHSCPGCGATDHGAP
+ALRRAGDGTTPGGAPGDDGGPVLPAVSLTHVDGPRPVTVLAWCTPSVAGTAWGIGVDAED
+PTAPQTLRAFAAGADGAAEIDAVAFAAEERAALAGLSPEGALAERVRLWTVKEALVKARG
+TGLDRDPAEVRPQLGEAVVPLADPRLPPGVVGTVAWRPAS
+>GCF_023573625.1_01392
+MSAATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACAGCGSAAH
+GVPALTGLPPGRVALVSFTHVRMPGAEDRARIGAWWAPARPADGLGLGVDVERADAAAFA
+DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV
+PADVVLVDLTDRLPGGLLGALALRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001195.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001195.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a86c90699f691af6f100508a7ee0d503ec96ad4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001195.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01447
+MFESTRKRVRVRAWRGRRDAPTVVAMTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDA
+VGILADRGVTAEAVELPCAFGAAGPALTAALDRVRPEVAIAVGLAGGTATVRVERVAVNL
+QDARIPDNAGEQPVDRPVRADGPAALFATLPAKRAVAAIREAGVAAEPSLSAGAFVCNHV
+MYSLLDGPGTARAAGFIHVPWDTEHRPTPDTPALPAADLARAVAEAALTALAGGPDLDVP
+GGTLH
+>GCF_003691675.1_01179
+MTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDAVGILADRGVTAEAVELPCAFGAAGS
+ALTAALDRVRPEVAIAVGLAGGTAAVRVERVAVNLQDARIPDNAGDQPVDRPVRADGPAA
+LFATLPAKRAVAAIRAAGVAAEPSLSAGAFVCNHVMYALLDAPGTARAAGFLHVPWDAEH
+RPTPDTPALPAADLARAVAEAALTALAGGPDLDVPGGTMH
+>GCF_005280335.1_01452
+MTTPASASAVRVLLTGFEPFGGDGHNPSIVAARDAVALLAERGVAAEAVELPCAFAAAGP
+ALAAALERTRPEAAVAVGLAGGTAAVRVERIAMNLQDARIPDNAGDQPVDRPVRAEGPAA
+HFATLPVKRAVEAVRAAGVPAEPSLSAGAFVCNHVLYALLDAPGTARAAGFVHVPWDLAH
+RPRPDAPALPAEDLARAVAEVALVALEGGADLDVPGGTLH
+>GCF_020097155.1_01356
+MTDPVRVLLTGFEPFGGDDHNPSIEAARAAAAALTADGTPAVAVELPCVFAAAGPALAAA
+LEAHRPEIAVAVGLAGGTAAVRVERVAVNLQDARIPDNAGDRPADRPVRSGGPAAHFATL
+PVKRAVAAVREAGVPAEPSLSAGSFVCNHVMYSLLDAPAPARAAGFVHVPWSREHAPTPQ
+TPALPAADLARAVAAVARAALVEGPDLDVPGGALH
+>GCF_023573625.1_01397
+MTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDAVGILADRGVTAEAVELPCAFGAAGP
+ALTAALDRVRPEVAIAVGLAGGTATVRVERVAVNLQDARIPDNAGEQPVDRPVRADGPAA
+LFATLPAKRAVAAIREAGVAAEPSLSAGAFVCNHVMYALLDAPGTARAAGFIHVPWDTEH
+RPTPDTPALPAADLARAVAEAALTALAGGPDLDVPGGTLH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001199.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001199.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac71a94769ae8bb0df8d4ac6d440e6cd818fcde4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001199.fa
@@ -0,0 +1,33 @@
+>GCF_002008305.4_01452
+MTPHAEPMTHPRAERVRAVAALAGRSARRRTGTFLVEGPQACREALRAHLGEGPTAAAGQ
+WRAGRVLTQVYVSGGLVDRDPALAELVARVRDRPTPGGERVLVREASDEVLTAMADAVTG
+QDIVAVARMPEPQAVEAVLEEARLAAVLCRVQDPGNAGTVIRAADAAGADAVVLTPGSVD
+PFNPKVVRSTAGSLFHLPVATAVPAEAAAAAARAAGLQVWAADGYASDRLDALAPGVVAA
+PTAWLFGNEAQGLDDGELALADRRVAVPLYGAAESLNVGTAATVCLYSSAMAGARRAG
+>GCF_003691675.1_01184
+MTPPAEPLTHPRAERVRAVAALAGRPARRRTGTFLVEGPQACREALRAHLGEGPAGAARQ
+WPAGRVLTQVYVSAGLADRDSELAALVERVAADGPDGGERVFVREASDEVLTAMADAVTG
+QGVVAVARVPDQPALEDAFDGAALAAVLCRVQDPGNAGTVLRAADAAGADAVVLTAGSVD
+PFNPKVVRSTAGSLFHLPVLAGVQAEDVAVTARAAGLQVWAADGHGSDRLDALSPASLGA
+RTAWLFGNEAQGLDEAELALAERRVAVPLYGAAESLNVGTAATVCLYASAMASPTTRD
+>GCF_005280335.1_01447
+MARVKRAVNAHKKRRTMLELASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVKTAREALPAD
+VNAPRRLPLVGPGTPGSPPRVRRGHRRRRGGPSDEEARPVGVCAPAPRRTRPGEPMTPPA
+EPLTHPRAERVRAVAALAGRPARRRTGTFLVEGPQACREALRAHLGEGPAGAVRQWPAGH
+VLTQVYVSAGLAERDPDLAALVERVADGGPGGERVLVREASDEVLTAMADAVTGQGIVAV
+ARIPDQPPLADAFDGAALAAVLCRVQDPGNAGTVLRAADAAGADAVVLTAGSVDPFNPKV
+VRSTAGSLFHLPVLTGAEAAAVADASRGAGLQVWAADGYGDDRLDALAPETTAAPTAWLF
+GNEAQGLDEAELALADRRVAVPLYGAAESLNVGTAATVCLYASAMAAAVRRDG
+>GCF_020097155.1_01351
+MSRAPQPDDELMQNPRAERVRAVAALAGRAARRRSGTFVVEGPQSCREALRAHLGEGPER
+TRAQWRPGAVLTQLFVAPDLFARDPGLGDLVARLHDLTGPDRVLVREATDEVLTAMSDAV
+TAQGIVAVARIPQPLTAEDAWSDARLAAVLCRVQDPGNAGTIVRAADAAGADLVAFTAGS
+VDPFGPKAVRSTAGSLFHVPLVVGTEADAAADAARAAGMQVWAADGYGADRLDALEQDVL
+GAPTAWLLGNEAQGLSAAELELADRRVAVPLYGAAESLNVATAATVCLYASAMAAPHA
+>GCF_023573625.1_01402
+MTPHAEPMTHPRAERVRAVAALAGRSARRRTGTFLVEGPQACREALRAHLGEGPAAAAGQ
+WRAGRVLTQVYMSVGLVDRDPALAELVARVRDRPTPGGECVLVRQASDEVLTAMADAVTG
+QDIVAVARMPEPQAVEAVLGEARLAAVLCRVQDPGNAGTVIRAADAAGADAVVLTPGSVD
+PFNPKVVRSTAGSLFHLPVVTAVPAEAAAAAAWAAGLQVWAADGYGSDRLDALAPGVVAA
+PTAWLFGNEAQGLDGGELALADRRVAVPLYGAAESLNVGTAATVCLYSSAMAGARRAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001202.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001202.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf4102b2cbe58fdfb607e896a68ee6c0c3fa6b97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001202.fa
@@ -0,0 +1,19 @@
+>GCF_002008305.4_01456
+MVYGKLTTMTDERQAQDATPMDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSP
+DARELIDLDEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGK
+GPGEKFTGPVN
+>GCF_003691675.1_01188
+MDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSPDARELIDLDEARKLITALAG
+LVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTGPVN
+>GCF_005280335.1_01444
+MTDERQAHDANDQDSPAEVRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSPDARELVDL
+DEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTG
+PVN
+>GCF_020097155.1_01347
+MTDQNQHQHAAGEDVPTEVREIHEVPAVEVITTTAVHLMTAAAVKVGLADSPDAREMTDL
+DEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTG
+PVN
+>GCF_023573625.1_01406
+MVYGKLTTMTDERQAQDATPMDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSP
+DARELIDLDEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGK
+GPGEKFTGPVN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001203.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001203.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7db44fdacc62bd605bffc7d06429e9d84371b2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001203.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01457
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAAVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA
+>GCF_003691675.1_01189
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA
+>GCF_005280335.1_01443
+MAQSRRPDPVDPREAPAAPAPEGPRTGGRAPVAALVVAAALALQAAALLWLAGDAIAHLG
+DGVLPAGARVMLIVIYVLLGLWILVTSVALLRGRAWSRGAATAVQLFGVLLSSRLLSVGE
+PVVGGVLLAVSGIALVTLFSRPVTAHLSQAAREPSAE
+>GCF_020097155.1_01346
+MSSSIPASPSGRRRMPAQAVVVAGVLGLEALTLVWLAVDGVAHLGAGALPTAAGVFLVVV
+YVLLAAWVGAVCGGMVRGRRFSRGAAVAIQLFAVILSTWLMSIGAPIAGGLLLVGSGAAL
+LCLFSGAVQAHLAGPDAGRPDAGRPDVG
+>GCF_023573625.1_01407
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001204.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001204.fa
new file mode 100644
index 0000000000000000000000000000000000000000..554b02be55e28b7b05315da6a4879c4f9bce177b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001204.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01458
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>GCF_003691675.1_01190
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>GCF_005280335.1_01442
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>GCF_020097155.1_01345
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRTCEVIDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>GCF_023573625.1_01408
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001206.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001206.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f22aa69761b69df4cb8ec47cc8a1a5a315363a7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001206.fa
@@ -0,0 +1,51 @@
+>GCF_002008305.4_01460
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDLAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRTERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRGADEPDDAGPGAAPAA
+ATPDGGPATADEGADPAPSPEEGEPAGPARESLVTVVWGPTGAPGRTTVAVNLAAEHAVA
+GRNTLLIDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAARERWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEVAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDTGRPARRRTLIPWSVRSRRTP
+>GCF_003691675.1_01192
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRDADEPDDAGPGAAPAA
+ATPDDGPATAGEGADPAPSPEEGEPTAPARESLVTVVWGPTGAPGRTTVAVNLAAEHAMA
+GRNTLLVDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAAREHWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP
+>GCF_005280335.1_01440
+MTVRIALATTVLPGLDHIGPLERHQTRITVVRRAEDLAELLAIARSGLVDAVLVAGATEA
+VTGAFLEELARLPRPVGAAAISEVRAERRRLRALGVPCVRADAGPEPLAAAVVEAALAAA
+DGRRARADAVAEDEGGEDPVDGLDGIELTYGVLDDDPRLGPPLLGGDPERSAVSAARPEA
+GAGDEAVDDGRRGGRAGDDLVPADAAQGGVTRDGVAQDRAQDGFARDDAQDFAAWDADAA
+GRSVPDVDRPDPRDPDGDAAEHAEDRPDVEASGTPGDARVIVVWGPTGAPGRTTVAVNLA
+AEHAVAGRSTLLVDLDTYGPSVGAHLGLTEESAGVARAVRRADHGPLGPADLEAAGVRVR
+VAGAELTVLTGLTRVDRWPELRPSALTSLLAAARGRWERVVVDVGFGLEQDEELSFDVPA
+PQRNGATLAALAAADEVLAVGGPDAVSLPRLVRGTEELVEAAPEARLRVVVNRLRPAAAG
+VSPRSQVEAVWSRYASAGIPLAAFLPWDPAAADRALLGGQVLAEAAPNSALRRALAELAD
+VDPRGARRTGRRRRPTGQGPAGAARRHPQDEGAARPSRRRTLMPWSARSRRTP
+>GCF_020097155.1_01343
+MRVALATTLMPGRDHVGPLEQAQAEVTVVRRAEDLAELLAAARSGLVDAVLVAGDLSALA
+RGFVDEVREAPRPVAVVAMGEVRAERERVRTLGVPCLSADADPLALAAAVQSAVRARLTG
+ARPELGSETPPADPPAPAPGTPDGGDPEAVRVAAVRDREGTPRLPEPNPVRVDALAASEV
+DALFTEETSPVAAADEAGPASPDAAGPDAVTASPADTAPEDGPEGGPERGRTGRTVAVWG
+PTGAPGRTTVAVNLAAESAVAGLRTLLVDLDTYGPSVGVHLGLTEETAGLARAVHRAERG
+SVTREDLVDAAVRVRVAGGDLDVLTGLTRPDRWPEVRPGALREVLQAARDGWDRVVLDLG
+FCVEEDEELSFDVPAPQRNGATLAGLAAADRVLVVGGADAVAMPRLLRAVEALPAGVEQD
+RVRVVVNRVRPQASGVAPQAQVAGVWERYGPPIPLVAQLPWDPGAADRALLGGQVLAEAA
+PGSALRAAVLELARLDPAVAARTQSAGRGRRPAVRGLRRRLAPWSAPSPRTP
+>GCF_023573625.1_01410
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRDADEPDDAGPGAAPAA
+ATPDDGPATAGEGADPAPSPEEGEPTAPARESLVTVVWGPTGAPGRTTVAVNLAAEHAMA
+GRNTLLVDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAAREHWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001207.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001207.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0b897cbd703c9fb63f8f34e8d0687e05ca3cdf6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001207.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01461
+MSASAEGGRLRRPRWRDPRLLVGLVLVLASIAGVVALVASAQQTAAYWTAAEDLPPGTPI
+ASGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV
+ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVAAEQNGFGGSGTTRV
+QLLAPEETLPRIVDAKVKDARVTLVPAHGVR
+>GCF_003691675.1_01193
+MSASAEGGRLRRPRWRDPRLLVGLMLVLASIAGVVALVASSQRTAAYWTAAEDLPPGTPI
+AAGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV
+ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVTAEQSGFGGSGTTRV
+QLLAPEETLPRIVDAKVKDARVTLVPAHGVR
+>GCF_005280335.1_01439
+MSTSTSASAEGGRLRRPRWRDPRLLVGLVLVLASVAGVVALVASSQRTSAYWAAAVDLPP
+GTPLEAGQLRAVEVNLADAEGKYVAAAPDSAPSGRMVASTVRAGELLPAAALVDADPEGR
+RPVGVRLREPLAGGVGVGDRVDVWVAMPAEGGRGHADPERLAEALEIAEVATEQGSIGGS
+GETRVQLLAPEATLPRVVDAQVKDARITLVPAHGVR
+>GCF_020097155.1_01342
+MTTDPTAPAEGARLRRPRWRDPRLLVGLVLVLASLAGVTAIVAGAQRTQTYWAAARDLAP
+GAPVPADAFVPVDANLADAAGHYLRADAPAPAGKVVGAVVRAGELVPADALADVDPQRRR
+PVGVQLAEPLPAGTSAGDRVDVWVAARQDDGRDYEAPRRIAEGLEISELTEAEGGFGTGA
+TTRLQLMAGEDVLAQLLDAKVSEARITVVPALGEG
+>GCF_023573625.1_01411
+MSASAEGGRLRRPRWRDPRLLVGLVLVLASIAGVVALVASAQRTAAYWTAAEDLPPGTPI
+ASGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV
+ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVTAEQNGFGGSGTTRV
+QLLAPEETLPRIVDAKVKDARVTLVPAHGVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001210.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001210.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c850b33b3f68569a70e8e1af1abe157a3376b06b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001210.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01464
+MERSTSPAGPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGTSAPGAELTRVLGLG
+AGLAGLGLLAWWAVGLIGLALVALGRRAGRPAWARLGRSLTPALLGRVAGAVVGAQLLAA
+PAAWADAAHPVPDASWTVAAVPAHATGVEAPAPDAAWTPRPPAPAPPGAGTGRADPDHPT
+VTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRRVIGDDPHLLLPGTVLTSPVFT
+PHAGVDGPRP
+>GCF_003691675.1_01196
+MERSTSPAGPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGTSAPAAELTRVLGLG
+AGLAGLGLLAWWAVGLTGLALVALGRRAGRPAWARLGRSLTPALLGRVAGAVVGAQLLAA
+PAAWADAAHPVPDASWTVAASPTHATGVEAPAPDAAWTPRPPAPAPPGAGTGRADPDHPT
+VTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRRVIGDDPHLLLPGTVLTSPVFA
+PHAGVDGPRP
+>GCF_005280335.1_01436
+MQRITEPARRGRAALSEADGHRADGHRVDTVDAVGLVVLALAAPALLIGAAALLEPGEGA
+ASSELVRLLGLGAGIAGLGLVAWWAVGLLGLVLATVGRRTGRLGFARLGARLTPALLGRV
+AGAVLGAHMLAAPAAWAEQPAVGPVPDAGQTVSHAAPASTTASAPAAVPEAAWTPRTPVP
+APPGATAARNLSDRPTVTVRRGDCLWDIAAAELGPDATPREIDARWRRWHEANRRVIGDD
+PHLLLPGTVLTAPVFSPHAAPQEGLAMTPRPRTTPTTTRPQEPAMTALAARPPSPPSTAA
+PAVSPGTPTVAPTVPPPRCCTVPPTARPCCPAARRSPAGPPSSRAGRSCVGSAPWPR
+>GCF_020097155.1_01339
+MSFVASQPPAAGVHAPRASALDVAALAVLAAAVPALGWAAATLLGPAAPTPDAALGRALG
+LGAAGLGLALAAWWALGLLGLAALALGRRTGHRGWSRLGERMTPALLRRAGAAVLGAQLL
+AAPAAWADAPPAPSAAVVDASWTSAAASPTLPDAAWTPGAPPTPQPGSPAAPRDTGDRPT
+VTVRAGDCLWDIAADELGPDATPREVDRRWREWHRHNRDLIGEDPNLILPGTVLTAPDFT
+PHVQRGGTP
+>GCF_023573625.1_01414
+MERSTSPAGPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGTSAPGAELTRVLGLG
+AGLAGLGLLAWWAVGLIGLALVALGRRAGRPAWARLGRSLTPALLGRVAGAVVGAQLLAA
+PAAWADAAHPVPDASWTVAAVPAHATGVEAPAPDAAWTPRPPAPAPPGAGTGRADPDHPT
+VTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRRVIGDDPHLLLPGTVLTSPVFT
+PHAGVDGPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001211.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001211.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2274ce896f40e08935f935aca62193ee50fb6647
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001211.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01465
+MTTLATRPRAASDRRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPKSA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG
+>GCF_003691675.1_01197
+MTALATRPRTASARRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPASA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG
+>GCF_005280335.1_01435
+MIAVACVEVETGRRALRDLSAWLSPEVLDKMTRRMDLLGLAEQDRPRARSAAAGVSRAPA
+AAPRPVGARVCEVAPGRVEASATVLCDGRARAFALRLERRISRWKVTSVEIG
+>GCF_020097155.1_01338
+MTHSVRADRTMIRTSADRPAHRPAQEDPMTTLAPALAHGPTRPRPVSRTAPSRRDTESAL
+LRGPARRMSAVPTGEDLVRRAEQEDDREELRRLRSLAAVVAVACVETEAGRRPVRDLAGW
+LAPETYEKMCRRVDLLERTGTRPPSGSAPRPVGARVCAVRPGAVEASATVLVAGRARAVA
+LRIERRLSRWKVTHLEIG
+>GCF_023573625.1_01415
+MTTLATRPRAASDRRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPASA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001212.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001212.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9cede7ebe882f160eab541a85e621f4eae97e077
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001212.fa
@@ -0,0 +1,85 @@
+>GCF_002008305.4_01466
+MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV
+VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAQAEAAVED
+AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVMNRQREAIYTDR
+RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL
+DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPASTSLP
+GVQDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS
+RRQAERRGRRG
+>GCF_003691675.1_01198
+MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEANTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNREPQRVDRNDVVYKNEKVKFDAV
+VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVED
+AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVLNRQREAIYTDR
+RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGQATDWDLDQLWRDLAEIYPVGVSQEDVL
+DEVGGRGRLTAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRHWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLP
+GVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS
+RRQAERRGRRG
+>GCF_005280335.1_01434
+MPSIIDRVLKISDNRVLRRMQGTVDAVNLLEEDFRALSDAELRAETDTLKARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+TGRGVHVITVNDFLASYQAELMGRVFRFLGMETGVVVAGQLPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEEGSDYEVDHKKRTVGVLGPGIEKVEDHLGIANLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYDKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV
+VEDIAERHERRQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPQVLAEAEAAVED
+ANREVLEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVMNRQREAIYADR
+RSILEGEDLKDRVRRFVEDAVGNIVDATTEEGHAADWDLDQLWRDLSELYPVGITQEDVL
+EEVGGRGRLKAEDLRRELVSDALLAYEDREAQVGSEALREAERRVVLSAIGRRWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAGIREDSVSTLFKAQITAAPAPTSLP
+GIKDARGLTMTPQISVEGVEAPQRPSQLRFTGPSEDGQGAVTRAGTETGATVEAGTNRRS
+RREAERRERRS
+>GCF_020097155.1_01337
+MPSIIDRVLKISDNRVLKRMRGTVDAVNLLEDDFRALSDAELRAETDSFKKRLADGETLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGLALHQGNIAEMKTGEGKTLVATAPAYLNAL
+TGKGVHVVTVNDFLASYQADLMGRVYRFLGMETGVIVSGQDPATRRAQYAADITYGTNNE
+FGFDFLRDNMAWSKEELVQRGHHFAIVDEVDSILIDEARTPLIISGPAQGDISRWYGEFA
+RLVRSLERGTDYEVDEKKRTVGVLEPGIEKVEDHLGIANLYESQNTTLVQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLAGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLSGMTGTAETEAAEFTSTYGLGVVVIPPNREKQRVDRNDLVYKNEKVKFDAV
+VKDIAERHATGQPVLVGTTSVEKSEYLSTLLTKAGVRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLEQAEAAVQD
+AREKVREAGGLYVLGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDDLMRNFNPGAA
+QRIMNSASIPDDMALEFKMVSSAIQNAQSQVEGRNAEQRKNVLKYDDVMNRQREAIYADR
+RAILEGDSLGERVRGFVEDAVGAVVDAATEEGAPVDWDLEKLWETLREVYPVGISPEDVL
+EQVGGRGRLKAADLKRELVSDALLAYDDREAQVGSEALREAERRVVLAMIGRHWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGFTMFQAMLAAIKEDSARTLFHAQIAAAPAPTQLP
+GVKDARAMTMVPQISVEGVETPRQPARLHLSGPSEDGEGVEEKDLAADGAQTPAGANRAS
+RRAEARRRRRGED
+>GCF_023573625.1_01416
+MPSIIDRVLKISDHRVLKRMQATVDAVNLLEDDFRALSDAELRAETDALRARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV
+VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVED
+AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLQYDDVMNRQREAIYTDR
+RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL
+DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLP
+GVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS
+RRQAERRGRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001213.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001213.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbca836e9dc92ee96e399b4221e2a36fe9cdb95e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001213.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01467
+MTMDVSYIARNLRLPESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRLRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
+>GCF_003691675.1_01199
+MTMDVSYIARNLRLPESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
+>GCF_005280335.1_01433
+MTMDVSYIARNLSLPESFRDHVAERTERLHTLAEGAETLEVRVTKSSHHKHSDETVRVEL
+TARGPREVVRAEADADDKQVAFDMAVTRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPNGAQMAAEDAAREQDIPEEGTPVRIREKAFPATPMTVDEAVDAMELVGHDFFLFQ
+NSETGVPSVVYRRRGWSYGVIRLDESLPADHVSATEGERAYQAREA
+>GCF_020097155.1_01335
+MTLDVSYIARGITLSDRFREHVEERLEKIEPLAEGAETLEVKVSRSSHHRHSDEGMRVEL
+TLRGAREVVRAEGDADDKAAAFDAALSRIAERLRRMRDRRKDRRHGKGSAASRGAGEIPF
+VPPLPAVGQADAPADEAPESGTPVSIRAKRFPATPMSVDRAVDAMELVGHDFYLFQDETT
+GVPSVVYRRRGWSYGVISLDESLPAHHVAPVEGERVYQASREADAE
+>GCF_023573625.1_01417
+MTMDVSYIARNISLSESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001215.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001215.fa
new file mode 100644
index 0000000000000000000000000000000000000000..622f84c835c9c6f1b06e7f440f0b139a70e27a95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001215.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01469
+MTTVDPQPPRPPRVAVVAVIVALVLALSGCTQIPQSSEVRSADPVDGASAAADAPQFHPP
+GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD
+GDGDYQIQVEVDSEIDEYGLRTVAPPGTTRAWAVTVQERPQGMRITSTENGTLLSQAQFG
+QLFAPHELAFYDTAKRYIVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVETAFPLRTG
+TDLAAPTVPVDDDGVAHVDLTQAAAEGADAERRHRMREQLELTLRGLQSVKEVEVTVAGA
+QLSTSGDDGPAPVQTDPAVRSVQVGIDAATGGLVYVQGSSVTPVGGAPDVTALDPVRPTM
+SGDRSRFAFVTGDRTAVHVAGTDGSLREVLRGTGLTVPSLDLLGWVWAADRGTTSRIRAV
+SAQPGGQERIVTATWLRPGERIVDLRLARSGARAAMLVDDGQRTTLRVSGVVRGSDGVPN
+ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAEKPDERVVPRIVSIDGTVRELNPLGGLRG
+ISAGDDGAYYAETEELVFLLVGSSWRAQELDRGVRDLSFPD
+>GCF_003691675.1_01201
+MTTVDPQSPRPPRLAVVGVIVALMLALSGCTQIPQSSEVRSADPVDGATADADAPQFHPP
+GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD
+GAGDYQIQVEVDSEIDEYGLRTIAPPGTTRAWAVTVQERPQGMRITSTENGTLLSQAQFG
+QLFAPHELAFYDTAKRYVVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVDTAFPLRTG
+TDLAAPTVPVDDDGVAHVDLTQAAAEGADAERRHRMREQLELTLRGLQSVKEVEVTVAGA
+QLSTSGDDGPAPVQTDPAVRSVQVGIDAATGGLVYVQGSSVTPVGGAPDVTALDPVRPTM
+SGDRSRFAFVTGDRTAVHVAGTDGSLREVLRGTGLTVPSLDLLGWVWAADRGTTSRIRAV
+SAQPGGQERIVTATWLRPGERIVDLRLARSGARAAMLVDDGQRTTLRVSGVVRGSDGVPN
+ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAAKPDERVVPRIVSVDGTVRELNPLGGLRG
+ISAGDDGAYYAETEEFVFLLVGSSWRAQELDRGVRDLSFPD
+>GCF_005280335.1_01431
+MSPTRPTGPRRARRLAGVGLAAALALALGGCTQIPQSSDVRSAEPLDGATAAPEAPQFRP
+PGPSADDTAEDVIRGFLLAGTSPQDDYAVAREFLDGPAAARWAPGQRTLVYSAQPRITRG
+EGTGNYQVQVEVDSEIDEFGLRTIAPEGTTRAWQVSVQERPEGMRITATENGTLLSQSQF
+GQLFAPHELAFYDTAQRYAVPDVRWFVNRGTTVTAVTRALLRGPAPYLTGAVETAFPLRT
+GADLAGPTVPVDEDGVAHVDLTEAAAEGADADRRHRMREQLEITLLGLQSVSDVRVTVDG
+AELSASGENPPPPVQDEPTTGSVQVGIDSATGDLAYFQGMSVGPVGGAPDVSALDPVDPT
+MSRDRSRFAFVTRDRTAVHVAGTDGSLREAMRGTGLTSPSIDGLGWVWAADGAETSRVRA
+VPAEPGQEARIVTATWLRPAERIVDLRVSRSGARAALLVDDGDRRTVRVAGIVRGSDGVP
+SALTEPILLPSTGRAASVEWAGDTNLLVSPRAATPDERVVPRIVSIDGTVRELNPLGGLT
+GVSAGDGGALYAETDELVFLLVGSSWRAQELERGVRDLSFPG
+>GCF_020097155.1_01333
+MRPSGPARPRRRLCAAALAGALALAGCAQIPQSSPVRSGAPLDVGSRAADAPQFRPPGPA
+EDATAEQLVRGFAQAGIAPEDGYAIARQYLSAEASDGWEPDRGVVVYSGEPTVTRGLGEG
+TYEVQLEVESEVDEFGQRTMAPPNTTQAREVTVEEVDGVLRITGVQDGVLLSRSQFAQLY
+APHPLYFFDQSQAFAVPDVRWFVNRGTAVTALTRALLRGPAPYLTGAVATAFPLRTGADL
+TGPSVPVAEDGTAAVDLTGATVDGADPARLSRMREQLERTLTGVSGVERVEVTVEGRSLT
+SSAPSGSVPSARIGEDPGTVQVGVSDAGELVFFQGLDAVPVGGLPSVADLGPEDPAMDRE
+RRRFVFLDRTRTVLHGVGTDGGEHRLLDGGRLTAPSLDSSGWAWTVDRARSSRISVVRAD
+GSEPARVVTTPWLAEGESIVALHIGPAGARAALIVDDGQQRTLRVAGVVRGGDGVPTALT
+PPVYIPTLDPPDDVEWMGDGSLVSTPLAPDAETRVRPEVVSLDGTSRQLNPLAGLTGISA
+REEGTLYAETAEDVFLLVGSSWRAQDVATPVHDLAFPD
+>GCF_023573625.1_01419
+MTTVDPQPPRPLRVAVFAVIVALVLALSGCTQIPQSSEVRSADPVDGATAAADAPQFHPP
+GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD
+GAGDYQIQVEVDSEIDEYGLRTVAPPGTTQAWAVTVQERPQGMRITSTENGTLLSQAQFG
+QLFAPHELAFYDTAKRYVVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVDTAFPLRTG
+TDLAAPTVPVDDDGVAHVDLTQAAAEGADADRRHRMREQLELTLTGLQSVKEVEVTVAGA
+QLSTSGDDGPAPVQTDPAVGSVQVGIDTATGGLVYVQGTSVTPVGGAPDVTALDPVRPTM
+SGDRSRFVFVTRDRTAVHVAGTDGTLREVLRGTGLTVPSLDLLGWVWAADRETTSRIRAV
+PAQPGGQERIVTATWLRPGERIVDLRLSRSGAQAAMLVDDGQRTTLRVSGVVRGSDGVPN
+ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAEKPDERVVPRIVSIDGTVRELNPLGGLRG
+ISVGDDGAYYAETEELVFLLVGSSWRAQELDRGVRDLSFPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001216.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001216.fa
new file mode 100644
index 0000000000000000000000000000000000000000..705bae328f0a3ec8db690b2895d1142eb8b9b51f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001216.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01471
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>GCF_003691675.1_01203
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPTFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCKLIRAESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHQVTRAGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>GCF_005280335.1_01429
+MSRAKILVVDDDEALAEMIGIVLRNDGFEAAFAADGTAALPAFHRERPDLVLLDLMLPGM
+DGIEVCKLLRSESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLQIGDLEIDVAGHQVTRDGAAISLTPLEFDLLVALARRPRQVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>GCF_020097155.1_01331
+MSKARILVVDDDEALAEMIGIVLRNDDFEPSFAVDGTSALPAFRSARPDLVLLDLMLPGI
+DGIEVCKQIRAESDVPIIMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEQRPAEALAIGDVRIDVAGHQVSRGGAPISLTPLEFDLLVALARKPRQVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRAKVEPDPENPTVVLTVRGVGYKAGQV
+>GCF_023573625.1_01421
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001217.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001217.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76fdcd8cf369ed967ecfd45eead769fce8c7420a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001217.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01472
+MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPDRGPGADATGR
+SAALLQQLAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWREDAHRWADTAGAEGAVVERLA
+VRVRGPLSLLACLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAGRLGVVVD
+EPWAAAVLAGTLPTASGYRTVRSLPREEARGLWRAALDGLTALPDVARVWLAPGRRAASP
+GAELPGPAALSTLTGESLPRPDAAADAPAPAPVSLVVGVGALDDGADGTPGTREAWEAAA
+GWADIGRGLTLAPEPGVRPVEVVRTWERLGVDPGRVGDVGLTAAGLHDPVVLHTLRRDAE
+ELTARLAELRG
+>GCF_003691675.1_01204
+MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPDRGPGADATGR
+SAALLQELAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWHEDAHRWADTAGAEGAVVERLA
+VRVRGPLSLLAGLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAGRLGVVVD
+EPWAAAVLAGTLPTASGYRTVRSLPREEARGLWRAALDGLTALPDVARVWLAPGRRAASP
+GAELPGPAALATLTGESLPRPDAAADAPVPAPVSLVVGVGALDDGADGTPGTREAWEAAA
+GWADIGRGLTLAPEPGVRPVDVVRTWERLGVDPGRVGDVGLTAAGSHDPAVLRTLRRDAE
+ELTARLAELRG
+>GCF_005280335.1_01428
+MPEAHDDGARPVALGGSPWAGTDAAEAQRVTLGELGAEHWPVLPELPSRGPGADATGRSA
+ALLSELAVDLQPHGWRVSPPGAAGSGMDRRRAASFWREDAHRWADTAGAEGAVVERLAVR
+VRGPLSLLGGLWLPGGERVLADHGARRDVAASYLEGLLEAVPRLRAATGAAGLGLLVDEP
+WAAAVLAGALPTASGYRTVRSLPRDEARGLWRELLAGLTALPGVASVWLAPGRRTASAAD
+VPATAELAALAGECLPAAGGEDDDAGAPVRLVVPVGDLDDGPDGTAGTRAAWESAAGWAD
+AGRGLTLSPAAHLRPADVVTTWERLGADPAHLRGTGLTAPGRHDATVLRRLRTDAAELAA
+RLDDALG
+>GCF_020097155.1_01330
+MPEASDDVGAVRVAALGGAPWRGTDAAEAQLATLGELGAEHWPVLPELPDRGPGADATGR
+SAALLHELAVDLQPHGWRVSPPGVVGSGMDRRRAASFWREDAHRWADTAGAEGAVVERLG
+VRLRGPLSLLGSLWLPGGERVLVDHGARRDVAASYVEGLRDAVPRLAAATGARTLGVVLD
+EPWAAAVLAGALPTASGYRTVRSVPRDEVRALWRDALAALADLPGVGRVWLAPGRRSAGV
+DVPLPDVSALAALAGESLPAAAPSADDDAPAPTRVDLVVPVGALDPGPDGTGGTRAGWET
+AAGWTDAGRGLTLSTATGVRPADVARTWERLGADPGHLAGVGLTVPGPHDAAVLGRLRAD
+AEELAARVGELLG
+>GCF_023573625.1_01422
+MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPERGPGADATGR
+SAALLQELAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWREDAHRWADTAGAEGAVVERLA
+VRVRGPLSLLAGLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAARLGVVVD
+EPWAGAVLAGTLPTASGYRTVRSLPREEARGLWRAALARLTALPDVARVWLAPGRRAASP
+GAELPGPAALATLTGESLPRPDAAADAPARAPVSLVVGVGPLDDGADGSPGTREAWEAAA
+GWADVGRGLTLAPEPGVRPVDVVRTWERLGVDPGRVGDVGLTAAGPHDPAVLRTLRRDAE
+ELAARLAELRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001218.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001218.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cce9e712c0b535b6dc9813d7d6e3bda22cda80e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001218.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01473
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GESPGDADD
+>GCF_003691675.1_01205
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GESPGDADD
+>GCF_005280335.1_01427
+MSPDYDPHASSLTGRTDPEVLAELYAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHE
+LPPSDPGREAAQIERLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALASGAGPEAPAGD
+PAADSLPDGTRTDAGDDPRRGGADA
+>GCF_020097155.1_01329
+MSHDYDPHASSLAGTADQDILEELYEIRGSIDNIDASLVYLLAERFKFTQRVGRLKARHA
+LPPSDPGREAAQIERLQDLARDADLEPEFAEKFLNFIIAEVIRHHRAIAEDEAPVARPAE
+ASDAGSADA
+>GCF_023573625.1_01423
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GAGSGDADD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001220.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001220.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27e15df02ca2db76601df8a9bfb0366f83cced54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001220.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_01475
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLRLEEARERIAAAL
+GAHPTEVILTSGGTEADNLAIQGLYRARRAAAPERTRIVLTGIEHHAVLDVVDWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALATAPERTALATLMWANNEIGTVQPVAEAARLAADHGV
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALLVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGQALSPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFTLGRTTTPAEAAALIDALRTLLGPGV
+>GCF_003691675.1_01207
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL
+GAHPPEVILTSGGTEADNLAVQGLYRARRAVAPERTRIVLTGIEHHAVLDVVDWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGI
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALFVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGEPLPPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFALGRTTTPAEAAALIDALRTLLGPGV
+>GCF_005280335.1_01425
+MPSAATPRPLGERVHLDHAATTAVRPSALAALAEAAALPGNPASLHASGRRAKLALEQAR
+EAVAAALGAHPSEVVLTSGGTEADNLAVQGLFRARRAADPQRLRIVLTGAEHHAVLDAVD
+WLAAHEGAEPVIVPVDADGVVDLAAWEAALAAAPERTALAALMWANNEIGTVQPVAEAAR
+IAAAHGVPLHTDAVQAVGAVPVDFAASGAATLAVSGHKAGAPVGVGALLVRRDVALTPVV
+HGGGQERRLRSGTVSVALAAALAAALTEAVAEQPAEAVRLGVLRDRVIEAVEALETVVLT
+GPRDADPATGEPLPPGTRRLPGNVHVTVPGRTADALLFTFDTAGLDTSSGSACTAGVAEP
+SHVVAALPGRTEADARATQRFTLGRTSTSADVDALIAALRALAPAPRRGAPTPKGAPTTK
+EESR
+>GCF_020097155.1_01327
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL
+GAHPTEVILTSGGTEADNLAVQGLYRARRAAAPERTRIVLTGIEHHAVLDVVGWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGV
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALLVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGEPLPPGTRRLPGNVHITVPGRTADALLFFFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFTLGRTTTPAEAAALIDGLRTLLGPASRLDRPSVVERGVRP
+>GCF_023573625.1_01425
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL
+GAHPSEVILTSGGTEADNLAVQGLYRARRAVAPERTRIVLTGIEHHAVLDVVDWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGI
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALFVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGEPLPPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFALGRTTTPAEAAALIDALRTLLGPGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001221.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36925d0b80b73cbf557869605a37191bb1901a8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001221.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01478
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA
+>GCF_003691675.1_01210
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA
+>GCF_005280335.1_01424
+MRQNVAMALTELALRHPVRRFARREVDFRRRILTMAVVNRTPDSFYDDGAAFALEAAVDQ
+ARAAAEAGAEWVDVGGVPFAPGPALDPGEEARRVVPLIAALRGEAAEHSEAVAGLILSAD
+TFEPAVAEAAIAAGADVVNDTSGLVHADLGRVVAASQAHLVLTHSLAHVHGPRAVVPRPR
+YGDVVAEVREHLLRTVERAVALGVPEERIIVDPGHDLNKNTLHTLEITRRLDEIAGLGLP
+VLAAVSNKDFIGESLDQHRHERLAGSLAAAVACVHGGARILRMHDAAASVSAARLLECVF
+GWREPARLVHNMGEANPAPDRTSLAEHRAGRVRAGGTR
+>GCF_020097155.1_01324
+MPTPSVPLAHPVHRFAHHEIDFRRRIVTMAVVNRTPDSFFDDGAGFAFDAALAQVHTAAD
+AGAEWVDVGGVPFAPGRELDPAEEAARVAPFVAAVRAGRGEGASEAARRLILSADTFQPA
+VAEAAIDAGADVVNDTTGLYYPDLGRVVAASNAHLVVTHSLAHVSGPRTVVPRPRYDDVV
+AEVREHLLRTVDRAVALGVPEERIIVDPGHDLNKTTVHTLEVTRRLDEIADLGFPVLAAV
+SNKDFIGESLDRHRHDRLAGTLASAAFCALAGARILRMHDADASVSTAHMLECILGWREP
+LLAVHNTGDVNPAADRTTPADRVPADRPPAAVPAPTHDPEEARP
+>GCF_023573625.1_01428
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001222.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001222.fa
new file mode 100644
index 0000000000000000000000000000000000000000..529ebd329254acdb46f3a51c75c61ce99033aad8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001222.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01479
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHASPGPDPTP
+>GCF_003691675.1_01211
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHASPGPDPTP
+>GCF_005280335.1_01423
+MRRLAAVGPELSDEDLLALRRAPSTQDAPGPWVRAVFVSSLDGATALDGRSGTLGSPADR
+RQFALARTDADVILVGAGTVRAEGYAGPLVDAAARARRAARGLPEHPAVAVVTGSLDLDP
+DGEFFRAAPVRPWVIASERAVAAQPERAAALAEVADVLTAGVRDVEPRELLALLAGRGAR
+VVHCEGGPTLLGALAAAGAVDELLLTLSSLLAGGAGPRLIPAVEGIGLPARMLPHHVLTQ
+DGDLYLRLLHERHAALLADAPGLDGRAGTGR
+>GCF_020097155.1_01323
+MRLLTATGPEIDDDALLALRRAPAPDLVPGPWVRAVFVSSLDGAATLDGRAGGLGSPADQ
+RQFTLARTDADVVLVGAGTVRAEGYEGPLVGPAARARREEAGLPAHPGIAVVSGALGLDP
+DGDFLRQAPVRPLILTTQTALERCPDRAEALAARADVVASGAEVVEAPALVDALTARGHR
+VLHCEGGPRLFGTLAAADLVDELLLTISPLLAGGDGPRVLSGGDGPGLPTRLRPHHVLTE
+DGELYLRLVHERHAAVLAEAPGLEADPADADPAPGAP
+>GCF_023573625.1_01429
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHASPGPDPTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001225.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001225.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1243bdcd5df6284ee61f7b0d024cd4eb546150b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001225.fa
@@ -0,0 +1,47 @@
+>GCF_002008305.4_01482
+MQTPDASEPHADRPDDAGQPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMFGPGD
+DAAAATVRTYLTAWEEASEAGLDLSEQDDATHRERQVFTWLEVLAHRVMTSLRRAGGSAA
+ERGRRPGPAGPAALPEDLMDRVDPDAFEAVRLAWLGGCTDREVADRLDLPADRARTLLRD
+GVRQVVAARRDITQDAARPSAPAPATGPALGADVREDVDAGRALELADLSAVHALDTAGH
+TAAFSAVQRRGGELARWRSRVDGARQAVAWAFRSVTAEPPSALLDEVLRRLPAQDVGMDL
+IGDESTPAGPPRDRLRWLKVTALLLLAALVLGIGGWTVWSQFTRPGIVHRIDQSKDLFTT
+SEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGTAPASLGTYDANG
+FGEPVTFRGLDRFAAMGISVEPSSGSEVPTSEPIVGVDLDPTAQTGPRYGGRPSTN
+>GCF_003691675.1_01214
+MQTPDASEPHVDRPDDAGQPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMFGPGD
+DAAAATVRTYLTAWEEASEAGLDLSERDDATHRERQVFTWLEVLAHRVMTSLRRAGGSAA
+ERGRRPGPAGPAPLPEDLVGRVAPDAYEAVRLAWLGGCTDREVADRLGLPADEARTLLRD
+GVRQVVAARRDLTQDAARPSAPAPATGPALGADVREDVDAGRALELADLSAVHALDTAGH
+TAAFSAVQRRGGELARWRSRVDGARQAVAWAFRSVTAEPPSALLDEVLRRLPAQDVGMDL
+IGDESAPAGPPRDRLRWLKVTALLLLAALVLGVGGWTVWSQFTRPGIVHRIDQSKDLFTT
+SEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGTAPASLGTYDANG
+FGEPITFRGLDRFAAMGISVEPSSGSEVPTSEPVVGVDLDPTAQTGPRYGGRPSTN
+>GCF_005280335.1_01420
+MQTPDASEPRADRSAAAGAPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLASAMFRSAD
+DAAEATTLTYLTAWEEASEAGLDLSEHDAASHRERQVFTWLEVLAHRVMTTLLRSDGLPE
+AGHGLLPDRAGPGSAGPAERPEDLDSRVDPAAFEAVRLAWLGGLSDRQVAARMGRPVAES
+RTLLRDGVRQVVEAHRALTRDAADRSPETSARPALATSVREDVEAGHALELADLSAVHAL
+ETAGHTAAVSAVQRRGGDLPRWRSRVDGARQAVAWAFRSVTAEPPSAVLDDVLRRLPAQD
+VGMDLIGEEAAPARPPKDRLRWLKITVMVLLAALVLGVGAWTVWSQFTRPGIVHRVDQSE
+DLFTTSENPARDGGTAQAFLSRDQNSGYVTVSGMPQLPDGQAYQVWLYPDDGTAPASLGT
+FDANGFGEPVTFRGLDRFAAVGITVEPSSGSEVPTTDTLVGVDLDPTAHTGPRYGGRPST
+N
+>GCF_020097155.1_01320
+MQTPQHPETPGADASTAPQQPSRRGVDELLHASARGDRAAFSAFYDATVPWVHGMATAMF
+RSRRDAAEATAQTYLAAWSEAPEAELDLSDRDAAAARERRVFAWLEVLAHRVMTGLLRTD
+ALPEQGRRLLPERAGLGTGGPTALPATLEGSVSPETHRAVRLAWLGGRTDAQVAEALDVP
+VDRARTLLRDGVQELVAAHRADQGLPAPVAGARPALAATTREDVDAGRGAELADLSALHA
+LDAAGHTAAAAAAQQRGAGELALWRTRVDAGRRAVAWAFRDVVAEPPSDLLDGVLRRLPA
+QDMGLELVEETAAPRGAAERRRGLKTVLLGLLALVVLALGVYAGWSQFSRDGITHRVHGA
+KDLYTTSEYPAAGGGTMQGFLSDSENSGYVTVSGMPQLEDGQTYQVWLYPKDGSAPSSLG
+TYDADGFDDPISFRGLDRFAAVSMTVEPSGGSPEPTADDVLLGLDLDPSNQSGPQYGGMP
+SNN
+>GCF_023573625.1_01432
+MQTPDASEPHADRPDDAGQPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMFGPGD
+DAAAATVRTYLTAWEEASEAGLDLSERDDATHRERQVFTWLEVLAHRVMTSLRRAGGSAA
+ERGRRPGPAGPAPLPEDLVDRVAPDAYEAVRLAWLGGCTDREVADRLGLPADQARTLLRD
+GVRQVVAARRDLTQDAARPSAPAPATGPALGADVREDVDAGRALELADLSAVHALDTAGH
+TAAFSAVQRRGGELALWRSRVDGARQAVAWAFRSVTAEPPSALLDEVLRRLPAQDVGMDL
+IGDESAPAGPPRDRLRWLKVTALLLLAALVLGVGGWTVWSQFTRPGIVHRIDQSKDLFTT
+SEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGTAPASLGTFDANG
+FGEPVTFRGLDRFAAMGISVEPSSGSEVPTSEPVVGVDLDPTAQTGPRYGGRPSTN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001226.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001226.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb982d2f34844270d9734a0feb187cc0620f6c94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001226.fa
@@ -0,0 +1,29 @@
+>GCF_002008305.4_01483
+MAVGAHPDDLDFGAAATLAGFSAAGLHIELCIVTDGDAGGFDSEGAEAMTARRHAEQRAA
+AAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDVVLSTHPERDWERMQAAHPDH
+LACGEAVVRAAYPAVENPYAYPELAAEGLEAFKIRNLLLYAAPAARRNTVVDVTGLAEQK
+LRALDAHLSQHPDVDAMRRHVLAQMAEHHRHAAGPAAGPGHAEAFHLVTVNGPGTIAGF
+>GCF_003691675.1_01215
+MTTTLTTPAALAAHHGWRRVLAVGAHPDDLDFGAAATLAGFSAAGLHIELCIVTDGDAGG
+FDSEGPEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDV
+VLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKVRNLLLY
+AAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRRAAGPAAAPG
+HAEAFHLVTVNGPGTIAGF
+>GCF_005280335.1_01419
+MTTPITPAALAAEHGWRTVLAVGAHPDDLDFGAAATLAGLSAAGLRVELCVVTDGDAGGF
+DSEGPEAMTARRHAEQRAAAAVVGAHEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDVV
+LSTHPERDWELMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKIRHLLLYS
+APAARRNTVVDVTGLEDVKLRALDAHISQHPDVAAMRRHVLAQMTEHHRRAAGPAAAPGL
+AEAFHLVTVNGPGTISGF
+>GCF_020097155.1_01319
+MSAVPESLPTPADLAVRHGWRTVLAFGAHPDDLDFDASATLAGLAAAGVRVELCVVTDGD
+AGGFDSDGPEAMTARRHAEQRAAAAVIGAADVHFLGERDGHLEPTHEVRRRIVELMRRVR
+PDVVLCPHPERDWESMQASHPDHLACGEAVVRAAYPAVENPYAYPELADAGLDAFRIRHL
+MLYTAPAARRNLTVDVTGLEDVKLRALDAHVSQHPDAPAMREAVRAKLTRRHREAAGPDA
+PAGSGEAYHLVTVNGDGVIAGF
+>GCF_023573625.1_01433
+MTTTLTTPAALAAHHGWRRVLAVGAHPDDLDFGAAATLAGFRAAGLHIELCIVTDGDAGG
+FDSEGPEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDV
+VLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAAENPYAYPELAAEGLEAFKVRNLLLY
+AAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRRAAGPAAAPG
+HAEAFHLVTVNGPSTIAGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001229.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001229.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b30b3f9e5aae1b7f19de205400e893ad739d630
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001229.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01486
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDASRSWGQKALAASQKADDFRAKGDTASADKFDNLAKVAIERQMDFERQAKS
+AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ
+AALTSGDVDADETLTLDYAAEGTAEETGTARG
+>GCF_003691675.1_01218
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDASRSWGQKALAASQKADDFRTKGDTASADKFDNLAKVAIERQMDFERQAKS
+AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ
+AALTSGDVDADETLTLDYAAEGTAEETGTARG
+>GCF_005280335.1_01416
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDAARSWGQKALAASQKADDFRTKGDAASAEKFDNLAKVAIERQMDSERQAKS
+AEPTITSQREIVERLKTGLDQMKVKRQQLVSKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQELAASSLDAQFESLEDLGEKTEVEARLAALKSGGAGQ
+SALTAGGSEGSDLALDYGAETTAEQGAEQTRVERG
+>GCF_020097155.1_01316
+MVKQSILGRITTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMM
+EDDYREDQEAARSWGQKALAASQKADEFRTKGEAANADKFDNLAKVAIERQMDAERQAKT
+AEPTITSQREIVDRLKTGLDQMKVKRQQLVSKRDELTARSRTAEAQTKVNEAVKSIDIMD
+PTSEISRYEEKVRREEARVRGQQELAASSLDAQFESLEDLGEQTEVEARLAALKSGSAPS
+ALTAGSEELTLDYSGAETGTQTGTAERA
+>GCF_023573625.1_01436
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDASRSWGQKALAASQKADDFRTKGDTASADKFDNLAKVAIERQMDFERQAKS
+AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ
+AALTSGDVDADETLTLDYAAEGTAEETGTARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001230.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001230.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb5a7e40e52109c15cbcb0907d4ef86f271e0b44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001230.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_01487
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLVLGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYASQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITSVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR
+>GCF_003691675.1_01219
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR
+>GCF_005280335.1_01415
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVIKPLQTLMIPASVIAGILGLVLGPNVLGWL
+PFSTQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGSFASYGVLIYASQVAIGALVALL
+VLQPLFSTPDSFAALLFAGWAGGFGSAAAVGQAYAANGDMTVTSLAYTSATVGMIVGVVG
+GIIQAKIGARRGHAKEFAGLTSIPDELRTGVLDQVQERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVTWITAVWPNIVGEDGPKLIIPAFAVAFILGLIGRVVFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIASIAPTVVVDYWQPLLVLFVIGLALALFLGLVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+IAGLSWAVVGIWGAIAIAAILAAIWLRRTDPGVRSPAQQAVRAASR
+>GCF_020097155.1_01314
+MTWFQGVWPSIVGPEGPKLMIPAFAVAFVLGIIGRLLLQVTKTATFLDSASLNSVSGTAT
+DILIVCGIASIAPKVVLDYWQPLLILFVVGLALAVLLGLVVAPHVMTESWFEKQLFTWGW
+ATGAVATGVAMLRIVDPKLKSGTMEQFGVAYITVVPVEIAAVSFVPLLIIAGLSWAVVGI
+WDAIAEAAIIAAVFLVRSDPARKSAVPA
+>GCF_023573625.1_01437
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+IAGLSWAVVGIWGAIAIIAIIAAVWLRRTDPGRRTPAQQAVRASSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001235.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001235.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1469c2dca8ffe81c98db07b0b5852a2673188eb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001235.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_01517
+MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL
+ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA
+ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP
+RRRGAKVAVCRTCGKPLETGAERKVGRCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV
+VFTDATLVAIAEAMPRTPAELLKVPGLGKAKLEKHGPELLELLHGTPTA
+>GCF_003691675.1_01226
+MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL
+ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA
+ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP
+RRRGAKVAVCRTCGKPLETGAERKVGRCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV
+VFTDATLVAIAEAMPRTPAELLKVPGLGKAKLEKHGPELLELLHGTPTA
+>GCF_005280335.1_01408
+MSTPDEILRGLDPEQRRAATALQGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQGMRMSVDRAGLRDLAGEIEWAKVSLHAPEGYAEAARGREMPAGWDATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPRIAATIRDQYRVFLVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERHPDATVVELVRDYRSSPQVVEAANRLL
+ADRTKAGQRDRTMPRWPDPLELVSQRPNGPDPVFAECTDDEAEAGWVADRIRALIDDGVA
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVPDRVRDVLASLGYSAQPPAATGAARERWESLHALVNLAEQLAGSRGAEFTLTELVA
+ELDERAQHQHAPTVQGVTLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRAREHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAPGAAKP
+RRRGATVATCRTCGKPLETGAERKVGRCLDCPATYDEAVLEQLRDWRSRTAAEMKMPAFV
+VFTDATLVAIAEAMPASPKELLAVPGLGRTKLEKHGEALLELLHGTPTA
+>GCF_020097155.1_01307
+MSTPDEILRGLDPEQRKAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVDGVQARTFHSAALRQLQYFWPQAVGGQMPTLVENKVRLLT
+EVAHRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAARDREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPKIAATVREQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRQDLCVVGDSSQTIYSFTGATSRFLTGFRERYPEATMVKLVRDYRSSPQIVGAANTLL
+AERTQAGLRDRSLPFWPEPLALSSQRPSGPDVVFAECQDDEAEAGWVAQRIQGLLDDGVP
+AAEIAVLFRTNGQSEAFETALSAAGIGYQLRGGERFFSRREVREGVLQLRAAAREAQDLV
+GADVVQRVKDVLSSLGYSDTPPSASGAARERWESLHALVNLADQLAGTREDFTLVQLVAE
+LDERAQAQHAPTVQGVTLASLHSAKGLEWDAVFLVGLSEGLMPISFADTPAEVDEERRLL
+YVGITRARQHLHLTWTLARSGGGRANRRPSRFLRAIDPTLGGTREHAPAAAMPARRPRRG
+ATVAVCRTCGRPLETGAERKTGRCVDCPALYDEGVLDTLKDWRSRVAKTDKVPAFVVFTD
+ATLEAIAETMPATPAELIKVKGVGKSKLDRFGQDVLDLLHGTSAA
+>GCF_023573625.1_01444
+MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL
+ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA
+ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP
+RRRGAKVAVCRTCGKPLETGAERKVGSCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV
+VFTDATLVAIAEAMPRTPAELLKVPGLGKTKLEKHGPELLELLHGTPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001236.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001236.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86e9b5c8e185bd4f770ec0f15a300322d25c20e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001236.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01518
+MASCPPSSSDPTVAPPLALPLAREELDRGAVARLDPGHLAASWAREGTEVLWLQGGRAPV
+ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA
+VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE
+QFPRTDPAVIVAVIDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGV
+TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELARLAREGDV
+TLPGAVSIARALIEDWYGGTLPDAQTLIT
+>GCF_003691675.1_01227
+MASCPPSSSDPTAAPPLALPLAREELDRGAVARLDPGHLAASWAREGTEVLWLQGGRAPV
+ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA
+VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE
+QFPRTDPAVIVAVIDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGV
+TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELARLAREGDV
+TLPGAVSIARALIEDWYGGTLPDAQTLIT
+>GCF_005280335.1_01407
+MPVPDPAAPAPEPRHDPAPAPAPAAPLALPLAREEVDRGAVARLDPGHLAAAWEREGTEV
+LWLQGGRAPVADGRLRFTTPSGPVPPQAAYLGRGTAADLGPGGRERAVVAVALEPPAVLP
+PDAAAALGDAAWVGLRDAAAALSDADAGLFVAAVANANWHAAHRFCSFCGGATAVEAAGW
+VRRCEACGREHFPRTDPAVIVAVTDPDGRILLGRNAAWPAGRYSCLAGFVEPGESLEHAV
+VREVAEESGVTVADPRYRGSQPWPFPRSLMLGFTAQAPAGAEPVADGTEILSVRWFEREE
+LAALAREGEITLPGAVSIARALIEDWYGGTLPDAQTLIT
+>GCF_020097155.1_01306
+MPVPSAPDAVPAALPHLTLAREALDRSGAEREDPGLLGRLAADPATGVLHLVGGRAPVRD
+GALVLVPPAGPFPPEAVFLGRRLTDAAAPSAAGRPLVLVARESAPGSSGDGGPTRPAEPT
+DAPTRDPLAGAAWLGLRDVAAGLSDADTGLFVEAVAIANWHAGHGFCSRCGGRTDTESAG
+WVRRCRDCSARHFPRTDPAVIMAVMDDQDRILLGSNAAWPAGRHSCLAGFVEPGESLEHA
+VAREVLEEAGIVVVDAAYRGSQPWPFPRSLMVGYRAHALPGQEPVADGHEIRSVRWFTRD
+ELAAEVRAGAVTLPGAVSIARALIEDWYGGTLPDPTTLIS
+>GCF_023573625.1_01445
+MASCPPSSSDLTAAPPLALPLAREELDRGAVARLDPGHLAAVWAREGTEVLWLQGGRAPV
+ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA
+VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE
+QFPRTDPAVIVAVTDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGI
+TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELAHLAREGDV
+TLPGAVSIARALIEDWYGGTLPDAQTLIT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001239.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001239.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ec03eda5a074ce823a843d97fc0bafd69ebcf1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001239.fa
@@ -0,0 +1,104 @@
+>GCF_002008305.4_01521
+MTREHGVDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHNAVLVLGAPG
+TGRTTVAVEYAARRIEAGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPADVAP
+AVEARGFRREVRELVDRMSELGLEPGRLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAAERDRLAVLVVEDLHEATPAVHDLLT
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPGVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAEVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLV
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVVTAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAVL
+AADGVGVADPRRWWGLLPLSTEAALVDPEREVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGVPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLERPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR
+>GCF_003691675.1_01230
+MTREHGVDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHNAVLVLGAPG
+TGRTTVAVEYAARRIEAGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPDDVAP
+AVEARGFRREVRELVDRMSELGLEPGCLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAEERDRLAVLVVEDLHEATPAVHDLLS
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPEVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAAVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLL
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVATAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAAL
+AEDGVTVADPRRWWGLLPLSTEAALVDPEREVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGVPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLEHPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR
+>GCF_005280335.1_01404
+MTWQADEDLLLDDDAAAPERAARLVSPAAAPAERVALTLEQEAVAAMGPGHGAVLVLGAP
+GTGRTTVAVEYAARRLESGTDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVR
+TWTSYAFDLLRRARVTGPLSHLPVAPRLLTGAEQDTVIAELLEGYAAGHAEAPRWPQDVA
+AAVETRGFRREVRELVDRMSEFGVEPGRLQELGAAHARPVWEAAAVLLQDYRDRIDLGLA
+EAFDAAGLISAAVRVLTERHPEDPERDAAALAFAAAERERLRTLVVEDLQEATPAVHDLL
+AVLGRGRDVLLTAGPDTAVEGFRGARPDLVSRYPQALDPDPVPGAPEAPSSGERTRVLTQ
+GHRMAPEVQDAFLRVARRVRQRTAAVEHTRTQTAPADGPGTVRGHVVPTRAHEDQLVLER
+VLRVHHEDEVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTL
+LAAAGVLADDPEAGVEDVLDPDEVVALLTGRYGMAGALHVRRLRQDLLAAERGRGGRRSS
+DALLAAALLDPALAGPEHERHRALRRVHWMLRAGIEAARAPSASPEAVLWALWSASGRAE
+RWRSTALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGAAPEAFAVYMESQDL
+PVDTLARRAEAGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLADLL
+TLPEGGAWPTDHRTRLREVRQDELRMLAAAVSRARRQVVVTAVRSAEDAPSDFLDLVDPP
+ERLPAPARDEAGVRRLTAVPDPITAPALAGTLRRRLEEDPGQGPAAAGLAALARDGVGVA
+DPRRWWGLLPLSTDAGLADPAQDVVALSPSRVETALHNPLNWLLYHVGATAGGTLAQSVG
+TLVHSVAEHHPEGVPEQVRAELERRLPELGLPEGWITEIEHERARALVDAYIGYWSIARD
+AGRRPVAQEVRLLAELTWGGTTVRITGVVDRLEADAEGRPFIADLKTGRSAPTGPEMARQ
+PQLAAYQVAVLAGGLAQIRDDPDADPALRAALADLARPAAPAGAALVQLGAGTQKTKVQE
+QPALGPEDDWALEQVFTAARRTVGPRFLAIHEAGGRRCALPSVCPLCSEGRQVTEWPR
+>GCF_020097155.1_01303
+MSTTPHPSEPRTEPTPQAADADPADLAALLAEPDEEPPHAAPVPARLVRGVGQDRAGVVL
+TVEQEAVAGLGEGHGAHLVLGAPGTGRSTVAVEYAARRLEAGLDPESLLVLAPSREAAAR
+LRDALTERLAAAGHGTRAVTPVRTWASYAFDLIRRARVTGPLRGLSRPPRLLSGAEQDTV
+IAELLDTYAAGLAPAPEWPRDVAQAVDTRGFRREVRELVDRMSEFGVEPGVLQELGRRHG
+RPVWEAAAELVQDYRDRLDLGMAEAFDAAGLISTAVRLLTERFPDDPERDAAALAFAEAE
+QARLRAIVVDDLQEAGPAVHDLLVHLGRGRDVLLTASPDTTVQGFRGARPDLVSRYPAAL
+DPDAVPGASSPDPDARTHVLTAGHRMSAGVQEGWLRAARRIRQRTVGVELTRTRTVPAGE
+GGAVEGHAVPSRAHEDQLVLERVLRVHHEDGVPLDGLAVIARSGARAAALGRHLEAAGVP
+VRREAAGEVLKDEPAVAPLLTLLRAVSDQAEDPEAGVALEADEAVALLRGPYGRATALNI
+RRLRQDLLAAERARGGRRTSDELLVAAFGDPALAGEETDRHRALRRLAWMHRDGLAAARE
+PGATAETVLWAVWAASGRADRWRAAALGRAEGAEGRREARRADADLDAVVALFRIAERFV
+DQFPGAAPADFSRYMESQDLPMDTLARRAETGDAVHVLTPAGAAGREWDTVIVVGLQEGA
+WPNTALRGQLLGATDLTDLLTAAAVDGAWPTDHRTRLAEVRQDELRMLAAAVSRARRRVV
+ATAVRNEDETPSDFLDLLDPVADVAAGRPLTEVPLPLTAAALVAAARRRLEAPDLPEALV
+GLEDPAAAAVLAALAEDGVAAAAPDRWWGLAPLSTDAPLTDITAEPVRLSPSRAQTALEN
+PLNWLLYHVGAQAGGTLAQSIGVLVHSVAEHHPDGEPGAVRAELERRLPELGLPEGWTTD
+LQHARARRLVEAYIRYWSQMRAEGRRPVAQEVALHVPLAWGDERVEISGVIDRLEVDATG
+RPYVVDLKTGSSKPDTAELERLPQLAAYQVAVRARGLELLAEDPATDPALRRALSAIEAP
+AEPGGAALVQLGAATKTKATVQPQPAVTADDDWALDQVFTAARRTVGPRFLAVHRPGVRC
+ALPSVCPLCTEGRQATEWHR
+>GCF_023573625.1_01448
+MTREHGEDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHGAVLVLGAPG
+TGRTTVAVEYAARRIEEGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPADVAP
+AVEARGFRREVRELVDRMSELGLEPGRLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAAERDRLAVLVVEDLHEATPAVHDLLT
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPGVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAEVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLV
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVATAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAAL
+AEDGVTVADPRRWWGLLPLSTEAALVDPKHEVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGMPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLERPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001240.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001240.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d423135ee9fd27a0df32f0db98c3ad768e33f93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001240.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01522
+MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGRAVSYGGLAGLLGVGGPRQAGRAMAE
+SSPGTPWWRVVRADGSLPPELAARAAVEHEREAMPRTPAGRVDLPRARWEPDDGAARAIR
+AIADRIVSGPGARMRP
+>GCF_003691675.1_01231
+MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGHAVSYGGLAGLLGVGGPRQAGRAMAE
+SSPGTPWWRVVRADGSLPPELAARAAVEHEREATPRTPAGRVDLPRARWEPDDGAARAIR
+AIADRIVSGPGARMRP
+>GCF_005280335.1_01403
+MTTPPADPRPVPDGPLTLGEGLEAVARLVPAGRAVSYGDLAGLLGVGGPRQAGRAMAKSA
+PGTPWWRVVSADGSLPGELARRAAVEHAREGTPVRPGGRVDLPRARWEPDEAALGAVAAI
+AARIVSGPGARMQA
+>GCF_020097155.1_01302
+MSPVPSTPPDPDPHLPTDGPVTLGEALAAAARLIPSGRAASYGALAGLLGRGGPRQAGRA
+MAESEPGTPWWRVVRADGSLPEPLRRQARERWAAEGTPVRGSGTVRDQRVDLAQAGWEPD
+AAARAALADLAARVG
+>GCF_023573625.1_01449
+MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGRAVSYGGLAGLLGVGGPRQAGRAMAE
+SSPGTPWWRVVRADGSLPPELAARAAVEHEREGTPRTPAGRVDLRRARWEPDDGAARAIR
+AIADRIVSGPGARMGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001241.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001241.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cfc448ba9e8b0fb4305ab79baafb5ff9dbd73960
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001241.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01523
+MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEQGRAASSAEWLVDPGVPIPAEAAEV
+HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARHHGLTPL
+EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAARY
+EQLRVAPVDLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVEAER
+>GCF_003691675.1_01232
+MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEQGRAASSAEWLVDPGVPIPAEAAEV
+HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGLTPL
+EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAAQY
+EQLRVAPADLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVDAER
+>GCF_005280335.1_01402
+MSPVNWHQSIRAGFDLETTGRDPRSALIVTATLVMVDAQGRATASAEWLLDPGVPIPAEA
+AEVHGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGL
+APVEARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALA
+ERHEQLRVDPAELHERQVRWKAEQAESFEEYLRRKDPQATVSRDWPVESGR
+>GCF_020097155.1_01301
+MSWNEQIRAGFDLETTGRDPRQARIVTATIVMVDAAGKAVSSAEWLLDPGVPIPEEAAAV
+HGVTTERARAEGLEARRGVSEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGVAPL
+EPRPVVDPYVVDKQVDRFRKGKRTLGAVSEHYDVVLEDAHTSAADALAAVQVMDELVRRH
+PKADLPLDELHAAQARWKAEQAESFEEYLRRKDPQATVSRAWPVEPDV
+>GCF_023573625.1_01450
+MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEHGRAASSAEWLVDPGVPIPAEAAEV
+HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGLTPL
+EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAARY
+EQLRVAPTDLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVEAER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001242.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001242.fa
new file mode 100644
index 0000000000000000000000000000000000000000..284776f58d2fcc46449cff243687453bd0b9d965
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001242.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01524
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDVWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGLDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSLLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG
+>GCF_003691675.1_01233
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSMLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG
+>GCF_005280335.1_01401
+MTTSTRTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGREYVDL
+VCSWGPMLLGHGHPEVTDAVHAAVDRGLGFGTSTLEETALAELIAAKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRDALEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITARHGALLIW
+DEVLTGFRATATGGWGLSGQVDGWTPDIWCFGKVIGGGMPAAALAGSAEIMNHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADDAVYAAVQRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSVAFGTSGTGVRDYRDAQAQEAFRYAPFFQSMLESGVYLPPSVFEAWFVSAAHDDAAV
+QRVLDALPAAAKAAAAATPQG
+>GCF_020097155.1_01300
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGTEYVDL
+VCSWGPMLLGHRHPEVLEAVHAAVDRGLGFGTSTLEETALAELIASRVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAALEAVFAEHGERIAAVITEAVPCNMGVVEPAEGYNAFLREITAQHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALAGSAEIMNHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADDAVYAAVQRASDAVREGLAAALTAEGVDHSIQRAGT
+LFSVAFGTSEHGVRDYRDAQGQDVFRYAPFFQTMLESGVYLPPSVFEAWFVSAAHDDAAV
+ERVLAALPTAAKAAAAATPQG
+>GCF_023573625.1_01451
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSMLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001243.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001243.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e35bd59031582ec63a7efbbf75d9b1f0ce44e37b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001243.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01525
+MSFPLHRPRRLRRSAAMRRLAAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGAVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL
+>GCF_003691675.1_01234
+MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL
+>GCF_005280335.1_01400
+MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAPEPIAIASMPGVVQHTSDT
+LKAAAAEAAELGLGGIMLFGVPETRDAVGSISLDPEGVLNQAIRDVKSEVGDALVVMSDL
+CLDEFTDHGHCGVLTEDGAVDNDATLEIYAQMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LDAAGHVDTGILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRTEALHEVALDLE
+EGADMVMVKPAMSYLDIVRDVAELADVPVSAYQISGEYAMIEAAAANGWIDRKASIVESV
+LSIRRAGADTVLTYWATELGRWMKEGSL
+>GCF_020097155.1_01299
+MSFPLNRPRRLRQSAAMRRLVAETRLHPNELILPAFIKEGAAEPVPIASMPGVVQHTTDT
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALREVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL
+>GCF_023573625.1_01452
+MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRGVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001249.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab63cb9fbf18ae9c03f539b8c7ca9b5651d7db23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001249.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01531
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMAMEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA
+>GCF_003691675.1_01241
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMALEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFIVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA
+>GCF_005280335.1_01394
+MSTAPENAAAASPAPEPRADAPVHAGPRAGVAPTLRAPEEAAAGVDFDVCGVMAPKEYDA
+LLLASFGGPEGQDDVIPFLRNVTRGRGIPDERLEEVATHYRANDGVSPINAQNRALKAAI
+EAELAARGLALPVYWGNRNWEPYVPDTLERMHADGHRRILTVTTSAYSCYSSCRQYREDM
+GMALRRTGLEGVVDLDKTRQYFNHPGFIEPFRDGLRADLASLREELGEDARIHVLFATHS
+IPTSDAAAAGPRGLAADLRAQAGAEPGEEGADVYSAQHLDVAREILAGVPEAADVPWSLV
+YQSRSGPPSVPWLEPDINDAMEHLAGEDAEADAAGRAVAGFVVVPLGFVSDHMEVLWDLD
+TEARQTAADLGVAFRRSPTPGTDPRFVSGLVDIVEERMGRREGRASLGCFGAWYDVCRPD
+CCSKVMRDGTVRPTTSAVDADVRGLAEHEAGTAPAGRTEES
+>GCF_020097155.1_01285
+MTAVPTHRVPEDARRPVHEPERAAAGVDYDACGAMAPKAYDALILASFGGPEGQEDVIPF
+LRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALISAIEAELVRRGLELPVYFGNR
+NWEPYFPDALQRAYDDGHRRILTVTTSAYSCYSSCRQYREDMGLAMERTGLEGKVDLDKT
+RQYFNHPGFVEPFAEGLRADLASLREEVGEDARVHLLFATHSIPTADAAAAGPRGLAAAL
+REQAGGEPGDVEGADAYSAQHLDVIREVLARVPEAEGVDWSLVYQSRSGAPHVPWLEPDI
+NDALEALAGPDAPADADGRALAGVVVVPVGFVSDHMEVVWDLDTEAKDTAAELGVAFRRT
+PTPGTDPRFVSGLVDIVEERLGRREGREAVGCFPAWYDVCRPDCCVKVMRDGSVRPTTSA
+VDAPVRGLAEHRGEQDGADDAGAQDS
+>GCF_023573625.1_01458
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMAMEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001252.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001252.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14b2bdd94eaa07d48ce05283baa3ed63f184f56c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001252.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01534
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGAETAEREERA
+>GCF_003691675.1_01244
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGVETAEREERA
+>GCF_005280335.1_01391
+MSDLSQTSEIRAGAPALPADHPLRTQDPARSTAASPLVRALRGQRPDRHPVWFMRQAGRS
+LPEYREARAGIGMLESCLMPDLVREITLQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGRAVRTAEDVAALPVLEDSALDVIREAVSSTVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHGDPEAWAALAGWAATVSGQFLRAQLEAGASAAQLFDSWAGSLA
+AEDYLEHVQPHSRAALAHVDDLAGPGVDGGAPLLHFGTGTGEFLHHLRDAGASAVGVDHR
+LTLSEAHRRLSERPGPDGRTVVPLQGNIDPALLAAPWPVVEAHVRDVVASGAAAPGHVVN
+LAHGVPPETDPTVLTRVVELIHSLPVPEREGQDPAPPAGAAAGEGRA
+>GCF_020097155.1_01282
+MSAMTTPPGLPAEHPLSTADPARSTADAPLVCALRGRRPHRHPVWFMRQAGRSLPEYRKA
+REGVGMLESCLRPELAAEITLQPVRRHDVDAAIFFSDIVVPLKLAGVGVEIVPGVGPVLD
+HPVRTAEDAAALPELEDSALDVIREAVSRTVAELGPTPLIGFAGAPFTLAAYMVEGRPSR
+DHLGPRRMMHGDPQTWAALAAWAATVSGQFLRAQLEAGASAAQLFDSWAGSLSAADYRKH
+VQPHSAAALSAVSDLAGPGVEGGAPLLHFGTGTGEFLDLMRDAGASAVGVDHRITLAEAH
+RRLSSRPGPDGRAAVPLQGNIDPALLGAPWEVLEAHVREVVASGAAAPGHVVNLAHGVPP
+ETDPEVLTRVVELIHSIPVADGAEK
+>GCF_023573625.1_01461
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGAETAEREERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001253.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001253.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55edeb0dfb79aa81c3f6d52b86936077b5f951fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001253.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01535
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEADAAGV
+EAARAGLLSAVAASTSLPDEDVHAAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAVCPAHEDEGGAARIA
+>GCF_003691675.1_01245
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEADAAGV
+EAARAGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAACPAHEDDGGAARIA
+>GCF_005280335.1_01390
+MADVVTVFSLVASHQHLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEAD
+ESGVEAAREGLVAAVAAHSSLPDEAVRSAFRVLDSEATARHLFEVGAGLDSAVVGEREIA
+GQVRRALSMARESGTASGSLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLTEELRG
+LADDDAKAAFWADASVLLIGTGAYAGTTLAQLAERGATAVAVHSASGRAEQFVEDRGGWA
+LALGGGAVAGAVAEADVIIGSSGGERQISPERLQELREDVDRPLTVVDLALSRDFDPAVG
+DLPDVDLITLESVRLAAPEQARAAVAEARVLVDGAVAEYRAAQRGRSADASIKALRRHTL
+AALDREMERVRARHGCTAAAEEVEFALRRMVNQLLHEPIVRAKRLAAEGRLDRYEDGLEA
+VFGIEPPGSTSSPAERPDAGCPAHEDEAGTARIA
+>GCF_020097155.1_01281
+MDVAVTVFSLVASHKDLSLDTVARLSAGSAGVGSALASSTDDGAVVLATCNRVEVYADAR
+DADAARERIVAAIAEQSGLPEDAVRSAFRVLDDDASARHLFEVGAGLDSAVVGEREIAGQ
+VRRALVDARDAGTATGSLTRLFESATRTAKDVGSHTALGATGRSVVSVALDLAEELRGLT
+DAMARRTFWQEANVLLIGTGAYAGTTLAQLADRGAQAVGVHSASGRAAQFVADRGGWALA
+LGGADVAGAVAEADVIIGSSGGDRQISPERMAGLRRGAERPVTVVDLALSRDFDPAVGEL
+EGVDLITLESVRLAAPEQAQAAVAEARGLVETALEEYTSARRGRTADAAIKALRGHTMAA
+LDREMERVRARHGCTAAADEVQFALRRMVNQLLHTPSVRARELAAQGRLDEFEHALEVLF
+DIPVPGTRPADAPGDACPATEADDARRTA
+>GCF_023573625.1_01462
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAIVLATCNRVEIYAEADGAGV
+EAARTGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELREGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAACPAHEDDGGAARIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001254.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001254.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96149d570bfc755ec2247b7f84a2badd9d408fbd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001254.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_01536
+MTDHPAATAPDEPGRGRRLPRQERRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRDNRERVRATVAAVFEYMASPERTHRL
+IFDSGIDGDPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDALVWRGLASLPSADDAPR
+>GCF_003691675.1_01246
+MTAHPAATAPDEPGRGRRLPRHERRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRDNRERVRATVAAVFEYMASPERTHRL
+IFDSGIDADPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDALVWRGLASLPSADDAPR
+>GCF_005280335.1_01389
+MFAAEGYAGASMDQIAERAEVSKPVLYQHFPGKHELFLELLDAEVADLQERLGAAMDTRR
+GRDNRERVRATVAAFFEYMGAPERTHRLVFDSGADQDPEVRSRSEAVHRLLSSEITRTIS
+ADTSVGEAEAEVLSRGLVGLLLGAARHWADRLDVQARPPAAEMARTVDALVWRGLATLPT
+DDDAL
+>GCF_020097155.1_01280
+MAAPARLPRAERRGQLLEVARVVFAAQGYVGTSMDEITERADVSKPVVYQHFGGKQELFL
+ELLDAEVERLRALIVEGTASTQDNRTRARSAVHAVFRYMDSPTSAHRREGGRGRGERAVA
+GPGRDRGPRRRRVLSRAALRPGVNARRPPGARPRLP
+>GCF_023573625.1_01463
+MTAHPAATAPDEPGRGRRLPRHKRRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRGNRARVRATVAAVFEYMASPERTHRL
+IFDSGIDGDPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDDLIWRGLTSLPSADDAPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001257.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001257.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15b38a4093320bc14198c940d9b850a7c444906f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001257.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01540
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAQAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGRARDARLTRAQEMVRRLGADFSI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG
+>GCF_003691675.1_01250
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAHAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGLARDARLIRAQEMVRRLGADFPI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG
+>GCF_005280335.1_01385
+MSRYDLHTHSVESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWEAAAEAALAEGIAFV
+PGMEMSCMAADGTSVHVLSYLHDPADPSLLREIGTARSARLTRAQEMVHRLARDYPITWE
+LVQEHAAEGATIGRPHLADTLVTLGVVEDRSAAFAHILTGRSKYYVPHYAPDPAIAVELI
+RSAGGVPVFAHPRAVTRGRVVGVEVIEEMIDAGLAGLEADHRDNPEEERSWLREVAARHD
+LFVTGSSDYHGTGKPNLLGEFSTGEDVLAEIERQGTGAAVVRG
+>GCF_020097155.1_01276
+MSTARYDLHTHSTESDGTEPAADVVHAAALAGLDGLALTDHDTTAGWAAAADAARETGLL
+LVPGMEMSCMAADGTSVHLLSYLHDPADPSLLAELGASRDARLTRAQSMTDRLAEDFPIT
+WDLVREHASENATIGRPHIADALVTIGAVPDRSAAFSSILRGGSKYYVPHYAVDPVEAVR
+LVRAAGGVPVFAHPRARLRGRIVGDDVLEAMIEAGLAGLEADHRDNPEQERTWLRETATR
+HGLFVTGSSDYHGAGKPNLIGEFTTGPEVLAEIEHQGTGAAVVRG
+>GCF_023573625.1_01467
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAHAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGLARDARLIRAQEMVRRLGADFPI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001258.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001258.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de767644a2b87eba7303f95376cc1c1845309d64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001258.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01541
+MTDAAQHPAQTTPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMASDWA
+PSSQALPDPDASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAFAHLT
+GLGVDHEPDAVLVLEPTDPGAGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWIGPRP
+TLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAGVDLA
+AAAEADAQTAEFLSELRLVKDAWEVDRMRASVAATIAGFEDVVRALPRAVGHDRGERVVE
+GAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLYTADI
+TRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGWGLLP
+VSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEPGLYF
+KEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAALPRTPDEIEAWMARLQA
+>GCF_003691675.1_01251
+MTDAAQHPAQTTPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMASDWA
+PSSQALPDPDASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAFAHLT
+GLGVDHEPDAVLVLEPTDPGAGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWIGPRP
+TLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAGVDLA
+AAAEADAQTAEFLSELRLVKDAWEIERMRASVAATIAGFEDVVRALPRAVGHDRGERVVE
+GAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLYTADI
+TRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGWGLLP
+VSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEPGLYF
+KEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAVLPRTPDEIEAWMARLQA
+>GCF_005280335.1_01384
+MTDAAQHPAQHADQDRPQDPAATPEAGVDAEGAVSPQPLAQRVENRSQRPSSDAFRAFMG
+ADWAPSSDELPAQDASAPHAARRRAAVSARYPGERIVVPAGRLKVRSNDTDYRFRAHSAF
+AHLTGLGVDHEPDAVLVLEPTDPGAGDGGSDHAATLYFRPLAGRDTEQFYADARAGEFWI
+GPRPTLAGLAARTGLRTAGLEELESAVTKNVCADGTAVRLLREADQDMDALLAGVRAEAG
+MDAEAAASADAQVAEFLSELRLVKDAWEVERMRASVAATIAGFEDVVRALPRAVGHDRGE
+RVVEGAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGTVREGDLLLLDAGVEDDSLY
+TADITRTLPVSGSFTDVQRRIYQAVLDSADAAYAIVRPGIRFREIHAEAMRVLVERLADW
+GLLPVSAEVALSEDGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEP
+GLYFKEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAALPRTPDEIEAWMARLQA
+>GCF_020097155.1_01275
+MTDASAQQNDDLAPEAAADSGAALSPQPLAERVENRSQKPTSDAFRAFMASQWAPASREL
+PGPDASAPFAARRRAAVSAMFPGERIVVPAGRPKVRSNDTDYRFRAHSAFAHLTGLGVDH
+EPDAVLVLEPTDAGAGDAGTDHAATLYFRPLAGRDTEQFYSDPRAGEFWIGPRPTLAELA
+ARTGLRTAGLEELENAVTKDVAATAVRLLREADQDMDAVVAAARADAGVDAQAAGAADAA
+LAEALSELRLVKDEWEVERMRASVASTIAGFEDVVRALPRAVGHARGERVVEGAFFARAR
+EEGNDLGYDTIAASGNNATVLHWIRNTGRVREGELILVDAGVEDDSLYTADITRTLPVSG
+TYSDVQRRVYQAVLDAADAAFALVKPGIRFREIHAEAMRVLAGRLHGWGLLPVSPEEALS
+EAGQHHRRWMPHGTSHHLGLDVHDCAQARRELYLDAVLEPGMVFTIEPGLYFKAEDLAIP
+EEYRGIGVRIEDDILVTEDGAENLSAALPRTPEDVEAWMARLQG
+>GCF_023573625.1_01468
+MMGGMTDAAQHPAQTAPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMA
+SDWAPSSDALPDADASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAF
+AHLTGLGVDHEPDAVLVLEPADPGTGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWI
+GPRPTLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAG
+VDLTAAAEADAQTAEFLSELRLVKDAWEVERMRASVAATIAGFEDVVRALPRAVGHDRGE
+RVVEGAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLY
+TADITRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGW
+GLLPVSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEP
+GLYFKEEDLAVPEEYRGIGVRIEDDILVNEDGAENLSAALPRTPDEIEAWMARLQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001259.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001259.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecc7ced4054ab67d0505df7a0efb77de893e3f3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001259.fa
@@ -0,0 +1,59 @@
+>GCF_002008305.4_01542
+MGIDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDLATAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARDPSGIVTEPSRVWLAAGPHDAVAVAD
+RPDGAVVVPLAAPDGKTLAGLQRGDEIELTDARGAHRRLEVERVSGEGVLVRADKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFA
+DATVGDRVSLDDGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L
+>GCF_003691675.1_01252
+MGIDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GLPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARDPSGIVTEPSRVWLAAGPHDAVATAD
+RPDGAVVVPLADPEGTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLVRAEKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEEIVLARSLEPVPAVDTPPYRIGLTLAQAFA
+DAAVGDRVSLDDGRIGARITAVSADEITLEVTQAGPRGAKLKAEKGVNFPDTHLAIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L
+>GCF_005280335.1_01383
+MDIDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQDALS
+DVGLSSLGRMEAGVLGHVDAVLAAARALDGEDAPSPDDDALTPARGREILARDADRLLGP
+ARPDRAARIMVTLPSEAAQDPDLVARMAEAGMDLARVNCAHDDEAAWAAMIEAVRACATP
+ERPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARTPAGLVTEPSRVWLAAAGAADAPAGA
+VVVPVTEAGAEVLAGLAAGDEVELTDARGSHHVLTVEQAGAAGALVRADKTVYWGTGLAV
+DTPRGTLTVGELAPLEQSMRVRRRDQVVLTRSLDPVPAASAPPYRIGLTLAQAFEDVAVG
+DRVSIDDGKIDAVVRAANADEITLEVTEAGPNGTKLKAEKGVNFPDTALSIPALTDEDLA
+HIPFVARHADMVNLSFVRSAEDVAQLIDALAAEDATDVDITLKIETVGAFEQLPRMLLEA
+MRWRDVGVMIARGDLAVEAGFERMAELQEEILWLCEAAHVPAIWATQILESLAKTGLPSR
+AEITDAAMAQRAEAAMLNKGPYIEEAITALGDILGRMGGHARKKRDMLRRLESWSL
+>GCF_020097155.1_01274
+MSTLPENAPDSRPTAESPVVAPGAAVTELIEAIDALRARIVAAEQAHAERLDRVADRHRA
+SARNLVHYVTLRGEDLRPLQDALSAVGLSSLGRMEAGVLGHLDAVRTALHPLGGRPAPDP
+ADDDPLSPAEGRALLAANAESLLGPSRPGRETRIMVTMPSEAATNAALVQGMADAGMDLA
+RVNAAHDGEAAWAAMVANIRGVARDGGRPAPRICMDLAGPKLRTGPLEPGPGVVKVKPRR
+DVDGTVLERSRVWLGEADAPEAADAVVLPLDPAGSGHSPVLSALRPGDHAMLTDARDSDR
+TLHVLAATEAGVLLACRKTVYWHTGLEVDTPRGTLVVGALPSVPQAMRVHAGDEIVLTRS
+MDPRPAVSEGPFTIGCSLPQAFQDVRPGERVLIDDGKITGEVVSNDGEAITLTVTEAGPT
+GAKLRAEKGVNFPDTDLRLPALTDEDRSHLPFAAAHADVVNMSFVRSPADVAALIDALDA
+EDARGVGVSLKIETVGAFERLPAMLLEAMRWNDVGVMIARGDLAVEAGFERMAELQEEIL
+WLCEAAHVPAVWATQILETLAKQGLPSRAEITDAAMAQRAEAAMLNKGPYIDEAIGALSD
+ILTRMGGHADKKRDMLRRLRSWSL
+>GCF_023573625.1_01469
+MGIDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPTRDPSGTVTEPSRVWLAAGPHDAVAAAD
+RPDGAVVVPLADPEGTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLVRAEKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFA
+DATVGDRVSLDDGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001261.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a222843a131cc919eca6742a9c84749204f077b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001261.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01544
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT
+>GCF_003691675.1_01254
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT
+>GCF_005280335.1_01381
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAVPPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAADLFDRRVRLTDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLDWDEARWTGQAEPQAATSFLAAHEDLKPA
+DLADMLHEMPEKRRVEVARELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEEAEDVRRLLEYEEGTAGSVMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAVGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTSIPVVNEHHRVVGAVSVDDVLDHILPDDWRAMDHDDHDPRP
+AA
+>GCF_020097155.1_01272
+MNSPRIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGRGARSAATGLVIEVPGKKRVFVPM
+TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAGDLFDRRVHLTDGSGRAVVEDLGIEQQR
+NGDWLVTDYYVRRDDGRTAFGRPRGEHLLVSWDEVAWGAAAEPQGASSFVAAHDDLKPAD
+LADMLHEMTDKRRVEVANELQDERLADVLQELPDDDQVQILSHLDIERAADVLEEMDPDD
+AADLLNELPDSQQELLLELMEPEDAEDVRRLLEYEEDTVGSIMTPVPVVLPPEATVAEAM
+ATIRQQEISPALASLVIVARPPLETPTGRYLGVVHFQRLLRYPPPEAIGNIMDKDLEPVS
+DMDSVAHVTRELATYNLTSIPVVNAQHRVVGAVSVDDVLDHILPEDWRAMDPEDHPETEG
+QD
+>GCF_023573625.1_01471
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVARELQNERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEAV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001263.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001263.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98f7d35a08a7cf759760893ba55e0c5f0aada3b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001263.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01546
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ
+IAQRVAVRPRGLAGRRLPVTPR
+>GCF_003691675.1_01256
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ
+IAQRVAVRPRGLAGRRLPVTPR
+>GCF_005280335.1_01379
+MSDLGLHVPEVRTDLERRVLDRLATVQDPEIRRPVTELGMVESVVETAPGTVEVTVLLTI
+EACPMRGTIQGDVAAAVADVPGCDAVDVRTGVMSPERRLALQDALRAARPANPFGEGSLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTASPTKLDRM
+ILPPVVRDVKVISIGMFLDEDRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQAVAGVIENMGPMTLPDGTVL
+DVFGAGGGQEVAERLERVLGSAVPLLGSVPLDPALRRGGDAGDPVVLSAPDSPAGRALAG
+VAERLAVRPRGLVGRRLPLSPR
+>GCF_020097155.1_01270
+MSAPALPRPEVRTPLEAAVLAALDGVVDPEIRRPITELGMVRSVAETGGGHVAVEVLLTI
+AGCPLKGTIQADVAAAVADVPGCAGVDVRLGVMTPTERAALQEALRGARPANPFAEDSLT
+RVLAVASGKGGVGKSTVTANLAVALAGRGLSVGLIDADVHGYSIPGLLGVQASPTRVGEL
+ILPPVSRGVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELVVVTTPQHAAAQVAARAGQLAAQTGQRVAGVVENMGPMALPDGTVL
+DVFGAGGGQEVADRLSGALGTSVPLLGTVPLDPALRRGGDAGEPVVVSAPESPAAAALQE
+VAARLAVRPGSLRGRGLPVSPR
+>GCF_023573625.1_01473
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVADVPGCGSVDVRVGVMEPERRLALQDALRAARPTNPFGKDTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLGTQVPLLGTVPLDPALRAGGDAGDPVVVSAPESPAGRALAE
+IAQRLAVRPRGLAGRPLPFTPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001264.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001264.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c2120d5079375ed2d5ea2d44852351fb31db6ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001264.fa
@@ -0,0 +1,23 @@
+>GCF_002008305.4_01547
+MFGINGSEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGISAEDVHGGLTRQDLTDMDP
+RTLFRRPAGAGSTAAAESGAAAAQTRSTEPAAGAAAVGGAAAALMASGRAEALTEERPAA
+VETEPDPLELLGLAPAPFDVDAT
+>GCF_003691675.1_01257
+MFGINGSEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGISAEDVHGGLTRQDLTDMDP
+RTLFRRPAGAGSTAAAESGAAAQTRSTEPAAGAAAVGGAAAALMASGRAEALTEERPAAV
+ETEPDPLELLGLAPAPFDVDAT
+>GCF_005280335.1_01378
+MHGGLTRQDLVDMDPRSLFRRPAGAGSSAAPAASSGSAAPAAGASLATGAAVGGAAAALM
+ASGRAEEAVAEERPAVEPDPLELLGLAPAPYDVDAT
+>GCF_020097155.1_01269
+MFGINGSELIVLIVLAFVVLGPEKLPEYTRALAQGIRKTRDMAEGAKTQFKEETGTDFDS
+VDWRRYDPRQYDPRRIIRDALREPADGSTAAARAQELTGVAAEDLQGGLSAQDLRDMDPR
+SLFRRPSGDGSTAAPAGGGASAPSDAPTPEDVPSAAVPVAAASPSPAGAAAAGVAAALLA
+SGRAEEVLTDPAPLQHLGTDPDPLDLLGKAPAPFDVDAT
+>GCF_023573625.1_01474
+MFGINGGEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGVSAEDVHGGLTRQDLADMDP
+RTLFRRPAGAGSTAAAESGAAAQTRSTAPAAGAAAVGGAAAALMASGRAEALAEERPAAV
+ETAPDPLELLGLAPAPFDVDAT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001266.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001266.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12a3349def0af6edd8439276eeb2c9cf41aff084
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001266.fa
@@ -0,0 +1,10 @@
+>GCF_002008305.4_01550
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA
+>GCF_003691675.1_01260
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA
+>GCF_005280335.1_01375
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQG
+>GCF_020097155.1_01266
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEAKELQQCLEGVTQA
+>GCF_023573625.1_01477
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001267.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001267.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54afc4f82a0659a1518a03171ff73f6836d98f3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001267.fa
@@ -0,0 +1,18 @@
+>GCF_002008305.4_01551
+MRAPLGGEGRRVSGPQWIVLVAVLVVVLAALAAALAGRLTLRADDPAGRTPGHPVLLPER
+PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQCEDEVTALRARVAELEAADPSRSD
+PAGRA
+>GCF_003691675.1_01261
+MRAPLGGEGRRVSGPQGIVLVAVLVVVLAALAAALAGRLTLRADDPAGRTPGHPVLLPER
+PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQREDEVTALRARVAELEAADPSRSD
+PAGRA
+>GCF_005280335.1_01374
+MSTPLWIAVIAALVVVVAALAAAAAGRLTLRAGEPAGQAPVHPVALPERPRADDVAFVRL
+AVAVPGYQRDQVDAVLLRLRDALADHEDEVAALRARLAELEADAARDAERTGPR
+>GCF_020097155.1_01265
+MTQPIWIAVLVVAVVAVAALAAAALGRALPRPADPAGQAPPHPVLLPEHPRAADVDRLRL
+ATAVPGYQRDQVDEVLARLRAALAADEERIAALEARLGEGDGVGR
+>GCF_023573625.1_01478
+MRAPLGGEGRRVSGPQGIVLVAVLVVVLGALAASLAGRLTLRADDPAGRTPGHPVLLPER
+PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQREDEAAALRARLAELEAADPSRSD
+PAARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001268.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f58d442150289744fb6e6d283f110604142c948
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001268.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01552
+MAPHEHPSGGDVAAKPQRVRRGGQVLRGDAAHTPTFDQLLLDGRRPGDAARPAADVASTT
+SEAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVI
+TGGGPGTMAAANRGAHEAGGESVGLGIDLPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQ
+GFIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWSPLVDWIRGTLVERGMISPE
+DPDLFHLVDTAEEAVACVLRSAGRADA
+>GCF_003691675.1_01262
+MAPDEHPLDGDVAEPEHVRRGGQVLRGEAERTPTFDQLLLDGRQPGDATQPAADIASTTS
+EAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVIT
+GGGPGTMAAANRGAHEAGGESVGLGIELPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQG
+FIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWGPLVDWIRGTLVERGMISPED
+PDLVQLVDTAEEAVACVLRSAGRADA
+>GCF_005280335.1_01373
+MDPDQHPRTDAVPAPERVRRGGQVLRGEAARRPTSDQLLLDARRPGDALPPAADLASTTS
+EAWRVLRIQAEFVEGFGTLAGIGPAVSVFGSARTPEASPEYALAREVGARLAEAGFTVIT
+GGGPGSMAAANRGAHEAGGESVGLGIELPFEAGLNEWVHVGVDFRYFFARKVMFLKYAQG
+FVVLPGGFGTLDELFEALTLVQTGTVTRFPVVLVDSTFWGPVVDWIRGTLVERGMISPGD
+PEIFHVVETAEEAVDCVQRVCGPGAP
+>GCF_020097155.1_01264
+MTDKPDPARADRVDRHRVHRGGQILRGDAAASPTFDQLLLDARRAPAGKTRTPSTSSTSD
+AWRVLRIQSEFVEGFGTLADLGPAISVFGSARTGEGTDEYALGVEIGRRLAEEGWAVITG
+GGPGAMESANRGADEAGGVSVGLGIELPFETGLNPWVGIGVDFRYFFARKVMFLRYAQGF
+VVLPGGFGTLDELFEALTLVQTGTVTRFPVVLVGTEFWGPLVDWIRGTLTARGMISPGDA
+DLITVVDTAEEAVAHVSATCGGARA
+>GCF_023573625.1_01479
+MAPHEHPSGGDVAAKPQRVRRGGQVLRGEAARTPTFDQLLLDGRRPGDATQPAADIASTT
+SEAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVI
+TGGGPGTMAAANRGAHEAGGESVGLGIELPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQ
+GFIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWGPLVDWIRGTLVERGMISPE
+DPDLVQLVDTAEEAVACVLRSAGRADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001269.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001269.fa
new file mode 100644
index 0000000000000000000000000000000000000000..79990a7c9fff4cb9ca7f07a6a49d55eb648bd8e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001269.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01553
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAQQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
+>GCF_003691675.1_01263
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAAQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
+>GCF_005280335.1_01372
+MTQITPEEPHGAHARDEAAPRRPRAAPGDDLIVLENVNKHFGDFHALKDIDLRIPRGQVA
+IVVGPSGSGKSTLCRTINRLETIDDDGGRILLDGQPLPAEGKQLAQLRAEVGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRKADAERHAMELLERVGVAQQAKKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPESFFTAPQHERARDFLGKILAH
+>GCF_020097155.1_01263
+MSEITSGTVHGSTAASGPAPAAASDALIRLEHVNKHFGEFHALKDIDLAIPRGQVAIVLG
+PSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPSEGRELARLRAEVGMVFQSFNLFAHK
+SILENVTLGPIRVKGRKKAEAERHALELLERVGVAHQAKKMPAQLSGGQQQRVAIARALA
+MEPQALLFDEPTSALDPEMVQEVLDVMVGLAREGMTMVVVTHEMGFARKAGDRVVFMADG
+EILEDTDPESFFTRPQHPRAQEFLGKILVH
+>GCF_023573625.1_01480
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILVDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAQQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001274.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001274.fa
new file mode 100644
index 0000000000000000000000000000000000000000..390bb25ecc6b5aeb47c22863465fc17247ba0c66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001274.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01558
+MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAAHTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
+>GCF_003691675.1_01268
+MTQTAAQQPSPRLVSGHGLATTAADGAVLDVWFPTPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLARPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
+>GCF_005280335.1_01367
+MTETAAQHPSARLVSGHGLATTAADGTVLDVWFPAPVAGPLADADATLAETLRSLAADDA
+DRGTTQSVVELEADLDAAPATAEDAWLRLHALSHRLVRPNELNLDGVFGLLANVVWTNFG
+PCAVEGFELTRARLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLL
+GANSGVGISIGDDCVVEAGLYVTAGALVTVVRPGEEPRTVKAVELSGVPNLLFRRNSATG
+VVEVLPRAGRTVELNAALHAN
+>GCF_020097155.1_01258
+MTDTSQTSSARLVSGHGLATRAADGAVLDVWFPAPVTGPLASADASLAGTLEGLAAADAD
+RGTTQDIVALEADLDVAPASAEDAWLRLHALSHRLVRPNELNLDGVFGLLTNVVWTNFGP
+CAVEGFEATRAKLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTVM
+HEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLLG
+ANSGVGISIGDDSVVEAGLYVTAGTVVTVVEPGRKPRTVKAVELSGVTNLLFRRNSVTGG
+VEVLPRDGRTVALNAELHAN
+>GCF_023573625.1_01485
+MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001275.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001275.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b272ccee5f57494aabbccc76f6a931bcfe9af48e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001275.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01560
+MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSALSTFYPDSLDPHDQEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPAAKIGRPRQIYVGE
+QLRQYPQR
+>GCF_003691675.1_01270
+MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTY
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSALSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE
+QLRQYPQR
+>GCF_005280335.1_01366
+MTQNESVRLTVGEQSLDLGVERATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF
+IDGDEGILRYRGYAIEDLAANSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSGLSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYEIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRTIQSDGIKPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILSKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE
+PLRQYPQR
+>GCF_020097155.1_01257
+MSEIESARLTVGEKTLDLGVEKAAEGNDGIVVAPLLKETGKVTYDPGFMNTANAKSAITY
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKEALEAWETNILRHNMVHEDL
+KMFFNGFPRDAHPMPVLSSSVSALSTFYADSLDPKDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNNLNYVENFLRLCFGVPAEEYEIDPDMVKALDLLLMLHADHEQNASTST
+VRLVGSTDANLFASVSAGINALYGPLHGGANEAVLNMLRRIQAEGIKPEDFMEKVKHKED
+GVRLMGFGHRVYKNYDPRAKIVKKTAEDILAKLGGNDELLEIAMRLEEKALADDYFVERR
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELTEDPATKIGRPRQIYVGE
+QLRQYPQR
+>GCF_023573625.1_01487
+MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSGLSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE
+QLRQYPQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001276.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001276.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b5df4ec8befdd0bd387911fef9b88c6056e375c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001276.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01561
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDDLRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADDLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARDV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPQLVATLINTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGELADLGIIAGPGVFYGAGGDGYVRVA
+ITATDEAVARAAARLTARGPRTG
+>GCF_003691675.1_01271
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDALRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADGLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARGV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPELVATLVNTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGDLADLGIIAGPGVFYGAGGDGYVRVA
+ITATDEAVARAAARLTARGPRTG
+>GCF_005280335.1_01365
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPELIRRALTEAADAHGYPTTHG
+TADLRRAVVDWYARRRGVAGLDPEAVVPTVGSKEFIAWLPTLMGLGAGDVVVHPEAAYPT
+YAMGALIAGAEAVAADDLASLAPEVRERVRLVWTNSPANPTGAVLDAAALKRVVDDARAL
+GAVVCGDECYAELGWDEWDGELVPCILSEEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPGLVATLVNTRKHAGMIVPAPVQHAMAVALADEGHVAQQKDRYRRRRDALRAALEASG
+HAVDHSEAGLYLWTRRADTDPAAATEQDSWDLLGELADLGIIAGPGVFYGAGGHGYVRVA
+ITASDEAVEQAARRLAARGPLRR
+>GCF_020097155.1_01256
+MLTLPDYPWDTLAPYRERAAAHPEGTVDLSIGTPVDPTPALIRDALTAAADAHGYPTTHG
+TAELRQAVVDWFARRRGVPGLDPEAVLPTVGSKELIAWLPTLLGLGAGDVVVFPATAYPT
+YAIGAQIAGAEAVAADTLAELDDDVRSRVRLVWTNSPANPTGAVLDAAELRAIVDDARAL
+GAVVCGDECYAELGWDEWEDRVVPCILAPEVSGGDLTGLLSVYSLSKQSNLAGYRAAFVG
+GDPELIAPLTNTRKHAGMIVPGPVQHAMAVALRDDAHVAAQRDLYRERRAALKAALESAG
+YAVDHSEAGLYLWTRRADLAPGQGTAQDSWDLLGELAELGIVAGPGVFYGAAGHGHVRVA
+ITASDEAVAAGAARLTARGPLPR
+>GCF_023573625.1_01488
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDALRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADDLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARGV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPELVATLVNTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGDLADLGIIAGPGVFYGGDGYVRVAIT
+ATDEAVARAAARLTARGPRTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001277.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001277.fa
new file mode 100644
index 0000000000000000000000000000000000000000..327fd7bdd323329f3a85f3e0cb1a24b34f58ebb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001277.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01562
+MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPEEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA
+>GCF_003691675.1_01272
+MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPEEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA
+>GCF_005280335.1_01364
+MTYVIALPCVDVKDKACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPEEWADYYKANVEFFDDLGSPGGAAKLGMIAKDHPIIAALPPQNADA
+>GCF_020097155.1_01255
+MTYVIALPCVDVKDKACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD
+VPEEWADYYKANVEFFDDLGSPGGAAKLGQIAKDHPLISALPPQGEGA
+>GCF_023573625.1_01489
+MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPDEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001280.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001280.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc1908eb0b7e3fee7852b9d167a4e0abc8934404
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001280.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01566
+MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSLLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGGGAHRRLRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEEAGGSARISDADEDGQR
+>GCF_003691675.1_01276
+MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEAAGGSARISDADEDGQR
+>GCF_005280335.1_01360
+MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRVKAGKSYSQGALVRKRFFRHKAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGANMGILPLALVLGLVTWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRVIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISLYQNS
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAAAGRKRGLFSRRAAKTDAGAT
+TAGGLGTAPTARDGEADDLIADPDAPEHRRGGAGGPAGGVGQ
+>GCF_020097155.1_01251
+MTMSHSAQQNPRSTSPAVVDLAEAEDLKLQQKTGKSYSQGALIRMRFFRHKAAMVSLVVL
+AFIALMAFTSIGFAGIPGWWDESYSAASTVVDGGRPTLSVVPQFLGGEGLRWGAHPFGQT
+STGTDFFALVMRGTQQSLIIAFIVGLISTAIGALVGAASAYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGKMAGGLQLGILPLAFVLGIVSWTSLARLVRGEILSLREKEFVAAAVAMGA
+KPGRIIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSYLGFGVKSPDSSLGLLISDYQTA
+FTTRPWLFWWPGMTILAIALSVNFLGDGLRDAFDPRQSGSGRRKRGLFSRRAAVTEATPT
+TAGGLQASPASAPAGHADVVTDSRGLDAPAAWTVTDADGTSRPAGDDVDTTEGDAR
+>GCF_023573625.1_01493
+MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHKAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEEAGGSARISDADEDGQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001282.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001282.fa
new file mode 100644
index 0000000000000000000000000000000000000000..926f35e39e43af9e2db44db19a2282dfcca5d73a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001282.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01568
+MKYTKLSAAAALAAGSALILSACAPGGGNAGDSSSNSASGASQGGDSGAGNVIEGDKGQK
+LTAEASGPGKADLGDVKTQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMFSSFWY
+FGTDGSIIPDKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANNDTIKA
+EGAETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAKEA
+GMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGGWQAGQ
+SITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGED
+VNVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNL
+REVFPFQDKYQEVVDAAYPKEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRRTETVA
+LIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALFAWAGSGQKASGANIYQSDGAQNQQ
+SYNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVR
+DTAAQSGALWNVEQWVRVQE
+>GCF_003691675.1_01278
+MKYTKLSAAAALAAGSALILSACAPGGGNAGDSSSNSASGASQGGDSGAGNVIEGDKGQK
+LTAEASGPGKADLGDVKTQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMFSSFWY
+FGTDGSIIPDKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANNDTIKA
+EGAETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAKEA
+GMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGGWQAGQ
+SITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGED
+VNVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNL
+REVFPFQDKYQEVVDAAYPKEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRRTETVA
+LIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALFAWAGSGQKASGANIYQSDGAQNQQ
+SYNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVR
+DTAAQSGALWNVEQWVRVQE
+>GCF_005280335.1_01358
+MKYTKLSAAAALAAGSALILSACAPGGGDDADNTASSGNGGASGSASQGGEAGAPEVTEG
+DKGQKLTAPVDGPGMADLGDVETQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMF
+SSFWYFGTDGSIIPNKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANN
+ETVKAEGSETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHI
+VAKEAGMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGG
+WQAGQSITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLE
+GLGDDVNVQTGDQLTWEHVDFNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADA
+QVMNAREVFPFQENYQEVVDAAFPEEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRR
+TETVALIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALYAWAGSGQKASGANIYQSDG
+AQNQQSYNNPEVDAAWDKLATSLDEDEQLEQVKTIERLLWEDFQAIPLYAHPGLVGHKAD
+VANVRDTAAQSGALWNVEQWVRVQE
+>GCF_020097155.1_01249
+MKHTKLSAAAALAFGSALVLSACAPAGPAASGSSSNGGGSSAASGSSAASGSDAAGGVTT
+GEKGEKLTAPADGPGMADLGDVKTEEGSVAYSVGKDDFLSYNGVQANTYSTYNSAIVDRL
+FSGFYYFGTDGTIVRNEEFGTFEKISDDPLKVKYTINEDATWSDGTPVTAADFIVQWAAD
+NPNIVDESGKADPKTGQKPQLFESITSEPGKYIPEAPEGDPKGKEFTVTYAEPYADWEIL
+ITTALPAHVIAKGADMSLDDLVAAAKAKDSTKLVPAAKFWNNGWDFNPGELPSADMIPSM
+GPYKIKDGGWVAGQSITLEANDKYWGTPAATKNLVIKFAAPETHVQALQNKELDVIEPQA
+TVDTVSQLEGLGDSVNIQKGDQLTWEHLDFNRGTGSTFADSKELREAFALCVPRQQIVDN
+LVKPINPDATVMNAREVFPFQDNYQEVVDAAYPKEMDQPNIEKAKELVAKSGVSKPTVRL
+GYQAGNQRRAETVKLIKASCDQAGFDVQDANSNVFFKEVMPTGDYDVALYAWSGSGQKAS
+GANIYQSDGEQNQQSYSNKTVDEAWDKLAGSLDEKEQLEQVKVIEKALWEDFQAIPLYAH
+PGVVAHQADLANVRDTVAQQGALWNVEQWKRVS
+>GCF_023573625.1_01495
+MKYTKLSAAAALAAGSALILSACAPGGGNADDSSSNGSGASQGGDSGAGNVVEGDKGQKL
+TAEASGPEMADLGDVETQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVVDRMFSSFWYF
+GTDGSIIPNEDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIFHWAANNDTVKAE
+GSETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAEEAG
+MSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGSYKFKDGGWQAGQS
+ITLEANPEYWGTPPATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGDDV
+NVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNLR
+EVFPFQDKYQEVVDEAYPKEMDEPNIEKAKELVEKSGVSTPTVRLGYQAGNQRRTETVAL
+IKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALYAWAGSGQKASGANIYQSDGAQNQQS
+YNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVRD
+TAAQSGALWNVEQWVRVQE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001284.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53d885ce3ea251b7196d8b70f4e65a8efa03bee2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001284.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01571
+MTPPGWPPRARRSPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHIHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGDQVAAVGNGGGQGHLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTADEVDGFAIPLEVAFDVVDQVLTGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRAVGDDASRMSRLV
+NDHNVGDRITVQWRTADGEVREAEAVLQPALVN
+>GCF_003691675.1_01281
+MTPPGWPPRARRAPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHVHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGETVAAVGNGGGQGHLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTAEEVDGFAIPLDVAFDVVDQVLSGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRPVGDDAFRMSRLV
+NDHNVGDRITVQWRTASGEVREAEAVLQPALVN
+>GCF_005280335.1_01353
+MSVPPGWPPRRRRSPLALAISFFGVLGALVLAVGVTLLVAGRMVDVVGAPDPVVSARESA
+PPDAGALAQELAGAHEGVAVDWDAPAHAGSELDPGLAVDHAPGILLVETVLGQRMGTGTG
+MVLTPEGLALTNYHVVEDSSEVFVVEADTGERHTATVLGRDAEHDVAVLDVHGVTDLPVA
+SVSLDPVRRGDEVAAVGNGRGQGHLTAVRGTVLGTDRSIMAASQGSDEYARLTGLIQTDA
+DVVPGYSGGPVVDDDGQVVGVTVAASDGTGAQEVDGFAIPLGVALGVVDQVLSGEETDTV
+SIGADGALGIMVAADPEAGVVVMQVDADSAAEAIGLVPGDVVLAVDGQAVEGNASRMSRL
+VNDHNVGDRITVTWRTASGEVREAEAVLQEAVVN
+>GCF_020097155.1_01246
+MAIAVFGVLGAVVLAVGLTLLAGGRLIAAVGAGSSSSAAAPSGPQVTTRSLDALAASLDH
+AHAGIAVPAADAPPADGSLDPGERVRRAPGVLLVETRLEAMQGTGTGMVLTSDGLALTNY
+HVVEDSTAVSVVVADTGARHAATVLGRDAKNDVAVLQIDGVSGLTTTSVSRDPVRPGEAV
+AAVGNGGGQGYLTSVGGEVLRVDQSILAATEGTDDFERLTGLIQTDADVVPGYSGGPLVD
+GEGQVVGVTVAASEGRTAAQVDGYAIPLSTAFDVVAQVLSGEETDSVSIGADGSLGISVA
+GSRDGVEVLSVDRGSAGEELGLRPGDVITAIDGRTLDGNATAMSRLVNDHEVGDRLSVQW
+RTADGEARQGEAVLQKARHN
+>GCF_023573625.1_01498
+MTPPGWPPRARRSPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHIHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGDQVAAVGNGGGQGYLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTADEVDGFAIPLEVAFDVVDQVLSGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRAVGDDASRMSRLV
+NDHNVGDRITVQWRTADGEVREAEAVLQPALVN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001285.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a10dfa28b67e3c6edcc9478aa18d3cf8ad86532
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001285.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01572
+MATTHMKSTPVHTVGELPQVGSPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC
+AASVREFDSRVADLGDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGGDYGVRM
+TDGPLEGLLARAVVMVDADGVVRHAQLVPEISEEPDYEAALAAARG
+>GCF_003691675.1_01282
+MATTHMKSTPVHTVGELPPVGAPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC
+AASVREFDSRVADLEDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGDDYGVRM
+TDGPLEGLLARAVVVVDADGVVRHAQLVPEISEEPDYEAALAAARG
+>GCF_005280335.1_01352
+MATTHMKSTPVQTVGDLPEVGAPAPDFTLTGADLSPVTLQELRGRRVILNVFPSLDTGVC
+AASVREFNSRATDLEDTTVLAVSADLPFAAARFCSAEGIENVRSGSVFRSSFGDDYGVTM
+VDGPLEGLLARAVVVVDAEGVVRHAQLVPEITEEPDYEAALAAAQA
+>GCF_020097155.1_01245
+MATTHFKGTSVHTVGELPEVGSAAPEFTLTGSDLSSVTLADLKGRTVVLNIFPSLDTGVC
+AASVRRFNQEAAGLEDTTVLAVSADLPFAAGRFCSAEGIENVVTGSVFRSDFGTAYGAEL
+ADGPMRGLLARAVVVVDAEGTVAYTELVPEITTEPDYEAALAVVRG
+>GCF_023573625.1_01499
+MATTHMKSTPVHTVGGLPQVGAPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC
+AASVREFDSRVADLGDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGDDYGVRM
+TDGPLEGLLARAVVVVDADGVVRHAQLVPEISEEPDYEAALAAARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001286.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001286.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01005563fe3d52a5198c4a4ed3527bc6bf49e1be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001286.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01573
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
+>GCF_003691675.1_01283
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFVPATMPISNGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
+>GCF_005280335.1_01351
+MRTPMTSNVTDTALLFEGGGMRASLTSAVVAELLRERIHVDFVAGISAGSSNSVNYLARD
+PERARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFQANPARL
+VLVGFDAVTGQTRWWDRSDMGTLADLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPVTAAEEAGFEKLFVVMTRERSYVKRPERFPAFYQRTFRRYPAVAEALISRWRRYNETR
+ERLFEMERQGRAYLFVPESMPVSNGERSVAKLAAAHELGLAQVRREMPAIREFLGL
+>GCF_020097155.1_01244
+MAEQQDHTAEALTSNVTDTALLFEGGGMRASHTSAVVAELLRAGVHVDFVAGISAGSSNA
+VNYLARDPLRARQAFVDFADDPRFGNWRTFLRGKGMFNAEYIYEHAGLPEADLPYDFAAY
+RANPARLALAGFDAVTGETRWWGREDMTTLQDLMVRVRASSTMPILMPPVHLEDTVYVDG
+ALGVDGGIPVTAAEEAGLAKLLVVMTRERSYVKRPERFPAFYQRAFRRYPAVAEALVTRW
+QRYNATRERLFEMEREGTAYLFVPEVMPVSNGERSVAKLAAAHELGLAQARREMPAIKEF
+LGL
+>GCF_023573625.1_01500
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFLRGKGLFNAEYIYEHAGLPEADLPYDFAAFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFKKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001288.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001288.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ed3238ec1eafa3a410ca701e5ee81effed42d81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001288.fa
@@ -0,0 +1,19 @@
+>GCF_002008305.4_01575
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMAAWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA
+>GCF_003691675.1_01285
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMAAWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA
+>GCF_005280335.1_01349
+MTGVTAADGLDLSGMAAWLRHQADEEIVHANKFIDHVTDRGSDAAGDLSSRPLLNWFLEE
+QIEGEATPPL
+>GCF_020097155.1_01242
+MSIDKDLTRKFNEQITLEFEASMVYRQLAIAADMQDLSGMAAWLRHQADEEIVHANKFID
+HVVDREASAVIGAIPAPDVPEHITPVQIFEAALAHERKVSEAIRELYRAAEAAGDLSSRP
+LLNWFLEEQIEEEATVGEIVGQLKLVGEDGSGLLRIDSALGARPVETTENAG
+>GCF_023573625.1_01502
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMASWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001289.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001289.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1be6823dfe15458e7dd0606073c71a7cea447d2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001289.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01576
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTETATSAVWGLLWGSVALGVV
+LLVGRLRGNKAAPAH
+>GCF_003691675.1_01286
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEETVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV
+LLVGRLRGKKAAPAH
+>GCF_005280335.1_01348
+MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMAGAAANREL
+PMIWRITKGSLRNKLLIILPALLLLDWLAPWVLPWLLLAGGTYLAYEGAHKVWGKLTGHS
+PERDEPAVEKGPEAEDKVVRGAITTDFILSAEIMVISMNEVADVDFWLKAVILVVVAILI
+TAVVYGAVALIVKMDDVGLHMTQNGRTAGGRRFGAGLVKAMPHVLTAITVIGTVAMLWVG
+GHIVLVELAALGVPWPYDVQHGIVHAVEAAGGFVAWLVETLTSALWGLIWGSLALGVVLV
+VNRLRGKKDTLAH
+>GCF_020097155.1_01241
+MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMEGAAAQREL
+PMILRIVRGSLRNKLVFILPGLLLLDWLAPWALPWLLLAGGTYLSFEGAEKVWHKLTGHH
+EPQEDTPAVEQGPEAEDKVVRGAITTDFILSLEIMVISMNEVSDQGFWMKAAILAIVAVV
+ITVAVYGAVALIVKMDDVGLHMHENAHTSGARRFGLGLVKAMPVVMGVISVIGTVAMLWV
+GGHIVLMELATLGLPWLYELQHTIVHAVEGAGSVIAWLVETLTSAIWGLVWGSLVVAVVG
+LVRRLRT
+>GCF_023573625.1_01503
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV
+LLVGRLRGKKAAPAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001290.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001290.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2e5a6ee728cae427cb6047db801d4a477dbc3a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001290.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01577
+MNTTAAASDPSDAPLASTRIGEGPRGVAFLHGLMGRGRNFTGPAKELGDDFTVELIDLPD
+HGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPELVDRLI
+VEDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRR
+TAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHPVLWLAGAESDYVQDEDVPRM
+KELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
+>GCF_003691675.1_01287
+MNTTAAASDPSDAPLASTRIGEGPRRVAFLHGLLGRGRNFTGPAKELGDDFTVELIDLPD
+HGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPDLVDRLI
+VEDISPRVSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRR
+TAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHPVLWLAGAESDYVQDEDVPRM
+KELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
+>GCF_005280335.1_01346
+MTISDQGSPRRLPDSLERVSTPDPSASAAPSDAALASDVIGDGPHRVAFLHGLMGRGRNF
+TGPAKALADDFTVELLDLPDHGRSPWTDRVDYQEIADRVAEHLRAGLAADGPVHVLGHSM
+GGKVAMVLALRHPDLVDRLIVEDISPRLLPQATDEFVHLLGTMLRMDLDSYESRAEADAV
+MAKHVHDARVRGFLLQNLRREGGRFAWQPNVAMLFEHLEAVGSFPDPAAPEDPDRVFDRP
+VLWLAGANSDYVRDEDVPRMKDLFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
+>GCF_020097155.1_01239
+MPTWSRASLSRVNTTAASAPSDAPLASTRIGEGSRRVAFLHGLMGRGRNFTGVATALADD
+FTVELIDLPDHGQSPWTDAVDYQDMADRVADHLRAGLAADGPVHLLGHSMGGKVAMVLAL
+RHPELVERLVVVDISPRMSPSATGEFVHLLGTMLRMDLASYTSRAEADAAMAEHVHDARV
+RGFLLQNLRREDGHFAWQPNVRMLFEHLDEIGAFPDPVVPEDPDRVFDRPVLWLGGADSD
+YIRDGDAPEMKALFPRVVRVTVRGASHWVHADQPEAFVSAVRTFLTAD
+>GCF_023573625.1_01504
+MNTTAASAPSDAPLASTRIGEGPRRVAFLHGLMGRGRNFTGPAKELGDDFTVELIDLPDH
+GASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPELVDRLIV
+EDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRRT
+AGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVVDHPVLWLAGAESDYVQDEDVPRMK
+ELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001291.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b88f92245147cd0c35d221de065b7ba1979fec2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001291.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01578
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPVLDDDGAAPASRPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DARR
+>GCF_003691675.1_01288
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGALEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DARR
+>GCF_005280335.1_01345
+MPAPEARVTVAVSTAVFGVRPDPSGAPRLHVALVPRMREPFLDRWALPGTWLAADEELAD
+AAARVAAETVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPSHGGGLD
+VAGLPAGVHVRWQRADAPPAMAFDHAEILTAAVARLRADLPRAGVAHALLGPSFTLAELR
+AVHEAVLGRTLDAANFRRATLATGVLEETGEVRAGTRHRPPKLYRYRPADGAPPPAAPDD
+PGDLS
+>GCF_020097155.1_01238
+MPVAEARVSVAVSTAVFGVRPDAHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPTLDDDGAAPASRPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRDGTPHRPPKLYRYRPAGPGTDPNPAGP
+DASR
+>GCF_023573625.1_01505
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001292.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001292.fa
new file mode 100644
index 0000000000000000000000000000000000000000..068ccc6b6462d80a6ddd3d2310c44f0680eaeb98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001292.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01579
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVAEPART
+ALERMLAVAPKQSAAQSAGAGT
+>GCF_003691675.1_01289
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART
+ALERMLAVAPKQSAAQSAGAGT
+>GCF_005280335.1_01344
+MTATPETTASVARTLTLVARDPARGSACSSDLTTGPWAFDAGLPAYGPGASQDDAIPADA
+PVQGRIPEEYQQASDEELHARIAAAKAALGDRAVVLGHFYQRDEVVRHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPEQAVILPNLAAGCSMADMADLDSVQDAWEQL
+EEVYGTEPDADGRVPLLPVTYMNCSAALKGFVGERGGIVCTSSNASAVLEWAFERAQRVL
+FFPDQHLGRNTGRAMGIELERMPMWNPRLPLGGNTEETLRDARVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVRVIVHPECPLPVVEAADESGSTDHIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPDAVADPARA
+ALERMLAVAPRQSVAQGAGA
+>GCF_020097155.1_01237
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPAAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRMPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALREAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPVSVADPART
+ALERMLAVAPKQSAAQSAAQSAGAGT
+>GCF_023573625.1_01506
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART
+ALERMLAVAPKQSAAQSAGAGT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001293.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001293.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75ce936b81c862a1b646fe8452af64bcc7ec7cdd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001293.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01580
+MTPADRAPATPAPQPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREPGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGSAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVERVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EVSPRR
+>GCF_003691675.1_01290
+MTPADRAPTTPAPRPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EGSPRR
+>GCF_005280335.1_01343
+MSAGTRGAWGPTPAPIADVERIVAAALAEDAPWGDVSSEAFVPADARITARVVAREAGVL
+SGTAALEAAFRLVDPATEVTLHLPDGTALAPGAVVAAVAGPARSVLRAERVALNLAQRMS
+GIATATAAHVAAVRAGGGHTRVADTRKTTPGLRVLERQAVRDGGGHNHRHGLSDAVMLKD
+NHLAALGFGGEDAPGEELTRALRAGKARLPHTVHVEVEVDRLDQLPAVLAAGVGTVMLDN
+FSLADLRAGVELVAGRAVVEASGGVSLETIGEIAATGVDVVSVGALTHSVRALDLGLDAV
+VDAADAPAPGRR
+>GCF_020097155.1_01236
+MTPADRAPATPAPQPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRSSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVGTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVRSLDLGLDAVVE
+EVSPRR
+>GCF_023573625.1_01507
+MTPADRAPTTPAPRPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+PNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EGSPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001294.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001294.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6e56c32b43b804bec06503055fe6503d3e6b0b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001294.fa
@@ -0,0 +1,43 @@
+>GCF_002008305.4_01587
+MSRSHSDALDASGPDSGGAVAVPRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG
+LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP
+LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD
+QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ
+YVVAGTIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC
+ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMIAAPGVPGGAIVAASGL
+LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER
+LDDEGAATGADAG
+>GCF_003691675.1_01298
+MSRSHSDALDASGPDSGGAVAVPRRRVGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG
+LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP
+LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD
+QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ
+YVVAGAIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC
+ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMVAAPGVPGGAIVAASGL
+LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER
+LDDEGAATGADAG
+>GCF_005280335.1_01335
+MSHASSGAAAPSDRAPQGAVSESCRRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATF
+NGLFSNVLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLFGGFGALLVCLLV
+FPLILTPGSFEAMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLRRGALHEG
+FDQLRSIIERVVMGLIVPLCATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLG
+VTMVAAPGVPGGAIVAASGLLSSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMI
+VDKIAGDRLIEDSEDEGLERLDDEEAATGADAG
+>GCF_020097155.1_01233
+MSHAAPSSSVPPAPPSSSATDGTAAPEKAPRRGLRRLGLLPRVLLGIVLGVVVGLVSPEW
+LTRTAVTGTSLFSAFLGFIVPVLIVALVAPAIAELGRGAGRWLSVTAAIAYGSTLFGGFL
+SLGVALALFPRILTPGSISGVTDPSEGGATPFFEIAMDPPFGVMTALLLSFVLGIGMTLI
+PRGVLQQGFEELRTIIERVVTGIVVPLLPFYIFGIFLAMAASGGVFEVIGTFLGVILIVF
+ALTVVLLLVQYAVAGVIAHRNPLTALKAMMPAYATALGTSSSAATIPVTLRQVVSLGVRQ
+PIAAFVVPLAATIHLAGSTVKIVAFSTAVIILTGGQVDVGLMVGFIFMLGITMVAAPGVP
+GGAIVAASGLLSSMLGFTEPQVALMVATYIAIDSFGTATNVTGDGAIALIMDRIAGDRIA
+ADPGVAEESPAA
+>GCF_023573625.1_01514
+MSRSHSDALDASGPDSGGAVAVPRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG
+LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP
+LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD
+QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ
+YVVAGAIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC
+ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMVAAPGVPGGAIVAASGL
+LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER
+LDDEGAATGADAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001296.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001296.fa
new file mode 100644
index 0000000000000000000000000000000000000000..352670aedf6079c28d9a34035ae1ccfd62afbc28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001296.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01591
+MAEPRPGDVRVTPGPGAPRGLVIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQRRNRVAARERLAALLREALAPPTPRRA
+TKPTRGSRRRRLEAKHRRSEVKRTRRRPGLD
+>GCF_003691675.1_01303
+MAEPRPGDVRVTPGPGAPRGLVIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQRRNRVAARERLAALLREALAPPTPRRA
+TKPTRGSRRRRLEAKHRRSEVKRTRRRPGLD
+>GCF_005280335.1_01300
+MADLRVEPGPGAPRGLVIPAAELMERFSHASGPGGQGVNTADSRVQLSLDLATTTALDES
+QRARALAVLGPRLAGTVLTVAAEEHRAQRRNRVAARERLAAMLREALIPETPRRATRPTR
+GSRRRRLEAKRQRSETKQLRRRPGV
+>GCF_020097155.1_01219
+MDDLRVPPGPGVPRGLRIPAAELSERFSHGSGPGGQGVNTADSRVQLSLDLAATTALTDA
+QRIRLLEGLAPRLAGTVLTVDAAEHRAQRRNRTAARERLAALLREALVPETPRRATKPTR
+GSQRRRLQAKARRSEVKQSRRRPRMD
+>GCF_023573625.1_01518
+MAEPRPGDVRVTPGPGAPRGLIIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQWRNRVAARERLAALLREALAPPTPRRA
+TTPTRGSRRRRLEAKRRRSEVKRTRRRPGLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001298.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001298.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86ddde4a14c710cda9ae8fe093a7cf55312c7390
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001298.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01595
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSTRADDGAPAWQILRHPAAERLEETIPAFRRVPNLFEILSYDYW
+RLNHGYELPPDACRRRDEYLATEAGRAHVRAVVTAKLRASGRSAEEAAAMSEAELIGASA
+AFFGGTHDVVIARRHFVDGAVDDHQLASSGTLTPDEHHAFMALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEVGAQNVAALDRLREDPQVFNQAALDVAVAHDLM
+IAANEHAVMFAGFGHRYPTVEVYSTSPVGQPWRQTAAELRAVSDLLHAAHAATGPDVPSN
+EEWHTRPPGVADPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELWAA
+GALADGMRIGADARVRPGMLRYAD
+>GCF_003691675.1_01307
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSMRADDGAPAWQILRHPAAERLEETTPAFRRVPNLFEILSYDYW
+RLNHGYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSAEEAAAMSEAELIGASA
+AFFGGTHDVVIARRHFVDGAVDDHQLASSGTLTPDEHHAFLALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEVGAQNVAALDRLREDPQVFNHAALDVAVAHDLM
+IAANEHAVMFAGFGHRYPTVEVYSTSPVGQPWRQTAAELRAVSDLLHAAHAATGPDVPSN
+EEWHTRPPGVASPMPWRVMLKWRVSTLAGFEGATKINVNTISPWDVRDRVLARLRELRAA
+GALADGMRIGADARVRPGALRYADGAARLTPPRGR
+>GCF_005280335.1_01301
+MPRTRPPAQDFLAELPDGTVKQRNPFSGTEVWTVPGRGHRPLGIARPAAQPLDPDDDGRH
+CAFCSARLLETPPEKSRVVRTEDGEHAILRDVPAEALFDTVPEFRRVPNLFEILSYEYWR
+LNHGFVPAPGVADRRAAYLATETGRAHVLAVVGNKLRAAGRSAEEVEAMPEEERIEAASG
+FFGGGHDVIIARRHFADGAQDDHALAGSGTLSPEEHRRFIALTVDSMRDLYAANPHARYV
+SVFQNWLKPAGASFDHLHKQLVAIDEVGVQNEAAIARVRRNPDAFAQDALGYAAKQGLMI
+ARNEHAAMFAGFGHRYPTVEIHSLSPTCEPWEQTDAERDAMADLIHAAHAATGADVPSNE
+EWHTRPTGVAEPLPWRVCLKWRVSTLAGFEGATKIYLNTVSPGSVRERVATRLQELQAAG
+AIADGIRIDDDGHGAV
+>GCF_020097155.1_01214
+MSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAFCEHR
+MLETPPEKARIVPTRADDDAPAWQILRHPAAERLGETTPAFRRVPNLFEILSYDYWRLNH
+GYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSAEEAAAMSEAELIAASAAFFG
+GTHDVVIARRHFVDGAVDDHQLASSGTLTLDEHHAFLALTADAMRDLYATTPAVRYVSVF
+QNWLKPAGASFDHLHKQLVAIDEVGAQNAAALDRLREDPQVFNHAALDVAVAHDLVIAAN
+EHAVMFAGFGHRYPTVEVYSTSPVGQPWRQSAAELRAVSDLLHAAHAATGPDVPSNEEWH
+TRPPGFASPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELRAAGALA
+DGMRIGADARVRPGALRYAD
+>GCF_023573625.1_01522
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSMRADDGAPAWQILRHPAAERLEETTPAFRRVPNLFEILSYDYW
+RLNHGYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSTEEAAAMSEAELIAASA
+AFFGGTHDVVIARRHFVDDAVDDHQLASSGTLTPDEHHAFLALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEIGAQNAAALDRLREDPQVFNHAALDVAVAHDLV
+IAENEHAVMFAGFGHRYPTVEVYSTSPVGEPWRQDPAELRGMSDLLHAAHAATGPDVPSN
+EEWHTRPPGVADPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELRAA
+GALADGMRIGADARVRPGMLRYAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001299.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001299.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bc4b970f90ad4dafdadb02c7251a8fa2f165374
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001299.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01597
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQT
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSPFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGESLSWHQRFLETGTMRQG
+>GCF_003691675.1_01309
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQT
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSPFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGESLSWHQRFLETGTMRQG
+>GCF_005280335.1_01298
+MSSRIQHAGLRAKVMSAQEAAAFIRPGTTVGMSGFTGSGYPKAVPLALAERISAAHARGE
+DFRIDLHTGASTSSEMDGALAESGGVALRTPFQSDPTMRAKINAGEVEYIDTHLSHLAQT
+VWNGFYGPMHTAVVEVSAIREDGTLVPSSSVGNNKSWLDLADEVILEVNSWQSEELEGLH
+DVYYGTALPPHRQPVMITDPADRIGQPYFECDPAKVVAVVETHGPDRNSAFKPADADSIA
+IAQHLVEFFEHEVAAGRYDERLLPLQSGVGNIANAVMAELVKSRFRGLTAFTEVVQDGML
+DALDSGTLSMASATAFSLSTEAAERFNSTVAQYKDKLILRTQEISNHPELVRRLGVLAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSVAKGGDISCIVPMVSH
+VDHTEHDVHVLVTEQGLADLRGLSPKQRARTIIAKCAHPDYRDQLQDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRHG
+>GCF_020097155.1_01207
+MSSRIHHPGLRAKVMSAEEAAAFITPGMTVGMSGFTGSGYPKAVPMALAERIKSAHARGE
+DFRIDLHTGASTSVEMDGALAEADGVRLRTPFNTDPTMRAKINDGSVDYIDTHLSHLAQT
+VWEGFYGPMDAAVIEVSAIREDGTLVPSSSVGNNKSWLQLADKVILEVNSWQSEDLDGIH
+DVYYDTALPPHRKPVPVNHPSDRIGRTEFVVDLDKVVAVVETHGPDRNSPFKPADADSIA
+IAQHLVEFFEHEVKAGRYDEHLLPLQSGVGNVANAVMAELVKSRFHGLTAFTEVVQDGML
+DALDSGTLAMASCTAFSLSTEVAERFNDNVLQYKDKLIIRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRQG
+>GCF_023573625.1_01524
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQA
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSAFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYRDPLRDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001302.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001302.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7164b4e33931a3c8f6ed707189f0f690c6bdcb2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001302.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01600
+MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQAEGDASAE
+TEASTPDAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG
+RALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR
+>GCF_003691675.1_01312
+MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQAESDASAE
+TEASTSDAAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE
+GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR
+>GCF_005280335.1_01293
+MDAAPTPSLALEDQLCFALHRATRAVTRGYGPLLSRIGLTYPQYLVMLTLWQVEGDASAE
+TEAPTPGAGALAVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG
+RALRASARTVPADALTRIPLDATERQVLMCLLNRITEAVGPR
+>GCF_020097155.1_01202
+MDAAPTPSLALEDQLCFALHRATRAVTRGYGPLLSRLGLTYPQYLVMLTLWQVEGDASAE
+TDAPTPGAGALAVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG
+RALRESARTVPADALTRIPLDATERQVLMGLLNRITEAAGPR
+>GCF_023573625.1_01527
+MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQVESDASAE
+TEASTSDAAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE
+GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001303.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001303.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28ec9e4a744c01d67f1c26c3b9a0e378fd7041c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001303.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_01602
+MSTPTRTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
+>GCF_003691675.1_01314
+MSTPTHTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
+>GCF_005280335.1_01292
+MSVDPYMRGRMNDVKSYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGLGWREHAV
+LDGDTVQAVDTSQFPDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAG
+QIARLLGASRVVGSAGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVG
+GDHLEAAIAALRVDGRVAMCGAIAQYNSTEPPAAPRNLALAIGKRLTLRGFVLQKYAAQV
+RPEFLERVGPWVAAGKIQWDETVREGLENAPQAFIDLLDGANTGKMLVRL
+>GCF_020097155.1_01200
+MSTPTHTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGLGWREHAVLDGDTVQAVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSTAGQIARLLGASRVIGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKRLTLRGFVLQKYAAQVRPEFLERVGPWVAD
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMVVRL
+>GCF_023573625.1_01529
+MSTPTRTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001306.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001306.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df2504670eb87505e422ec484b5460a2e9fa9fb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001306.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01611
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLVDAHPLTD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPVCSDCGQPIDPDGHDCTFPDS
+>GCF_003691675.1_01322
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGGIGLGWDPTTAQVLIDAHPLSD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPFCSDCGQPIDPDGHDCTLPDS
+>GCF_005280335.1_01287
+MTESPAHVHEFDWPDRVVIGTIGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMLDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLSD
+DDADPALEVDAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
+>GCF_020097155.1_01192
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALDGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLTD
+DDADPVLETDAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
+>GCF_023573625.1_01537
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLSD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001307.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..213f926d5a43fda16d4a40f8358900010074fa1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001307.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01612
+MSAADVPAGELMSGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAATLAR
+REVAASLVSEALGWDIVPRTWLRDGPFGKGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+VLEGEDEGGNRLVLAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VQDKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGQGLAELLGAEEVEALAARCAQLL
+DDGIFPAPSGLTPAVPWPLF
+>GCF_003691675.1_01323
+MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAASLVSEALGWDIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPAGQVPASGWLT
+ILEGEDADGNRLVLAHEDSAALRRMAVFDVIVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VADKLRTVLWGWLGEELSEEERDGVGRVLDGLDGELGRGLAELLSAEEVQALAERSAGLL
+DDGRFPAPSGLTPAVPWPLF
+>GCF_005280335.1_01286
+MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTSVVYKPVAGEAPLWDFPAGTLAR
+REVAAYLVSEALGWDIVPRTWLREGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+ILEGEDEGGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRYGVDHGLTFH
+VADKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGRGLVQLLSAEEVEALAERCAQLL
+DDGVFPAPSGLTPAVPWPLF
+>GCF_020097155.1_01191
+MSAADVPAGELVDGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAAHLVSEALGWEIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPAAGWLT
+ILEGEDEEGRRLALAHENSAALRRMAVFDVIVNNADRKGAHILAMPGGHRYGVDHGLTFH
+VAGKLRTVLWGWLGEALSEEERDGVGRVLDGLDGELGRGLAELLSAEEVEALAERGARLL
+DDGIFPAPSGRTPAVPWPLF
+>GCF_023573625.1_01538
+MSAADVPAGELVSGELTLTGRITTASNATFLGAVGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAAHLVSEALGWDVVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+ILEGEDEDGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VEDKLRTVLWGWLGEALSDEERDGVARVLDGLDGELGRGLAELLSAVEIGALAERSAGLL
+DDGTFPAPSGLTPAVPWPLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001308.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001308.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8769992302c864ed69a4703908d8a00047e15daa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001308.fa
@@ -0,0 +1,61 @@
+>GCF_002008305.4_01620
+MARRAAKAKPAKTLEQTLWDAADKLRGNQEPSEYKHVVLGLVFLKYVSDRFEERREQLKD
+ELAAEGIKPERIESFLEDRDEYASQNVFWVPSLARWGYVQSVAKQPEIGQQIDQAMDLIE
+KENPSLRGVLPRNYGRDGLDKRRLGELVDLIGSIGFTETDDHGADDVLGRVYEYFLGQFA
+GKETGKDAGAFYTPRSVVKTLVEMLEPFKGRVYDPAVGSGGMFVQSAEFVKAHGGKRTDI
+SVYGQEFTDTTWKLAKMNLALRGVEADMGSHSADSFTEDLHLDLRADYVIANPPFNVSDW
+WDAKLADDPRWKYGTPPKGNANFAWVQHFLHHLAPHGTAGFVLANGSLSSKSSGEGEIRQ
+RLVEAGLVDCIVAMPDKLFFNTGIPVSLWFISKGRDGNGHRARKGEVLFIDARKLGAMQS
+RRLRVLSDDDIAQIADTYHEWRNHDGCYEDVPGFAKSATIGEIEKHEFVLTPGRYVGAAE
+AEVDDEPIDEKIERLTNELLAEFERGRELENEVRLRMGSLS
+>GCF_003691675.1_01648
+MTIPATRGAASAPHRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAPH
+REFFAELAAKGHPDFVLDNLVESRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ
+NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPETVSNAEMGTLFEDLIRRFAAA
+SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSVLDERLRRMN
+PNAEVRLFGQELNDQSYAICKSELLGKGQAADGIARGDTLKNDAHMTERFDYVLSNPPYG
+GDWKASRAAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN
+GSPLFTGGAGSGPSEIRRWLLESDLVDVIVALPTDMFYNTGIATYVWVLDNNKPADRRGR
+AQLIDARTFFTKLRRNVGSKNKELSKADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGY
+REITVERPLQLRFEVEDATIAAALATKPADKLPDDGRSALEAALASLRGRVWDHQPTFVL
+DLKKALKEHGVTAGAPLVKALTGAIGVHDPKAEVVTNKKGEPEPDTSLRDTELVPFGRDI
+HEYFEAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDADLKQLTAEIIEL
+LQEVER
+>GCF_005280335.1_00900
+MTTPATPGAASAARRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAPH
+REFFAELAAKGHPDFVLDNLVESRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ
+NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPDTVSNAEMGTLFEDLIRRFAAA
+SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMN
+PNAEVRLFGQELNDQSYAICKSELLGKGQDADGIARGDTLKNDVHLTERFDYVLSNPPYG
+GDWKASRTAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN
+GSPLFTGGAGSGPSEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKSAERRGR
+VQLIDARTFFTKLRRNVGSKNKELSKADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGY
+REITVERPLQLRFEVEDATIAAALATKPVDKLPDDGRSALETALASLRGRVWDHQPTFVL
+DLKKALKEHGVTAGAPLVKALTGAIGVHDPEAQIVTNKKGEPEPDTSLRDTELVPFGRDI
+HEYFAAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLDEIDAELKQLTAEIIEL
+LQEVER
+>GCF_020097155.1_00838
+MPSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAQHREFFAELAAKGHP
+DFVLDNLVQSRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQNVADLFTYYEFDK
+TVAKLDEHDRLFLVLQQFASIDLSPETVSNAEMGTLFEDLIRRFAAASNETAGEHFTPRD
+AVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMNPNAEVRLFGQELN
+DQSYAICKSELLGKGQDADGIARGDTLKNDAHLTERFDYVLSNPPYGGDWKASRTAVEKE
+IAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLNGSPLFTGGAGSGP
+SEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKSAERRGKVQLIDARTFFTKL
+RRNVGSKNKELSTADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGYREITVERPLQLRF
+EVEDATIAAALATKPADKLPVDGRSALGAALASLRGRVWDHQPTFVLDLKKALKEHGVTA
+GAPLVKALTGAIGVHDPKAEVVMNKKGEPEPDASLRDTELVPFGRDIHEYFEAEVVPHVS
+GAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDAELKQLTAEIIELLQEVER
+>GCF_023573625.1_01879
+MTTPATRGAASAPHRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMDPH
+REFFAELAEKGHPDFVLDNLVQSRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ
+NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPDTVSNAEMGTLFEDLIRRFAAA
+SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMN
+PNAEVRLFGQELNDQSYAICKSELLGKGQDADGIARGDTLKNDAHLTERFDYVLSNPPYG
+GDWKASRTAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN
+GSPLFTGGAGSGPSEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKPADRRGR
+VQLIDARSFFTKLRRNVGSKNKELSTADRQRVLDIYRDFDAQSEDNAEFSKVLTAQDFGY
+REITVERPLQLRFEVEDATIAAALATKPVDKLPDDGRSALESALASLRGRVWDHQPTFVL
+ELKKALKKHGVTAGAPLAKALTGAIGVHDPDAEVVKDKKGEPEPDTSLRDTELVPFGRDI
+HEYFEAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDAELKQLTAEIIEL
+LQEVER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001309.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001309.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26a8cbe77509e7b9ba528842f300ff242d6cffd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001309.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01626
+MARPIDPFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASIDVDVEER
+TLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVLTLTIPVA
+EQAKPRKISVTHGGAAPVAGQTVEGETAETTGE
+>GCF_003691675.1_01332
+MARPIDPFREMERLMTGFARTSGAASMPMNLYREGDVFVAEVELPGVDPSSIDVDVEERT
+LTVRAERKEAPAGEDRRWLTKERPAGTFARQLNLGQGLALDKIEADYSDGVLLLTIPVAE
+QAKPRKIQVKHTGSAAQVEGEAVEGEAVEGSAAEASGE
+>GCF_005280335.1_01271
+MARPIDPFREMERPFREMERLVNGLTRTSGTASMPMNLFREGDRFVAEVELPGVDPASID
+VDVEERTLTVRAERKESPAGEDRRWLTRERSAGTFARQLTLGEGLALDRIEADYEDGVLT
+LTIPVAEQAKPRKISVKHSGAGAGAGQTVPGETAEVEERSAEQEAAQNGGAPQA
+>GCF_020097155.1_01181
+MARPIDPFREMERPFREMERLVNGLTTRATGTASMPMNLYREGDAFVAEVELPGVDPASI
+DVDVEERTLTIRAERKEAAASEGRQWLTRERSSGTFARQLTLGQGLALDRIEADYRDGVL
+VLSIPVAEQAKPRKIQVKHSAADQVEGQEVAGQESVQDSAAVEAPQQPSGE
+>GCF_023573625.1_01555
+MARPIDPFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASIDVDVEER
+TLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVLTLTIPVA
+EQAKPRKISVTHGGTAPVAGQTVEGETAETTGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001310.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001310.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e24c2fee8505869b74cb1a618a040fabd9be8f7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001310.fa
@@ -0,0 +1,23 @@
+>GCF_002008305.4_01628
+MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGDTVDEVLFVPYGETAEAAFRAALGHLEAPQTT
+DDEGDTGR
+>GCF_003691675.1_01333
+MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGGTVEEVLFVPYGDTAEAAFRTALDRVERG
+>GCF_005280335.1_01268
+MELLIAPGDITATTADVVVNAANSTLLGGGGVDGAIHRRGGPEILAACRRLRETELPDGL
+PVGQAVATTAGRLPARWVVHTVGPVWAKTIDKSATLASCYRESLRVAAELGARSVAFPAI
+SAGVYGWPMDDAARIAVTTCREVAAQGAGSVERVLFVPFGERAEAAFRAALDAPDETGAP
+AAS
+>GCF_020097155.1_01176
+MKLSIAPGDITATHADAIVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPDGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLRVARELGARTVAFPAI
+SAGVYGWPMDDAARIAVETSHAMADEVGDVVEEVLFVPFGDRAEAAFRAALEHLT
+>GCF_023573625.1_01557
+MQLTIAPGDITATRADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAETIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGGTVDEVLFVPYGETAEAAFRAALGHLEDPQAT
+DDEGDTGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001311.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001311.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e3e2402a989e26c4d6e877ce9b06371352d6b17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001311.fa
@@ -0,0 +1,19 @@
+>GCF_002008305.4_01629
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFNTLGRQPVFAPTILAVTADGQRGMWEHPDL
+QPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG
+>GCF_003691675.1_01334
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFDTLGRQPVFAPTILAVAADGQRGMWEHPDL
+EPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG
+>GCF_005280335.1_01267
+MEHVFDTLGRRPVFHPTILAVTADGQRGMWEHPDLEPEQAAAEVAKISPRPARAVAVFEG
+EAATEDGPRPAVAVEAFDAAALASVRLVFTYLPGVPGAGIAAQVDGDPQVVANGPNPLFG
+>GCF_020097155.1_01175
+MTPPTHEILPLVSLAVDHVFDTLTRQAVFDPTILAVTADGARGMWTLPDLAPEQAAAEVG
+RIQPLPQRAVAVFDGEVQTPQGPRPAVAVEAFDAGAVQSVRLVFEYVPGIPGTEITGRIE
+GEPHIVANGHNPLFGQIS
+>GCF_023573625.1_01558
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFDTLGRQSVFAPTILAVTADGQRGMWEHPDL
+EPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001312.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001312.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a87f8071713b001a11c3f497b2da2073a79dcc2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001312.fa
@@ -0,0 +1,42 @@
+>GCF_002008305.4_01630
+MEILSLLLALTLGLVLGALLGAWLMWRRAADGGEEARRAQAELAALRTEHQGAREALAAA
+RAEQRALTAARAEDAERQRAESQVMSTLAPLGQRLAALQEQVSVLERDRASQFGRLGEQL
+RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGRD
+GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAAQHAAAVRR
+HVDQLSAKSYWDGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT
+ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTAVDRYNQLVGSV
+ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAGVEEDELRRRRAESAREA
+>GCF_003691675.1_01335
+MEILSLLLALILGLVLGALVGAWLMWRRAAGGGEEARRAQAELAALRTEHQGAREELAAA
+RAEQRALTAARAEDAERQRAESQVMSTLAPLGQRLAALQEQVGVLERDRASQFGRLGEQL
+RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGKD
+GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAGQHAAAVRR
+HVDQLSAKSYWAGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT
+ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTAVDRYNQLVGNV
+ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAGVEEDELRRRRAESAREA
+>GCF_005280335.1_01266
+MDILSLLLALALGLVVGALTGAWLMWRRAAGGGEEARRAEQELAALRVEHQGAREELAAA
+RAEHRAVAAARAEDVERQRSEARVLSTLTPLGQQLTALQEQVGVLERDRAAQFGRLGEQL
+RAAAATDRDLLNQTTSLMATLRSTSARGHWGEAQLRRVVEAAGMLHHVDFSEQSTLSGRD
+GERLRPDLLVSLPGGKSMAVDAKAPIGDALAAEALADEPGEEAWERRQALAAQHAAAVRR
+HVDQLSAKAYWAGLEHSPELVLCFLPAESLLAAALDADGGLLDHAFSRNVALVAPVSLLT
+ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTTVDRYNQLVGNV
+ESRVLPAARKLREADPGLAPTPDIRTLESAPRVLSAPELVEGVEQDELRRRREDPAREEA
+VREDPAREA
+>GCF_020097155.1_01174
+MDFLTLVITLALGLLVGAAVGAWLMWRRMDGAADGSAGAELDALRREHAAVREELAGARA
+ESRALTQQRAEDAERARTDARVLETLAPLGRQLGALQEQVGVLERDRAAQFGRLGEQLRT
+AAANDRDLLNQTASLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFSEQTTMTGRDGE
+RLRPDLLVSLPGGKTLAVDAKAPIGDALAAGALAEEPGEEAAERRAALNARHAAAVRRHV
+DALSAKAYWTGLERSPELVLCFLPAESLLAAALDADGALLDHAFSRNVALVAPVSLLTAL
+KSVAYAWRQERLAENAQLIVSGARELYDRLGTMGSHLDRMGGSLRAAVDGYNRLVGNVES
+RVLPAARTLREADPGLPALADVRSVDNAPRPLTAPELVDGDGPVDEGWTPAGSAAAEDRP
+EPAPAFEESPLWEDDEWTEDAAWDTDRRTA
+>GCF_023573625.1_01559
+MEILNLLLALILGLVLGALVGAWLMWRRAAGGGEEARRAQAELAALRTEHQGAREELAAA
+RAEQRALTAARAEDAERRRAESQVMSTLAPLGQRLAALQEQVSVLERDRASQFGRLGEQL
+RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGRD
+GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAAQHAAAVRR
+HVDQLSAKSYWDGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT
+ALKSVAYAWRQDTLAENAHTVVASAKELYERLGTLGTHLDRMGGSLKTAVDRYNQLVGNV
+ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAGVEEDELRRRRAESAREA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001316.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001316.fa
new file mode 100644
index 0000000000000000000000000000000000000000..234a12cfa398fa5be79dab72b5cf6f5c56247428
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001316.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01634
+MDQPVTEGASAASDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVAMTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPRRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFEIREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDTRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVRDADQVAPDDRLDILVAAGRIAADVV
+ATHRTTPTPSHERTRQA
+>GCF_003691675.1_01339
+MDQPVTEGASAASDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVATTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPHRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFETREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDIRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVRDADQVAPDDRLDILVAVGRIAADVV
+ATHRPTPTPSHERTRQA
+>GCF_005280335.1_01261
+MDPSSTAHVEADALLDAGVPATASQTSAERPWPLRRLSENLKLHIERAPATWIEGQLIEY
+KTNRGNVYMTMRDLEEEYSLPVTAWRNVAVTFEGTVQQGSRVVARVKPNFWTKAGRLSMV
+VQEMRPVGLGDLLARVELLRRRLGEEGLLDPARKRPLPLLPGLVGLITGRDSDAKKDVLR
+NAQLRWPAVRFEVREVAVQGPEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADVRASTPTDAAKRIVPDAAQEAAGIAEA
+RRRLAAAVERRVQREGEGLAQLRSRPVLADPVVMVDGREQDLHAWRERARRATAHRLTRE
+RDAVEHLVARVRALSPQQTLDRGYAVVQQEGRLIRDAAQVAPGEDVDILVASGRISAEVT
+AVRPGRVGGVGTVQDEDEQAGTKEQA
+>GCF_020097155.1_01170
+MEESAAREEGTVVVPATASETSPERPWPLHRLSENLKLHIERAPATWIEGQLIEHKNNRG
+NLYMTMRDLEEEVSLPLTAWRAVAAGIDPSVQQGSRVVARVKPNFWVKGGRLSMVVQEMR
+PVGLGDLLARVELLRRRLAEEGLTSPARKRQLPVLPGVIGLITGRDSDALKDVVRNTHLR
+WPAAVFEVREVAVQGPDAPRQVAAALAELDARPEVEVIVIARGGGALEEVVLPFSDEALV
+RAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQESVGIREARLRLA
+GAVERRVRGEADALAALRSRPVLAHPHVMVDTRTEDLGRWQERGRVALGHRLAREADAVS
+ALRAQVRALSPQQTLDRGYAVVQHAGHVVRRAEDVTPGDDLDVLVAAGRIEAYVTDVTPV
+ETPSPTQEDA
+>GCF_023573625.1_01563
+MDQPVTEGASAAPDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVAMTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPHRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFEIREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDTRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVREADQVATDDRLDILVAAGRIAADVV
+ATHRTTPTPSHERTRQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001320.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8f548e96e0af4723e02e002a24e8a0cda38b932
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001320.fa
@@ -0,0 +1,38 @@
+>GCF_002008305.4_01639
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGTPITVVHGGEGLEGAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAVAADPAVALPSPPPPTSTP
+SSTPTGTEAGPSADAVPTPSATASTAVPSPTALPVGDPAADAQAAGRVLETLLAEETAAA
+GTPQDEAPAVLSSSAGVLRLTAVVTQTTAARLELESITDLNGWCESLTAVAPPPLTAAAD
+PDAATALRARLDRLAGCRPETWLADTEDPSAALVADEAQVALLTDTDPEIDANTLVPLED
+DGRVLPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGADPLPAAEAAQY
+WLVDHGLEDAPEDWFVPRGSWF
+>GCF_003691675.1_01344
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGAPITVVHGGEGLEAAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPPTPTPTP
+TPTGTEAGTSTGTVPTPSATASTAAPSPTALPVGDPAADAPAAGRVLETLLAGQTAAAGT
+PQDEAPAALSSSAGVLRLTAVVTQTTAARLELESITDLNGRCESLTAVAPPALTSAADAA
+TALRARLDRLAGCRPETWLADTEDPTAAVVADEAQVALLTGTDPEIDANTLIPLEDDGRV
+LPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGADPLPVAEAAQYWLVD
+QGLEDAPEDWFVPRGSWF
+>GCF_005280335.1_01256
+MPTASESSDAADASATPEPTPLPDGEPAADAAEAGRVVERLLQGDAEAGASPEPGDAVAV
+LGSSAGVLRLSAVVTATTAARLELDALEDLNGRCEGLTAALPAGLAGDPQANAALHARLD
+RLAGCRPGTWREEDASAAAVVVADQAQLGLLSATDPEIPASMLVPLEDPERVLPEGRLAA
+VGAPDALDDDAQRRIEEVLSALDEDGLRELERITTGADALPPAEAARYWLVDQGLEDVPE
+GWFMPRDSWF
+>GCF_020097155.1_01165
+MTRPAERPRTSRVRAAAGASALSLALALSGCGAPRAGAPADPTGAPVTVVHTSDPLDSAV
+AAVVARHLRHRGHPVTLEDAGDATPWSAAAGDTVAVVDTLRLALQADPAAVLPPEPEDAA
+ASRAAAAPTPSESSLEPIDPSAPARVPATGSATPSPTPLASGLPAADADAAQAVVDAALS
+RVAAGADAAAPTPAASRSAATPTGPSPRVLADSAGTLRLAAVVTATTASREGLDSIDDLD
+GRCGDLTLAVPAALAAAVSDGLLAHRLDDFAGCRPADWRTDAADVGPAVVADAAQVGLTY
+RTDPDIPPNGLVLLEDPDRVLPEGRIAVVGERETLDDDAQSALGEVMDRLDDDGIAELAR
+LTEGGDALPADEAAQYWLVSQRLEDAPEDWVVPADPWF
+>GCF_023573625.1_01568
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGTPITVVHGGEGLEGAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPPSPTSTP
+SSTPTGTEAGTSADAVPTASTAAPSPTALPVGDPAADAPAAGRVLETLLAEETAAAGTPQ
+AEAPAVLSSSAGVLRLTAVVTQTTAARLELESITDLNGRCESLTAVAPPTLTAAADADAA
+TALRTRLDRLAGCRPETWLADTEDPTAAVVADEAQVALLTGTDPEIDANTLVLLEDDGRV
+LPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGDDPLPVAEAAQYWLVD
+HGLEDAPEDWFVPRGSWF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001321.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001321.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18d8b8729bc8ce1a12986379835e14b4eb444bee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001321.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01640
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVLYTARITGGVLR
+PEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT
+>GCF_003691675.1_01345
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARITGGVLR
+PEVGGSSTDARWFDLAELSGLRTASWVTEALARAGVAT
+>GCF_005280335.1_01255
+MSPTPVPDAEPARADAPAGPFQTRAGAYALIVDGGRVLLSSWQGPEHLVWTLPGGGIELG
+ESPEEACRREVWEETGHTAELTGLLGVTTGVIPAERRLRGEALPLLTVQVLYTARITGGV
+LRPEVGGSSTDARWFDLAGLDAVRTAPWVREALARAGAAA
+>GCF_020097155.1_01164
+MSAASPTAASTAPGPFETRAGAYALIVEDGRVLMSAWAGPTGIVWTLPGGGIELGESPEE
+ACVREVEEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARLTGGVLRPEA
+DGSSVDAAWFALDGLADVRTSAWVDRALALAGLAADDAAGTAR
+>GCF_023573625.1_01569
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVVYTARITGGVLR
+PEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001322.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001322.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0406ca75ee05ef7376935e60d5e58c983e49fd1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001322.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01641
+MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAELESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
+>GCF_003691675.1_01346
+MDTPQDPPRRDDPSGGPVEPAVDAALDRVHALLRQARVIAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALVPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAGLESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDTALELTRRVIAVLGGLRAAGALLPIGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTVLPAARAVLASATTVRAIAAHELDRPTAALDLAFEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
+>GCF_005280335.1_01254
+MDAPQQTPAPADVGPTAVLARVRTLLAEARTSGAPEDAVDAAPVDHDARQWWELSLEAAL
+RDEPRESARCAESGLAALGPGEDGVRLSLLRALAVAADRLGDETGLTRWVEARAALLRTL
+GRPRQAALETQLGASLVREPDGFEAAVLAGVVEEEPGVPGEDPGDTVLPEAALALAVHRV
+HASDLDGALAAARRAVESLRGLRAAGAVLPVGSWSSAHLLLSRLHLWRGEHAEADEAAAV
+VTSLPAARAVLASATTVRAIAAHEQDRPTAALALALDAADRMARVGLRRGAASAAALAGR
+VAGDLEGHEEAAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRPDEAEPLLARLVR
+REAAQGHDVEQARALVDLGHAHHDQDRSENALPLWREAAGLFEAHGRWEDAARTLLAAGA
+LVNRERDELTRPSALDLFERAVAAARRAVDEDPAVLPAALHAHGYLLCESGRPEGLELLD
+EAVALVREAEAPWQVADYTDTRARALWSLEQGAEAVSTALHAADLFTAAQDPEGAAQAEL
+FAASVVAEDGSPEQAATLFRLVSESTQSTLVRLGALTGLHQCLSAVGDHDGAARVRDDLD
+AVREQLGAD
+>GCF_020097155.1_01163
+MAEDAPALLAGRDPLAAVEALLAAARDDAALPLPAGSDAPSLRERALEALLREDPASAAR
+AAEDGLDAPGGQDPALRLALLRLRATAAAHAGDEPALEEWTARRADLLRRLGRPRQADLE
+VQLGASLLREPDAFEATVLAGVAEDERGRITADPAALEDTVLPDALLALCAQRVQAHDLD
+AALEAAEEALAVIRAQETAGVVLGEAAEPHALLMLARLHLWREEHRASDDAARAVLARPC
+AAVVRASATLVRALAAHGQDRPEAALDFALRAAEAMSRAGLRRGAASAAALVGRVAGARA
+DRQDLAVAAWELSCVHAEKAEAPEAPSLAYWWAHQLLIAGRAEEAEPVLTALVRREAAAG
+DEAAQARALVDLGHACHELDRPSEALPLWREAAELFTRRGHHADAAHTLLAAGALCHRDP
+HDAAHAGALDLFEQAVDAARRSEGDSAVLASALHALGYLRCETGRGDGLELIDEAIALAE
+GSGAAWQKADYLDTRARSLWALHRGDDAVSAALTSADLFTDAGDPSGAAQAELFAAHVVA
+EDGRPEQAATLFRLVSESTHSDLVRLGALTGLQQCLAALGEHAEADRVRADADAVRRALG
+GRD
+>GCF_023573625.1_01571
+MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAGLESQLGGALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRYAGADWQVANYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001325.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001325.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e7c8088f004e5cbc24011ca5aff58975f8474dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001325.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01644
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGAGPASFGQ
+MVRWHGRQGRDGSAYTWGMALDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG
+RGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGAW
+RDHRTFAVTAEEVPDGLLAGWLATRPRP
+>GCF_003691675.1_01349
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGAGPASFGQ
+MVRWHGRQGRDGSAYTWGMVLDDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREA
+GRGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGA
+WRDHRTFAVTAEEVPDGLLARWLASRPRA
+>GCF_005280335.1_01249
+MSWQRSPWPVTLRHGTLSLRPLRRRDRDAWEAQRAHNHAWLTPWDATSPVPGAGPSSFGQ
+MVRWHGRQGREGSSFTWGVALDDDAPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG
+RGLTPTAVAMAADWAFRSAGLHRVEVNIRPENAASLRVVEKLGLRDEGVRRSYLHVDGDW
+RDHRTFAITAEEVPEGLLARWLASRPRA
+>GCF_020097155.1_01160
+MDVSGSLWPVALRHGTLTLRPLRRGDRRAWEEQRAANRDWLTPWDATSPVPGAAPASFAQ
+MVRWQHRQARAGTSYTWGMALDDDAPGRDRLIGLLSLGGVQHGSVMSGAVGYWIDRRQAG
+RGLTPTAVAMATDWAFHGLGLHRVEVNIRPENTASLRVAEKLGLREEGLRRAYLHVDGAW
+RDHLSFAVTAEEVPEGLLPRWLARREAAAGTAEPRDTAHTPGVAGDVPGPSGR
+>GCF_023573625.1_01574
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGVGPASFGQ
+MVRWHGRQGRDGSAYTWGMVLDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG
+RGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGAW
+RDHRTFAVTAEEVPDGLLARWLATRPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001327.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001327.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d36463e8af93646443aeaccfd61bea500206ed13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001327.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01646
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRKQYGSVGVSFKGSGFYRTDSRSG
+TGGTGSAGGSTSDSAAGSSTSSTSSSSSPAAD
+>GCF_003691675.1_01351
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRNQYGSVGVSFKGSGFYRTDSRSG
+TGGTGSAGGSTSDSAAGSSTSSTSSSSSAAAD
+>GCF_005280335.1_01247
+MPTYAYRCRDCGHAFDAVQSFTDDALTQCPECGGVLRKQYGSVGVSFKGSGFYRTDSRSA
+GSASSGSASSAGSASSSTSAGGSGTSSTSSGGSGSSGSSSSSSGSKD
+>GCF_020097155.1_01158
+MPTYAYRCKDCGHAFDAVQSFSDDALTECPVCGGVLRKQYGSVGVSFKGSGFYRTDSRGG
+APSSTPAAPSSGAASSTGTSSGSSD
+>GCF_023573625.1_01576
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRKQYGSVGVSFKGSGFYRTDSRSG
+TGSAGGSTSDSAAGSSTSSTSSSSSAAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001328.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001328.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af361551216fc61b9bd9276f47ae395200e3eb35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001328.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01647
+MPADGAPRRRGPRRADAPGTGPASADGREPRLPGMPRLIGQAGTSPATAPTGDVAGVESG
+PAEAERDRWLREQRPPHWG
+>GCF_003691675.1_01352
+MSADGAPRRRGPRRADAPGTGPAAADGREPRLPGMPRLAGQAGTSPVTAPTGDVAGVESG
+AAEAERDRWLREQRPPHWG
+>GCF_005280335.1_01246
+MGAEVPDPAPRRRGPRRADAPGTGPASADAPEPRLPGVGAGTDGARGAEGVRGAGGVRGA
+VGVRGAAGEPTADERDRWLLEQRPPHWG
+>GCF_020097155.1_01157
+MRTTPTASPEPGRRRGHRRADAAGTGPASADGPEPTLPEPTLPGPALPGAQTAGDATPSR
+PAVSRGRAVTSAAGADRPQPADELGRWLLEQRPPHWG
+>GCF_023573625.1_01577
+MSADGAPRRRGPRRADAPGIGPAAADGREPRLPGMPRLAGTSPATAPTGDAAGVESGPAE
+AERDRWLREQRPPHWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001329.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001329.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f10e78f8c1f1ddee2cbf8a4c9dfaec2fd307f01e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001329.fa
@@ -0,0 +1,110 @@
+>GCF_002008305.4_01648
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVSSLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPELDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHIQDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAPAEDDVAPADERLVVDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSSWRRLHLVEMSSVTRSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGEHVMGQVGQVRERLRRLEGVLAPEAVAEAPLE
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRDHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLAEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALD
+EVLPTLPLRTVHRPLERRLVRLLSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAADAEPFVIVPVVRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGDDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYAGVMDLAVLDPRADQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWSIDVFADPESVARELADRLGVEPADETDETDDDAR
+>GCF_003691675.1_01353
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVASLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPELDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHVEDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAPAEDDVAPADERLVVDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSSWRRLHLVEMSSVARSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLKDWNRHAAEPGTPPQVPDQGEHVMGHVGQVREHLRRLEGVLAPEAVAEGPLD
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRDHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLTEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALD
+EVLPTLPLRTVHRPLERRLVRLLSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAADAEPFVIVPVVRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGEDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYGGVMDLAVLDPRAEQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWAIDVFADPESVARELADRLGVEPADETDETDDDVR
+>GCF_005280335.1_01245
+MREQEFPRLARARAAARPEEGQTRPDPAAWVASLGSGAENDTMLRFAPSAANSIDVTAAN
+SSGVSQLLLGRRTRLSTLLPAGPALQAAEEVAAGLRAKVRELSEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRGELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYRQAAYATARLEQRPALARLREEAAALTGLQVEDRMLVSTFADLGETATLPASLEH
+LPVVEALYDAGTGMVPRPPALQPTEAPGEDDVAPADERLVLDLDAAQRRVVEHSAAGESL
+VVAAAPGTGQTQTAVAVAARLAWEGRRVLVVAERSAALADVHARLDEIGLRAAALDVPAH
+ADPEQLRRQLVQAVLRAERAEAPDAARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLPTPPATTVRLKRSVLDSTVNRQAVAEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFALDVPQLVAATATSTWRRTHLVEMSSVARSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGERVMGVVGDVRERLRRLERILAPEAVAEQPLA
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLKDHGLTELLTDLRDREVPTEALAAEL
+ELAWWQSALEAMISGDDFLAMMSGADLAEVERGFRELDRAHLERGADRLSAALGARWKEA
+LRTFRADAAVLRGLLKQGRPTVEALTTLAPEVLQPLVPVVTTSPMALSEFPSDWGADVVV
+LLEADATALATAVGALTRAPQVVAFGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALA
+EVLPTVALRTVHRPLERRLVRMLSALAYEGALEALPTAGEATGRDRTVTAEYLQEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEPHARRVAAAVQATAARASWA
+LDFLSRGRGEDAEGAEPFVIVPVTRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPGG
+ERMVAVALTRARQRLHLVSALRAADLDEDRLDGGAQWFLRLLEAYLGDGAPDPVGRVSDP
+LLADLRERLEERGARVLPRHGGVMDLAVVDPHPEDEDEDGDAPRPLALAGDGGDVYRALT
+VRERTRTLPERLEARGWDPRTLWAIEVFADPESVAQELADRLGVRPADESERDADDDGR
+>GCF_020097155.1_01156
+MTEQEFPRLARARAAVRPAEQDQERPDPAAWVASLGSGAESDTMLRFAPSAANSIDLTGA
+GTSGLSQLLLGRRTRLSTLLPAGPELDAAQEVAAALRAKVRELGEERGIDVGALALGVAT
+WSAVEDGRRERRTAPVLLARLAFSVRSGARGRDEVELQIVEHAHLNPALVRNLRRHHGLR
+LDPEAYQHAAYATSRLEPGPALALLREEAAGVEGLEVQETLLVSTFADLGDTATLPESLE
+HLPVVQALYDVGTGMVPRPAELRPTGRPDEDELPPADERLVLDADPSQLRALDHAAAGES
+LVVRTAPGTGQTQTAVNLAARLAWEGRRVLVVAERSSALADVHARLAQAGLRDAALDVPA
+HADPEDLRRQLVAAVLRAERASAPDRAAADAELEELRRRLREHVDSLHHVRPRWGCSPFQ
+AMQALASLTALDTPPATTVRLKRSVLDSTVDRHAVAGRLTRAGELGAFDRDATASRWFGA
+RVRNVQETEAAGELVEHLAGTLYTTRRAVEAAADQAGLRRPRTVDGWAEQSDLFARVERA
+LTAMDPSVFSLDVPQLVTATASSQWRRSNAVEMSSVQRSRLRRAAKDAVKPGVQVPDLHQ
+ELMEVEGILEDWRRWTAIPGSTPMVPDMADHARPAVRDVLDALDRLSQVLAPEATAGTPL
+AEQDVDDLMAAVDGLVADRPTLATLPERTLVLDELREHGLNELLEDLHAREVPVAALPAE
+LELAWWQSALEAMISGDDFLAMMSGADLTAVEQGFRAADRTLLDSGGARLAASLGAAWKA
+ALGTYRADAAVLRSLLKQGRPSVESLATITPGLLQALVPIVTTSPMALTEFPPDWDADVV
+ILLEADATALATVAGALTRAPQVVAFGDPAIGRPQSFQVSVDPTATAGPLRPLRSALSAL
+AEVLPVLDLRHVHRPLPRSLVRLVSHVAYEGAVDALPTAAEFTGRGRTLTAEYVAEGVGI
+PMTGGDVVESTDAEVARTVERVFEHIRDRPEESLAVVTVSEQHARRVAGAVQATAARAPW
+AADFLARGRTDGDEREPFVIVPVLRASTVTRDAVILTPGYGRTPHGRVVHHFGALSDPDG
+ERMLTVALTRARARMHVVTALRAADLDADRLDGGALAFRRMLEVALDDAEAAPAGRLSDP
+LLLDLRDRLAAEDALVAAHYGGAMDLAAADAAGERGRVRPLALVSDGGDAYREQSVRERS
+RRLPERLEARGWDTDTLWAIDVFADPESVAARLVGRLGLPLEEVDEDGEDDADGES
+>GCF_023573625.1_01578
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVSSLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPVLDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHIQDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAATEDDVAPAEERLVLDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSAWRRLHLVEMSSVTRSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGEHVMGQVGQVRERLRRLEGVLAPEAVAEGPLD
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRGHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLAEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAYDTLD
+EVLPTLPLRTVHRPLERRLVRLVSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAAEAEPFVIVPVVRAASVTRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGDDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYAGVMDLAVLDPRAEQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWSIDVFADPESVARELADRLGVEPADETDETDDDVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001330.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001330.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2c87729e0c92a0ed9e9c3f906f27a28fdb18a01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001330.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01649
+MTQNAPHPDTPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+KPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAQTGTREYG
+STRLDSVDADSVLFAGQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIY
+GVQWHPEVGHSSHGQRVLEQFLHVGAGLGADWTVSNVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE
+>GCF_003691675.1_01354
+MTQNAPHPDTPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+KPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAQTGTREYG
+STRLDSVDADSVLFADQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIF
+GVQWHPEVGHSSHGQRVLEQFLHVGAGLGADWTASGVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVISEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE
+>GCF_005280335.1_01244
+MTENAPHSDAPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+RPAALILSGGPSSVYEPGAPTLDPALLEAGVPVLGLCYGFQSIAHALGGTVAKTGTREYG
+STRLDSVDADSVLFAGQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDAERRIY
+GVQWHPEVGHSSHGQQVLEHFLHQGAGLGSDWTASNVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMRQGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPEATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRSADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPIVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE
+>GCF_020097155.1_01155
+MTQNEPTRDQPAPLHDVLPTVLVMDFGAQYAQLIARRVREANVYSEVVPSSTPAQEILDR
+RPAALILSGGPSSVYEAGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVARTGTREYG
+STRLESADGGSVLLAGQDAAQVVWMSHGDAVTEAPEGFAVTAVTAGAPVAAFEDRERRIF
+GVQWHPEVGHSERGQEILANFLTEGAGLSQDWTAENVIEEQVARIREQIGDARAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMRQGESDEIERAFGEAHGGAKLVMVDAREDFL
+AALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESAHDPNAPEVRFLVQGTLYPDVVESG
+GGDGTANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRQADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVTSEDAMTADWARIPSEVLSRISNRITNEVDGINRVVLDVTSKPPGTIEWE
+>GCF_023573625.1_01579
+MTQNAPHPDTPTPLSDVMPTVLVLDYGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+EPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAKTGTREYG
+STRLDSVDADSVLFADQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIY
+GVQWHPEVGHSSRGQRVLEQFLHVGAGLGADWTASGVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGINRVVLDVTSKPPGTIEWE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001331.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba4b00beb393467c169bbd9eb53516526b651a6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001331.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_01650
+MSTQHPGPEPVDPASLPDPEDITEADLPEPPPRPGREQRRFAGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFVVEKRMTRVVRDELHRFPDAAR
+RY
+>GCF_003691675.1_01355
+MSTQHPGPQPVDPASLPDPEDITEADLPEPPPRPGREQRRFSGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFMVEKRMTRVVRDELHRFPDAAR
+RY
+>GCF_005280335.1_01243
+MSHTEPVDPAALPDPEDITEADLPEAPPRPGRERRRFAGTQQQIRSATRFYVVCSWITGV
+MLLLLVAEMVFKYAWGQELFAGGTTVDGEQNILGLHPEDSVTGGVNLSLFILIAHGWMYV
+VYLLACFRLWSLMRWQPMRLLAMAGGGVVPFLSFVVEKKVTKVVRDDVHRFPDAARRY
+>GCF_020097155.1_01154
+MSQPHHDAGREAARAGEAPVDPATLPDPEDITEADLPAPPPRPGRAVRRFAGTRQQIVSA
+DRIYKVCAYITGVMLLLLVAEMVFKYGLHQELFAGGTTVDGEPHGFGLAPEKSVTGGVNL
+SLAILIAHGWMYVVYLLACFRLWSLMRWAPGRLLAMAGGGVVPFLSFVVERKVSGQVREE
+LAQFPDAARRY
+>GCF_023573625.1_01580
+MSTQHPGPQPVDPASLPDPEDITEADLPEPPPRPGREQRRFAGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFVVEKRMTRVVRDELHRFPDAAR
+RY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001332.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001332.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac5040ccbe21c980409268c56f280382c97f4303
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001332.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01651
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTEHAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLNGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREATAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AYVAAFEMVDAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAVAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEQSR
+>GCF_003691675.1_01356
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTENAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLDGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREAAAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AFVAAFEMADAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAFAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEHRR
+>GCF_005280335.1_01242
+MLRTALKPVWLATLVLALVAAGLFVALSKWQFETAETNAPPPRTQTEQPVPLTDHVRPYE
+PLLARDADQVVTVPGEFLPDTDVLVGPRLLRGDEGFWTVSAFRVAGAPDGEVIPVVRGWS
+AGADVVDPAPQGDVTVTGRLLPPDGPLPRTAAEADTADRLLYASLAPGQLVNVWDEPSYA
+AFVAAFEVADAAGAEVGAGASEGGLEPVWVAPQPEETEVIWLNVFYAVEWILFAGFALFL
+WWRFVRDDHLRDERERELDEEWAAQWRAEELARRREEARLAKERAYAAQAAARPSTDPEE
+NRP
+>GCF_020097155.1_01153
+MLRTALKPKWLATLVLALVAATAFVLLSRWQFASSETAAPPPRTQTENAVPLTEHVRPGE
+PLLASQADQVVSARGEFVPGTDALVGPRLSDGREGWWTVTAFRVAGAPDGETVPVVRGWS
+EAADVVDPAPTGEVTVTGRLLPPDGPVSPADAGEDTAGRPAFSTLSPGQLVNAWDVPAYA
+AYVAAFGVTDAAGADVSAGARDGGLQPVWVPPQPEESQVVWLNVFYGVEWLLFAGFALFL
+WWRFVRDDHLRDEQEAELDAQWAARWRAEELERRRERARREKEAAARAYAAWQAGETAPD
+AAHQEPQDGPAGPRKEGQA
+>GCF_023573625.1_01581
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTENAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLNGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREAAAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AFVAAFEMVDAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAFAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEQSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001334.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001334.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f0612e1ab15128374ad25584c24e488449e1834
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001334.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01653
+MARTRVAGLTPGHRIAETPVPKGVFVTTTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN
+ATDVIPADADPGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPREEWATRTVDTAMTRMPLVTAQEGVSRAETIRLFSQNRVEKLPLVDDAGRLTGLIT
+IKDFDKAEQYPDAAKDDEGRLRVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV
+FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPVA
+SVVHQLVGGLRQTMFYTGASTVTDLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR
+>GCF_003691675.1_01358
+MARTRVAGLTPGHRIAETPVPKGAFVTNTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN
+ATDVIPADADTGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPREEWATRTVDTAMTRMPLVTAQEGISRAETIRLFSQNRVEKLPLVDDAGRLTGLIT
+IKDFDKAEQYPDAAKDDEGRLLVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV
+FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPIA
+SVVHQLVGGLRQTMFYTGASTVADLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR
+>GCF_005280335.1_01240
+MARTRVAGLTPGHRIAETPVPKGAFVTTTSTGPSSEPVHSSADPFGFFGLTYDDVLLLPS
+ATDVIPAEADTSTQLTRNIRLNIPVVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPKATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPHEEWETRTVDTAMTRMPLITAREGISREETIRLFSQNRVEKLPLVDEAGRLTGLIT
+IKDFDKAEKYPDAAKDDEGRLRVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGAESVMLGSLLAGTAESPGDLV
+FYQGKQFKAYRGMGSLGAMQTRNGKRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPIA
+SVVHQLVGGLRQTMFYTGASTVDELKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR
+>GCF_020097155.1_01151
+MSTSTGPSSDPVYASEDPFGFFGLTYDDVLLLPNATDVIPADADTSTQLTRNIRLNIPVV
+SAAMDTVTEAPLAIAIARQGGMGIIHRNLSIEDQAKHVDTVKRSESGMISDPVTIGPKAT
+LAELDELCAQYRVSGLPVVAEDMTLLGIITNRDTRFIPHEEWDTRTVDTAMTRMPLITAQ
+DGISREEVLHLFSQNRVEKLPLVDDAGRLTGLITIKDFDKAEKYPDAAKDDEGRLRVGGA
+VGFFGDGWERAMTLVEAGVDALVVDTANGHTHGVLDMIARLKKEKAAAHVDVIGGQAATY
+AGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGVPQITAIYEAAKATRPAGVPLIADGGL
+QHSGDIGKALVAGADSVMLGSLLAGTAESPGDLVFYQGKQFKAYRGMGSLGAMQTRNGTR
+SFSKDRYFQADVPDEDKLIPEGIEGQVPYRGPIASVVHQLVGGLRQTMFYTGAPTIVDLK
+ENGRFVRITTAGLKESHPHDIMMTVEAPNYRSK
+>GCF_023573625.1_01583
+MARTRVAGLTPGHRIAETPVPKGAFVTNTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN
+ATDVIPADADTGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPREEWATRTVDTAMTRMPLVTAQEGISRAETIRLFSQNRVEKLPLVDDAGRLTGLIT
+IKDFDKAEQYPDAAKDDEGRLLVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV
+FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPVA
+SVVHQLVGGLRQTMFYTGASTVADLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001339.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001339.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4060516611ea2c154640feae178be6ccf9bfdb9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001339.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01661
+MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRMNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
+>GCF_003691675.1_01366
+MILDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLAGIVVTAVLVVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
+>GCF_005280335.1_01233
+MTDLHPGVADARTRLPEPGPGERVCWVPPTVLRPQRSRWQRTWPLLAGVAVTVLLAVVSL
+FVGVYDVGAEGGREMFAITRVPRTVALVLAGAAMAMCGLIMQLMTQNRFVEPSTTGTTEW
+AGLGLLVTMILIPGASIVTRMTGAVLFAFVGTMVFFLFLRRVRLQSSLIVPIVGIMLGAV
+VGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLVVCVAVFVIADRFTVAGLG
+KDVATNVGLNYNAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNIVSMVRGDNLRTNLP
+WVVMVGIWVVIVCDLIGRTVIAPFEVPISLILGLVGAVVFLGLLIRQAKHG
+>GCF_020097155.1_01144
+MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVLVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGSGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
+>GCF_023573625.1_01591
+MILDVRHHVADAPPRLEELGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFLIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001340.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001340.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b31af778529eec0f5442541113b3445ff611725
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001340.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01662
+MPRSVSAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASAAGGSSAASGG
+IAAGVTVTDMSGAEVTLPEEVDSVIATDNRAFRTLDDWGVELSAAPKQIMYKGEGGPSYL
+QDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTDFDVTQTP
+MDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLIASGGELSYVA
+PSTGRAIGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAIGEENA
+TAAELIERSEALQDVTAVKEGNIVYLPADFYVAEDIQNHTTVMEDLAKAFEGAQ
+>GCF_003691675.1_01367
+MPSSARAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASASGESSASASA
+AGGSSAASGGIATGVTVTDMSGAEVTLPEEVDSVIATDNRTFRTLDDWGVELSAAPKQIM
+YKGEGGPSYLQDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVV
+DTDFDVTQTPMDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLI
+ASGGELSYVAPSTGRAIGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMD
+RDAAVGEENATAAELIERSEALQDVTAVKEGNIVYLPTDFYVAEDIQNHTTVMEDLAKAF
+EGAQ
+>GCF_005280335.1_01232
+MQRSPRTPRLKALALASVAALALVGCSAGGAAEGPASGSADTGSAAGSGSASAPAGDGVA
+AGATVTDMSGAEITLPEEIDSVITTDNRTFRTLDEWGVELSAAPKQLMFKGEGGPGYLQD
+DEVADIGNHREPDMEVFVTAEPDVVFNGQRFNERKAEIDELTGDAAVIDTDFDPKQKPMD
+EGLKELTTLLGEATGHQDDAAALNKEFDDAVAKAKGAYDSEQTVMGLISTGGELSYVAPG
+TGRSIGPMFDILGLTPALEQAGSDNHQGDDISVEAIAQSNPDWLIVMDRDAATGEANATA
+AELIERSEALKDVTAVKEGNIVYLPQDFYVAEDIQNYTTVMDDLAKAFEGAR
+>GCF_020097155.1_01143
+MRTARLSTAAALASLAALTLAGCGAGGPAAEGSSPASSAASSSPASSAASSSATAGGVAA
+GVTVTDMSGTEVTLPEEVDSVIATDNRIFRTLDDWGVELSAAPKQIMYKGEGGPSYLQDD
+SVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTNFDVTQTPMDE
+GLKKLTTLLGEATGHEADAEKLIADFDAATQLAKDAYDPEQTVMGLIASGGELSYAAPST
+GRSIGPFFDMLDLTPALDQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAVGEENATAA
+ELIERSEALQDVTAVKEGNIVYLPADFYVSEDIQNHTTVMEDLAKAFEGAQ
+>GCF_023573625.1_01592
+MPRSARAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASASGGSSAASGG
+IATGVTVTDMSGAEVTLPEEVDSVIATDNRIFRTLDDWGVELSAAPKQIMYKGEGGPSYL
+QDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTNFDVTQTP
+MDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLIASGGELSYVA
+PSTGRAVGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAIGEENA
+TAAELIERSEALQDVTAVKEGNIVYLPADFYVAEDIQNHTTVMEDLAKAFEGAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001341.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001341.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e731b315baa96580e7e2979aea40664ff5a97145
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001341.fa
@@ -0,0 +1,43 @@
+>GCF_002008305.4_01663
+MARPRPAARPSRPSAAASEEDDTALAPVLESEGRALLDSLAGYREADALAVSSRLRAAGH
+PPERVAAALTQAALRSRAEARLGPEARRMLFTRDGLEQATRPLVAGLHADRLAAAGARRV
+ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP
+AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP
+AGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVHGGKTTTAQLVSGADFGDSPEV
+EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAVSWPVPTRQLDPHLAYLVAPEPVHDGL
+ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG
+RHATLVLARVGRSRFALEVTPLD
+>GCF_003691675.1_01368
+MARPRPASRSPRPTAAASEADDTALAPVLEPEGRALLDSLAGYREADALAVSSRLRAAGH
+PPERVAAALTQAALRSRAEARLGPEARRMLFTRDGLEQATRPLVAGLHADRLAAAGARRV
+ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP
+AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP
+EGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVRGGETTTAQLVSGADFGDSPEV
+EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAASWPVPTRQLDPHLAYLVAPEPVRDGL
+ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG
+RHATLVLARVGRSRFALEVTPLD
+>GCF_005280335.1_01231
+MLTQADLRARAVPRLGPDARGMLFTRDGLEQATRPVVAALHAQRMAAAGARTVADLGCGL
+GLDARAFADAGLGVVAVERDAVVAAAAEVNLTDRPGARVVHGDAVPWAREHVPAQADAVW
+LDPARRQVGGGGSARVFDPEAFSPPLSVVEELAATGVPVGVKLGPGLPHEAVPAGAEAEW
+VSVDGDVVEAALWFNAAARPGVRRAARVIDTRGGQATTAELVSGADFGDSPGVEAVGEEG
+MPGLVGRCSTSRTAPSSGPGSSRTWRSPGRRRPASWTRTWPIWWPPSTRPTRWPGRTGST
+RSTISTSSLCAGGRRRRGSAAWT
+>GCF_020097155.1_01142
+MARSQRPARPSRPRPRPADRPGRPRAAESAADATRLEPVLDPAGRVLLDGLGDVSGQDPL
+ALSSRLRAAGHDADTVAAALTQAGLRHAGRAKLGALADGMLLTRDGLEQATRAVVAEHRA
+RRLQEAGVRSLADLGCGIGADALVYARAGLDVTAVERDPTVAAAAAANLATLAPAGAASV
+VTGDAEAWAAAHADEVDALWLDPARRRLGSSGTARVFDPEAFSPPLSFVLGLADGGRPVG
+VKLGPGLPHEHVPAAAEAEWVSVDGDVVEVTLWFGPLAQAPGRRTATLLDTRGSAVHRLV
+PAAASSPAVEAVGEEGVDGLVGQVLLEPDGAVIRAGLVTDLAVELGPAVRLLDPHLAYLV
+APDAAPHPLARGYRVLAVHEFRTKALARWARETGVGRLDVKKRGVRETPEQVRAAVLGRG
+TPGGRHATLVLARVGERRVAFEVEPLPAG
+>GCF_023573625.1_01593
+MARPRPASRSPRPTAAASEADATALTPVLEPEGRALLDSLAWYREADALAVSSRLRAAGH
+PPERVAAALTQAALRSRAEARLGRQARRMLFTRDGLEQATRPLVAGLHADRLAAAGARCV
+ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP
+AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP
+AGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVRGGETTTAQLVSGADFGDSPEV
+EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAASWPVPTRQLDPHLAYLVAPEPVHDGL
+ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG
+RHATLVLARVGRSRFALEVTPLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001342.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001342.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1278feaa2a618eb9ffde2e703b68564f6a501f9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001342.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01664
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFADAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDADDAVAPLRAVVLDAAARTRASLDGRAG
+>GCF_003691675.1_01369
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRTLHATEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAARGISLFCQGTHPFADAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDTDDAVAPLRAVVLDAAARTRASLDGRTG
+>GCF_005280335.1_01230
+MNLPFADSTQSTLGIEWEVALVDAATGDLRSEAPAILHELHKEAGLAEGEDHPHVTGELL
+QNTVELVTGVHEAVPTAVAELGTIAARVARAAADRGLALYCQGTHPFGEAMTQPITPKER
+YGRMVDLTQYWGRQMLIFGVHVHVGLDDPAKAMPAVNRLISRFPHLLALSASSPFWVGAD
+TGYQSQRTQLFQQLPTAGLPFQFETWAEFEACVQQMTDVGMVEDVTECRWDVRAVPRLGT
+VEMRACDGMATLEEIAAVAAYTQCLVHELSADVERGRHMEILPPWYTQENKWRASRYGMD
+ATVIVDAAGTQVPLAEHLGADLERLAPIAEELGCAAELAHARVLMEHSPADRQRAVEAEA
+LAGPPAEGESAHDAAAPLRAVVLDAAARTRESLERVGG
+>GCF_020097155.1_01141
+MSLPFADSAQSTLGIEWELALVDPLTGDLRSEAPGILEELRAEAGLDADADHPHVTGELL
+QNTVELVTGVHGSVPDAVADLGGIAARVQRAAADRGLALFCQGTHPFGEAMTQPITPKAR
+YGRMVDLTQYWGRQMLIFGVHVHIGLDDRAKAMPAVNRLISRLPHLLALSASSPFWVGAD
+TGYQSQRTQLFQQLPTAGLPFQFETWEGFEHCVEQMTGVGMVEDVTECRWDVRAVPRLGT
+VEMRVCDGMATLEEIGAVAAYAQCLVHELSAQVEDDEPVAILPPWYTQENKWRAARYGLE
+ATVITDDAGTQVPLAEHLAADLERLAPVAEELGCAAELAHARVLMEHSPADRQRRVAAEA
+AAGPPRTGEDPADPVAPLRAVVRDAADRTRESLRAFQG
+>GCF_023573625.1_01594
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFAEAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEDFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDADDAVAPLRAVVLDAAARTRTSLDGRTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001343.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001343.fa
new file mode 100644
index 0000000000000000000000000000000000000000..392679bd5d32aad631e3b07aa02baa5d2148ad3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001343.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01665
+MRALTWQGKRNVVVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH
+EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGCGAALFG
+YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG
+TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT
+GGRGPDAVLDAVGMEAHASPVGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR
+RGGTVSISGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL
+TTHTAPLEDAPALYETFQKKEDGCVKVVLKP
+>GCF_003691675.1_01370
+MRALTWQGKRNVAVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH
+EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGSGAALFG
+YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG
+TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT
+GGRGPDGVVDAVGMEAHASPAGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR
+RGGTVSLSGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL
+ATHTAPLEDAPALYETFQKKEDGCIKVVLKP
+>GCF_005280335.1_01229
+MRALTWQGKRNVAVEDVPDPRIQEPTDAIVEITSTGICGSDLHLYEVLGPFMDAGDVIGH
+EPMGIVREVGAEVTHIKPGDRVVVPFNIACGRCWMCERGLQSQCETTQVREQGSGAALLG
+YSRLYGSVPGGQAEYLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYAQVPRGG
+TLAVIGLGPIGQLAARIGVHQGLRVIGVDPVPERRAMAARHGVEVLDSSDGGVAELLREC
+TQGRGPDGVVDAVGMEAHGSPVAKAAHTVVGLLPDALGRAAMKTAGVDRLDALHTAIDAV
+RRGGTVSLSGVYGGMQSPMPLLTMFDKQVTLAMGQCNVRRWVDDLLPLLDDPSDPLGVLD
+LTTHTAPLEDAPALYETFQKKEDGCIKVVLKP
+>GCF_020097155.1_01140
+MRALTWQGKRSVSVEDVPDPRIQEPTDAIIKVTSTGICGSDLHLYEVLGPFMDKGDVIGH
+EPMGIVEEVGSAVTNLSPGDRVVIPFNISCGHCWMCQHGLQSQCETTQVKEQGSGAALLG
+YSRLYGSVPGGQAEYLRVPHADYGPIKVPHTGPDTQWLFLSDVVPTAWQAVQYANVSKGD
+TLAVLGLGPIGQMSARIGVHLGCRVIAVDPVPERRHMAARHGVEVLDMEGSGTGVPDLLR
+QATGGRGPDGVVDAVGMEAHGAPVAAAAQTAAGMLPGPLARAAVKTSGIDRLTALHTAIE
+SVRRGGTVSLSGVYGGMQDPMPLLTMFDKQIQFTMGQCNVRRWVDDLLPLMDDPSDPLGV
+LDLVTHTAPLEDAPAMYEKFQKKQDGCIKVVLTP
+>GCF_023573625.1_01595
+MRALTWQGKRNVTVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH
+EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGSGAALFG
+YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG
+TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT
+SGRGPDGVVDAVGMEAHASPAGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR
+RGGTVSLSGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL
+TTHTAPLEDAPALYETFQKKEDGCIKVVLKP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001345.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001345.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1019826abacd3ee24871f7e00f8213cca33ab869
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001345.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01667
+MRTRTLTRRAALTGLLGSAALGFTACTSSGYPADPDGTLDRVTGGVLRVGVVHHPPHVDV
+SGAEPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHA
+SITRDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
+>GCF_003691675.1_01372
+MTITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHASIT
+RDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
+>GCF_005280335.1_01227
+MTITRRAALTGLLGGAVLGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDAEIAWTVSGEEALLTALEKGDVDLVAGGLTSDSPWTTHASLT
+RDYAEAAGPDGEPVKLVMAVPPGENQMLAALEAHLDAQAREAGR
+>GCF_020097155.1_01138
+MQTPRRTLLTGALAAAGVVLTGCTSSGYPADPDGTLDRITGGTLRVGASHHPPHVDAAGA
+EPQGPEPDLVRAFAAERDARVEWTVSGEEALMTALKQGDLDLVVGGLTKKSPWTTDAGLT
+RPYAETTGPDGEKAELVMAVPLGENQFQSALERFLDAHGEEAGA
+>GCF_023573625.1_01597
+MTITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHASIT
+RDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001346.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001346.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b040bd957683675505109cffe764fc8aff38eb8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001346.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01668
+MTRRDTRETGPSGRRFGATELPPEIERVVQQAKRLEWATLGVIVVTIVLVAFVMGSSQAM
+RAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG
+DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVL
+YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAILVGVSIVLDGWKNLKEAVTNLAD
+RRAATIDGARPHPLIDRAERVAWAEPWVRHAGARVRDEGHVFHVEMFVVPHEGADVTVAR
+CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE
+>GCF_003691675.1_01373
+MTRQDTRETGPSGRRFGATELPPEIERVVQQAKRLEWVTLGVIVVTIVLVAIVMGSSQAM
+RAAWIEDLLSLIPPIAFLIALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG
+DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLTLAEQLHDRVL
+YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWKNLKEAVTNLAD
+RRATTIDGARPHPLIDRAERVAWAEPWVRHAGARVRDEGHVFHVEMFVVPHEGADVTVAR
+CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE
+>GCF_005280335.1_01226
+MTHHASTTHRSPGGRRFGATELPPEIERALRRAVRLEWATLAVLAVTIALVAVVMGSSQA
+MRAAWIEDLLSLVPPIAFLVAVRVTRRHPTRARPYGSHRSVGVGHLVAAVALSVMGVILV
+ADSALGLVTGEHPPIGTLDLFGHTVWQGWFMMAVMALSIPGPVLLGRAKLKLAEQLHDRV
+LYADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWRNLREAVGNLA
+DRRATTIDGDRPHPLIDRAERVAWAQPWVRHAGTRVRDEGHVLHVEMFVVPHEGAGATVG
+RCAQLREEIVALDWKLEDVVVVPVAELPAEVHGGASGDEQSGEE
+>GCF_020097155.1_01137
+MSEKRTIGRAELPDDVARAAHQAVVLEWVSLGWLVLTVSLVAVVMGSSQAMRAAWIEDLL
+SLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVGDSLLGLLTA
+EHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVLYADADMNKA
+DWQTGVATIVGVAGIGLGWWWADAAAAIFVGVSIVLDGWKNLKEAVTNLADRRATTIDGA
+RPHPIIDRAERVAWAQPWVRHAGARVRDEGHVFHLEMFVVPRHGADVTVGRCADLRERIE
+ELDWKLEDVVVVPVAELPEEVHGGRSGDEQSKGSE
+>GCF_023573625.1_01598
+MTRRDTRETGPSGRRFGATELPPEIERVVQQAKRLEWATLGVIVVTIVLVAIVMGSSQAM
+RAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG
+DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVL
+YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWKNLKEAVTNLAD
+RRAATIDGARPHPLIDRVERVAWAEPWVRQAGARVRDEGHVFHVEMFVVPHEGADVTVGR
+CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001347.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001347.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7658c0659160f77873f411a9988c13e1420e229
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001347.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01670
+MTGPLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISAEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPHR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
+>GCF_003691675.1_01375
+MPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIPEIAARAHLEA
+LVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGTPLYGINHLVA
+HVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGSTIDDAAGEAYD
+KVARLIGAGYPGGPVIDRLAAEGDPTAFRFPRGLTAGKFVGSAEEPGPHRHDWSFSGLKT
+AVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLMLGGGVAANSR
+LRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWFGADPGQPVEV
+VSV
+>GCF_005280335.1_01208
+MTGPLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTVRRALEAADVGLKDLDAIAVTSGPGLAGALMVGVAGAKALATALDT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPHR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
+>GCF_020097155.1_01136
+MAPMSATATAPLVLGIESSCDETGVGIARGTALLAHEVASSVEEHVRFGGVIPEIAARAH
+LEALVPTVRRALDAAGVTLDEVDAIAVTSGPGLAGALMVGVAGAKALAVAADKPLYGINH
+LVAHVGVGLLDGVRPADWDDLPRDLGALLVSGGHTEILQVDRISSDVTLLGSTIDDAAGE
+AYDKVARLIGAGYPGGPVIDRMAQEGDPKAFRFPRGLTAGKFVGTAEEPGPHRHDWSFSG
+LKTAVSRAVEQFEAQGLEVPRTDIAASFQEAVADVITAKAVRACREHGLTHLLLGGGVAA
+NSRLRGLLADRCRSAGIELVVPPVNLCTDNGAMVAALGARLVADGVAPSDLAFGADPGQP
+VSAVSAA
+>GCF_023573625.1_01600
+MTGLLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPQR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001349.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001349.fa
new file mode 100644
index 0000000000000000000000000000000000000000..571afd2c2462489ace45983619c38c461a8b5bc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001349.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01672
+MALLLAIDSSAAASVAVLRDGEELARWATDDTHAHAEVLAPAVQTVLGEAGVTGTALDAL
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHEAGVDAFRHGIEEFVVATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWESATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA
+>GCF_003691675.1_01377
+MALLLAIDSSAAASVAVLRDGEELAHWATDDTHAHAEVLAPAVQTVLGEAGVTGTALDAL
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHAAGVDAFRHGIEEFVVATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWETATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA
+>GCF_005280335.1_01206
+MALLLALDSSAAASVAVLRDGEALARWATEDTHAHAEVLAPAVRAVLAEAGVAGAGLDAV
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVRGVRSLDALAHDAAVDAFRHGAEEFVVATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPAYGAGAGLYPEALRAVPGWETATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA
+>GCF_020097155.1_01134
+MPLLLALDSSSAASVALLRDGEPLAAWSTADTTSHAEVLAPAVRQVLAEAGVAGGDLDGI
+AAGVGPGPFTGLRAGLATAEALGFAWDVPVHGIRSLDALAHRAGTDAFAHAVEEFVVVTD
+ARRREVYWAHYAQVGGQPTLLHGPFVTPAAEVTPLPAYGAGAGLYPEALHAVDGWEGAVP
+DAVSLGRVDELALRRGRGVLPPTPLYLRESDATVPAPRTPARPAGA
+>GCF_023573625.1_01602
+MALLIAIDSSAAASVAVLQDGEELARWATDDTHAHAEVLAPAVQAVLGEAGVTGTALDAL
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHEAGVDAFRHGIEEFVIATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWETATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001350.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001350.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed58ddb44f699a35611854be012d418f04601aa4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001350.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01673
+MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAASAGEGEDGIVTDFS
+DEDGGQAEELRSAVVTGRGPRWAGVVLP
+>GCF_003691675.1_01378
+MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAAPAGEGEDGIVTDFS
+DEDGGQAEELRSAVVTGRGPRWVGVVLP
+>GCF_005280335.1_01205
+MSRHEPPAPDPALPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAT
+VDRSVTVVEWGRGLAESLAGFPEDPDASWLDVEIVRARGGEDPAPAGPGADDGGIVTDFS
+DEDGEQAEELRSAVVTGYGPRWAGVRLP
+>GCF_020097155.1_01133
+MIAGRRAEQPLPAPVWERRVPLDGAAGTREFGAALAGVLRAGDVLILTGELGAGKTTLTQ
+GLGAGLGVREGVISPTFVLSRIHPSLADGPDLVHVDAYRLRSAGELTDLDLEATADRSVT
+VVEWGRGMAESLAGFPEDPEASWLDVEVLRARGGADLPDGPAGGDAAPDAPVIVTDFSDE
+EGEAAEEVRTAVVRAHGPRWAAVALP
+>GCF_023573625.1_01603
+MSDHEFPAPGPTLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDGPAASAGEEDGIVTDFSD
+EDGGQAEELRTAVVTGRGPRWAGVVLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001351.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001351.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b3ada45f208e8625f52ca3b62a5f4ad6b926de5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001351.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01674
+MSRADVAPADTERAVRIDLAAVRHNVGVLQERIRRPDGSRPLLTAVVKADAYGHGAVAVA
+RAAAAAGADRLGVAHVREALALRAAGVRLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD
+AVADAVRGLRARGGAGPEARADLHLKADTGLGRHGCTPERWPALVARAAELEAAGLVRVE
+GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM
+VRVGLGLYGLSPFADVTAAEFGLRPAMSFVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG
+LVPLGYADGVPRVVEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS
+GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP
+>GCF_003691675.1_01379
+MSRADVNPADTERAARIDLAAVRHNVGVLRERIRRPDGGRPLLTAVVKADAYGHGAVAVA
+RAAAAAGADRLGVAHVREALALRAAGVPLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD
+AVADAVRGLRARGGAGPEARAVLHLKADTGLGRHGCTPERWPALVARAAELEAAGLVRVE
+GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM
+VRVGLGLYGLSPFADVTAAEFGLRPAMSFVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG
+LVPLGYADGVPRVVEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS
+GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP
+>GCF_005280335.1_01204
+MTQQDRSAGPAERTARIDLAAVRHNVAAVRARTVRQDGTRPLLTAVVKADGYGHGAVAVA
+RAAQAAGADRLGVAHVREALELRGAGLRLPILAWLHTVGTDFAAALEADVTLGVSGWDLD
+AVAAAVRALRPAPGTADSGPVRARVHLKADTGLGRHGCTPERWPAFVARAAELEAAGLVR
+VEGVFSHLGVADDPERAEETTAQLRRFEEAAAAAAAALGRPLLRHLANTPATLSRPDTHL
+DMVRVGLGLYGLSPFEGVDAAGLGLRPAMSLGTTLANVKPVPAGQGVSYGFRHVAPAPTT
+LGLVPLGYADGVPRIAEGARVHVGGRTVPVVGRIAMDQFVVDLGPDARDRPGDAVELFGP
+ASGIPADEWAAAAGTINYELVTRIGARVDRAHEGGEAPDAQEARA
+>GCF_020097155.1_01132
+MDDAPDLTPSAAEAAPAERRALVDLAAVRSNVAALRARLGRPDGASTALMAVVKADAYGH
+GAVPVARAALEAGADRLGVAHVTEALALRAAGVTAPILAWLHTRDTPFRAAVETDVALGV
+SGMWDLEAVAQAARAAGRRATVHVKADTGLGRNGCLLADLPALAARAAALQDEGVVDVEG
+LFSHLAVADELDRAAETDAQAAAFGEATVALDAAGLRPRVRHLANTPAALTRPDLHHDMV
+RVGLGLYGLSPFPDRAPAEFGLRPAMSLQTTLAAVKAVPAGQGVSYGFRHRTAEPTVLGL
+VPLGYADGVPRIAEGAPVAVAGRRVPHVGRVAMDQLVVDLGPGAAERVGDPVELFGPASG
+IPADAWAEAAGTINYELVTRISPRVPRVHVDGAAAGEVAA
+>GCF_023573625.1_01604
+MSLADVNPADTERAVRIDLAAVRHNVGVLRERIRRPDGSRPLLTAVVKADAYGHGAVAVA
+RAAAAAGADRLGVAHVREALALRAAGVRLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD
+AVAAAVRGLRARGGAGPEARAVLHLKADTGLGRHGCTPERWPAFVARAAELEAAGLVRVE
+GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM
+VRVGLGLYGLSPFADVTAAELGLRPAMSLVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG
+LVPLGYADGVPRVAEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS
+GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001352.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001352.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e24ea62ae593474219f159b6fcb3f7676613cff9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001352.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01675
+MTADDLTRIAVTGSAVRTAEEPLLAAGRGPELMRAAAWALAEHAAALLRERGPVAGTTVA
+ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRRDDDGAPRWHAEGWAALRAAGGRRADAV
+PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRAAA
+TVTFGALKSGLVLGEGAGRAGTVHVADIGLGPHLPTSPAARLGVMDEAAARAAHPAPAAA
+AHKYTRGVVAVVAGSERYPGAAVLASAGALHTGAGMVHHAGPQTTRDLVLAAHPEALVSA
+EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALLADASALDLVTAAELRSL
+RAAGTPVVLTPHAGEWSRLRERVPADGADAADPLAALRAWTAEHGATVLLKGPRTLVVAP
+DGEAWAVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA
+AWLHAQAGAEQARAGRITTATLPAALGARVARLWWPDDAEPEAVR
+>GCF_003691675.1_01380
+MTADDLTRIAVTGSAVRTAEEPLLTAGRGPELMRAAAWALAEHAAALLRERGPVAGATVA
+ALVGPGNNGGDALFALAFLRGRGVAAVAVPVRRDDDGAPRWHAEGWAALRAAGGRRADAV
+PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRADT
+TVTFGALKSGLVLGEGAARAGTVHVVDIGLGPHLPTSPAARLGVMDEAAARTAHPAPAAE
+AHKYTRGVVAVVAGSERYPGAAVLASAGALHTGAGMVHHAGPQTTRDLVLAAHPEALVSA
+EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALVADASALDLVTAAELRSL
+RAAGTPVVLTPHAGEWSRLRERVPADGADAADPLAALRAWTSEHGATVLFKGPRTLVVAP
+DGEAWVVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA
+AWLHARAGADQARAGRITTATLPTALGARVAHLWWPDDAEPEAVR
+>GCF_005280335.1_01203
+MSVEELRRVAVAGSAVRAAEAPLLAAGRGPAMMRDAAWALAEHAAALLRARGPVAGTTVA
+ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRHDDDGAPRWHAEGWAALRAAGGRRADAV
+PAAAALVIDGMLGTGFAGELTLPPAARALPRDAVVLACDVPSGVDADTGEVRGEALRADA
+TVTFGALKTGLLVGEGAALAGEVHPVDIGLGPQLPTSPAARLYLADEAAVRAAHPAPAPD
+AHKYTRGLVAVAAGSPRYPGAAVLSCSGALHAGAGMVHHAGPEATRDRVLAEHPEALVSA
+EGPAPDRADAWVAGPGLDTQDDARRRWEGVLSALAERPEAALVADASALELVTAAQLRAL
+REGGTPVVLTPHAGEWARLRERLPADGADAADPLAALRSWSAAHGATVLLKGPRTLTVQP
+DGEAWLVADGGPELAMGGTGDVLAGALGAVLAADVARRSRARRAEQAPGPVPTAALAAAA
+AWLHARAGAEQARAGRLTTRTLPAALGAVTARLWRAGDENGRTRG
+>GCF_020097155.1_01131
+MRAHTGTDVRAAERPLLDEGRGEALMRTAAWGLAEHVAAELRARGPVAGATVAALVGPGN
+NGGDALWALAFLRRRGVEAVAVPVRRNEAGEPVWHAAGWAALQAAGGRRSTAVPARAAVV
+VDAMLGTGARGGFTLPEPARHLPSGAAVVACDLPSGVDADTGAVPGEALAADLTVTFGAS
+KTGLLLGAGPGRAGRVVCVDIGLGPHLPADPAAGLHVVDDDAVARLHPVPARDAHKYTRG
+VVGVVAGSERYPGAAVLAVGGVLAGGAGMAHHGGPARAGDLVLAAHPAALTSADGPAPER
+ADAWVLGPGLGDGDGARERVRATVAAVLASGADGDRGPAALVVDASALDLVTGEDLAALA
+AVDARTVITPHAGEWARLRDRLPVPAADAVDVDEDGAGELARLRAWTAARGVTVLLKGPA
+SLAVAPDGQAWLMRDGGPQLGVAGTGDVLAGALGAVLAAETARARRGGDERHGAARGGRP
+SPAALAAAAAWLHARAGVRQAADGRATADTLPAALGDVVARRWWENDAHGRRP
+>GCF_023573625.1_01605
+MTADDLTRIAVTGSAVRTAEEPLLAAGRGPELMRAAAWALAEHAAALLRERGPVAGATVA
+ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRRDDDGAPRWHAEGWAALQAAGGRRADAV
+PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRADA
+TVTFGALKSGLVLGEGAARAGTVHVVDIGLGPHLPTSPAARLGVMDEAAARTAHPAPAAE
+AHKYTRGVVAVVAGSERYPGAAVLASAGALQTGAGMVHHAGPQTTRDLVLAAHPEALVSA
+EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALVADASALDLVTAAELRSL
+RAAGTPVVLTPHAGEWSRLRERVPADGADATDPLAALRAWTAAHGATVLLKGPRTLVVAP
+DGEAWVVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA
+AWLHAQAGADQARAGRITTATLPTALGARVARLWWPDDAEPESVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001353.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001353.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c383a742fe3439bc1d27204ac888cb9afda992ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001353.fa
@@ -0,0 +1,19 @@
+>GCF_002008305.4_01676
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA
+>GCF_003691675.1_01381
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA
+>GCF_005280335.1_01202
+MIVGVGMDVVDVPRFRAQLERTPALRERLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEAQGITHWHLSLSHDGDVAAAYVVAERRA
+GEDGA
+>GCF_020097155.1_01130
+MIVGIGVDVVDVPRFERQLARTPALRERLFTEEERDLSLRSLAARFAAKEAIAKALGAPP
+GMMWHHCSIPRPAHGDGRPEVRLTDSVRDRADELGVTHWHLSLSHDGDVAVAYVVAERHD
+>GCF_023573625.1_01606
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAVAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001355.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001355.fa
new file mode 100644
index 0000000000000000000000000000000000000000..adf6845211d671ed8e0573585bb7a9a1434787c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001355.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_01678
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDAVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA
+>GCF_003691675.1_01383
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDAVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA
+>GCF_005280335.1_01200
+MHTVDIGQPYPLGATVDETGTNFAVALAREAESVELCLVDEDGVETRLPVVERHGTTWHV
+HVAGVGHGQRYGYRVTGPWDPSRGLWHNPAKILVDPYARAFAGEHEWGQQHHSYDFDEPD
+RMDTSDNLGTTMLGVVTDDDFDWGEDAPPNIEMTDTVVYETHVKGMTMRHPAVPEELRGT
+YAGMAHPEVVRHLTDLGVTAVELMPVHQFVDDATLQEKGLSNYWGYNTLGFFAPHAAYAA
+SQEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSMRGLDNAGYYHLVEA
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRHWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSAFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGIWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNAANGEDNNDG
+ESHNRSWNCGVEGETDDPEVLTLRARQQRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAVDDSLVAFTRDLIALRHDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHTLTRGDEDEEGPYRDFYVLMNAWWEPVPYTLPG
+PLFPETWEVVVDTSSHVAPSGSRPRVRAGEVLEVPARSTVILRQVPEGA
+>GCF_020097155.1_01128
+MHTVDIGQPYPLGATVDEAGTNFAVAVGREVEAVELCLIAEDGSEERIPVTERHDTTWHV
+HVAGIGGGQRYGWRVHGPWDPARGLWHNPHKLLADPYARAFTGDYAWGQQHFSYAFDEPD
+RMDTADSRGTSMVGVVVDDDFDWGDDAPPQRLLTDTVVYETHVKGLTALHPDVPEELRGT
+YAGVAHPSVLEHLTSLGVTAVELMPVHQFVNDSILQEKGLSNYWGYNSLGYLAPHAAYSS
+ADTVGGQVHEFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPLLSFRGFDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGIWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRNPGASVNFVTAHDGFTLRDLVSYNEKHNHANGEDNNDG
+DSHNRSWNCGVEGETDDPEVLTLRARQQRNFLTTLMVSEGVPMLSHGDELGRTQKGNNNV
+YCQDNELSWIDWSTRDDALIAFTRDVIALRRDHAVFRRRQHFDGRPAERDVEAPLPDIVW
+LEPDATAKTEADWGAEARSIAFYLNGHDLQRREGEPDEAFRDFYVLMNAWWEPVPYTLPG
+PLFPGEWEIVVDTSSHVAPAGTRPHVVAGEVIEVPGRSTMILREVVRQEQG
+>GCF_023573625.1_01608
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+DAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDIEAPLPDIVW
+LEPDATAKTEDDWGAEARSLGFYLNGHTLPRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001356.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6fe6eaf07ad94c889370f3708a52675f1b7f0577
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001356.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01680
+MRRSRARSGILVRMCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQ
+LYHRKKAGKLANLAEELAEHPVPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLAFIHN
+GIIENYAELREELLAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAF
+TLLAVHVDHPDRVVASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITA
+DAVEISDFRGGPAEGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGA
+LMLDELRIDPEELKAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPI
+IDPHTLVVSISQSGETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEI
+AVASTKAFLAQITAAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAGKDQVKE
+LARSMADATSVLFLGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPV
+FVVMPSPLDRHSLHAKVVSNIQEVRARGARTFAVAERGDAAVRAQAEVVFEVPETQPMLM
+PLLTTVPLQIFALELATAKGYDVDQPRNLAKSVTVE
+>GCF_003691675.1_01384
+MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL
+AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL
+LAKGVEFLSETDTEVAAHLLADVYRHAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA
+DGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL
+KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPLDRHSL
+HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL
+ELATAKGYDVDQPRNLAKSVTVE
+>GCF_005280335.1_01198
+MCGIVGYIGQPSSTREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGELYHRKKAGKLANL
+AQELEEHPVPTGLVGIGHTRWATHGGPTDVNAHPHVADEGRLAMIHNGIIENYAELREEL
+LAKGAEFLSETDTEVAAHLLTDVYRNAGGQDLTRSLQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITAEGVEITDFAGSPA
+EGKRFTVDWDASAAEKGGYETFMEKEIHDQPQAVQDTLLGRMDAAGTLVLDELRIDPEEL
+KAVNKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPNTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLHAIPGKIQEILDDKEQVKELARSMADTSSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQAVFVVMPSPMDRHSL
+HAKVVSNIQEVRARGARTFVVAERGDQAVRSHAEVVIEVPETQPMLMPLLTTVPLQIFAL
+ELASAKGYDVDQPRNLAKSVTVE
+>GCF_020097155.1_01127
+MRMCGIVGYIGQPSSTREHDALEVLMEGLRRLEYRGYDSAGVAVVADGELYHRKKAGKLA
+NLAAELEAEPVPSAQVGIGHTRWATHGGPTDVNAHPHVADEGRLALIHNGIIENYAELRA
+ELLEKGVTFLSETDTEVAAHLLADVYRGAGEGDLTRTMQLASQRLEGAFTLLAVHVDHPD
+RVVASRRNSPLVVGVGEGENFLGSDVSGFIDFTKEAIELEQDQVVTITADAVEITDFQGA
+PAQGKAFTVDWDASAAEKGGFDTFMEKEIHDQPQAVQDTLLGRTDATGALVLDELRIDPE
+ELKAVRKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDDHTLVVSIS
+QSGETMDTLMAVRYAKEQGARTLSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQ
+ITAAYLLGLYLAQLNKKLFTGQIKDILADLAEIPGKIQEILDSSTPVRELARSMADTSSV
+LFLGRNVGFPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDEGQAVFVVMPSPLDRH
+SLHAKVVSNIQEVRARGARTFVVAERGDEAVRDHAEVVFEVPETQPVLMPLLTTVPLQIF
+ALELASAKGYDVDQPRNLAKSVTVE
+>GCF_023573625.1_01609
+MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL
+AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL
+LAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA
+EGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL
+KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPMDRHSL
+HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL
+ELATAKGYDVDQPRNLAKSVTVE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001357.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001357.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38b322b3c747737581179ef89604753cf40c0275
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001357.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01682
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAQHEVTRVLLRKV
+>GCF_003691675.1_01386
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAHHEVTRVLLRKV
+>GCF_005280335.1_01196
+MKDSTQPAPSVPEDLEDDLVSDHHRSPFVELERQTWARLATEMAQPFDQGDVERLRGLGE
+HLSLREVAEVYLPLSRLLSINVEASGALRSATNAFLGERTGRTPYVIGVAGSVAVGKSTT
+ARVLQEMLRRWPTTPRVELITTDGFLHPNAVLQERGIMARKGFPESYDRRALLRFMVDVK
+SGAQEVRAPVYSHITYDIVPGEEQVVRRPDVLIVEGLNVLAPPVTRADGTAGLSVSDFFD
+FSVYVDARADWIRSWYIERFMGLRSGAFADPRSYFHRYATLSDAEAQGTAESIWDSINGP
+NLQQNVQPTRGRARLVLTKNAQHEVTRVLLRKV
+>GCF_020097155.1_01125
+MRADAPPPPPPPCAVVLAGRRDAVAGRRPRACHDGPVKDTRDGGGGAPTAPADAPGPASA
+GDPHLSPFVELERQTWARLADQLDQPFDQDDVERLRGLGETLSLREVAEVYLPLSRLLGI
+HVEAAGALRRATNEFLGERTGRTPYVIGVAGSVAVGKSTTARVLQEMLRRWPSTPRVELI
+TTDGFLHPNAVLQERGIMDRKGFPESYDRRALLRFMADVKSGAAEVSAPVYSHVTYDIVP
+ERRQVVHRPDVLIVEGLNVLAPPLLRADGTPGLSVSDFFDFSVYVDARADWIRDWYVERF
+MGLRSSAFRDPDAFFHRYASLSDEEARETARSIWDRINGPNLAQNVQPTRGRARLVLTKN
+RQHEVTRVLMRKV
+>GCF_023573625.1_01611
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAQHEVTRVLLRKV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001358.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001358.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f6e42aac27c65285e575cea70c9fbdb61794fa1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001358.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01684
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMIEARNRRLGIDPAEEEVPADVAVLT
+EIRDLLAERRGGPTSGTTTL
+>GCF_003691675.1_01388
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMIEARNRRLGIDPAEEEVAADVAVLT
+EIRDLLAERRGGPTSGTTTL
+>GCF_005280335.1_01194
+MKGNVIDLAVAVVIGAAFGAVINAVVDSVLMPLIAALFAAPSFDDWLVLDINGVLVKFGV
+VLTAVVNFLLIAAAIYFAIVLPMNKMIERRNRRLGIDPAEEEVPEDVALLTEIRDLLSAQ
+RGGAAGTTHTTL
+>GCF_020097155.1_01124
+MKGNVVDLAVAVVIGAAFGKVVTALVDSVLMPLIAALFKAPSFDSWLVLNLNGVDVKFGV
+VLTAIVNFLLIAAAVYFCIVLPMNTMIERRNRRLGITPAEDEVAPDVAVLTEIRDLLARQ
+NGAPRV
+>GCF_023573625.1_01613
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMVEARNRRLGIDPAEEEVPADVAVLT
+EIRDLLAERRGGPTSGTTTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001359.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001359.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88e0d029b3650d2889f335574007f60c385d87ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001359.fa
@@ -0,0 +1,14 @@
+>GCF_002008305.4_01685
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP
+>GCF_003691675.1_01389
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP
+>GCF_005280335.1_01193
+MSSEAVPRPPRWSPFGALLAGLAVLWGAAFLAVDAPVCERHGAPVEWLPCLDRDRGDPDV
+APQR
+>GCF_020097155.1_01123
+MSPRRDPGRLRPLAGPAALLAALWVAAWLAVSVPVCDRGGPADWLPCVDPGRSVPAPGAP
+>GCF_023573625.1_01614
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001360.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001360.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bca5ff01c8a708f880ed6269d8cc5238a298f393
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001360.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01686
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD
+>GCF_003691675.1_01390
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDEHGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD
+>GCF_005280335.1_01192
+MSRLFGTDGVRGLANETLTVELSVQLAQAAAPVLGAEALEAGRRPVAVVARDPRISGEFI
+AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLGADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVEPRRPQGADVGRVKVFSDAEDRYVVHLLQALPHRLEGLKVVL
+DCAHGAAAGCSPEAFRDAGAEVVVIGASPDGLNINEGYGSTHLEKLQAAVLEHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVAMKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLAARVAETGRP
+LSALAAVMDRLPQVLVNVRGVDKSRAAEDVAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAEALADVVQRELRLHV
+>GCF_020097155.1_01122
+MSRLFGTDGVRGLANDVLTVELSVQLAQAAAPVLGADALAAGRRPVAVVARDPRISGQFI
+AAAVIAGLASSGVDVHDAGVVPTPAAAFLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDEQEDEIIQHLESEHPLRPTGAEVGRVRTFSDAEDRYVVHLLQTLPHRLDGLTVVL
+DCAHGAASGCSPDAFRDAGAQVIVIGAEPDGLNINEGVGSTHLEKLQAAVKEHGADLGIA
+HDGDADRCLAVDELGEVVDGDQIMGIMALALKDRGQLKEDTLVVTVMSNLGLKLAMRGAG
+IELVETQVGDRYVLAGMRLGEYSLGGEQSGHVIFADHATTGDGVLTGLQIAARVAETGTP
+LSQLAAVMTRLPQVLVNVRGVDKSRAAEDAAVQSAVREAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETARREAEALAEVVQRELRLHD
+>GCF_023573625.1_01615
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001361.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001361.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a767ba5c28816b98fd31b7663bcef5300604966
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001361.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01688
+MAENTSPTPDPRTRGEHGTEHTAQAPFAVTRDYAAEVDEIRELGRKLGGEKKTPTPDPQA
+WREGYPYKTKLSRKSYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGGAIKRF
+NEHLNPRGARTVALEKPTEEEASQWYFQRYIQHLEFMRETPELERMLLNSGVHIIKFWFS
+VSQREQLNRFAARETDPVRRWKLSPTDLASLDKWDDYTNAKEAMFFYTHTADAPWTVVKS
+NDKKRARLEAIRHVLHTLPYPDKDERIVHRPDPQICGPANELAEYGEVSGGSFPRVR
+>GCF_003691675.1_01392
+MGSFSWPLTAIKRFNEHLNPRGARTVALEKPTEEEASQWYFQRYIQHLEFMRETPELERM
+LVNSGVHIIKFWFSVSQREQLNRFAARETDPVRRWKLSPTDLASLDKWDDYTNAKEAMFF
+YTHTADAPWTVVKSNDKKRARLEAIRHVLHTLPYPDKDERIVHRPDPQICGPANELAEYG
+EVSGGSFPRVR
+>GCF_005280335.1_01190
+MTGRSPVRCAVRSNTTSGAAAAENTSTTTETTPAGGHAMEDTADAPWTVVKSNDKKRARL
+EAIRHVLHTLPYPDKDERIVHRPVPHICAPATELFETGEDSGGSFPRVR
+>GCF_020097155.1_01120
+MAENTTTPPTDPSADGVLAGEHPLESGRREQPFAVTEDYAAEVDEIRELGRTLHGDSLPS
+PDPTAWREGYPYKTKLSRKTYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGG
+AIKRFNEHMNPRGARTVALEKPTEAEASQWYFQRYIQHLPSGGEIVMFDRSWYNRAGVER
+VMGYCTPQQYLEFMRETPELERMLSNSGIHIIKFWFSVSRREQLNRFAARETDPVRRWKL
+SPTDLASLDKWDDYTNAKEAMFFYTHTADAPWTVVKSNDKKRARLEAMRHVLYTLPYPNK
+DERIVHLPDPQICASADVLSEIDEADGGSFPRVR
+>GCF_023573625.1_01617
+MQLWVKQTGQKVLIIVEGRDAAGKGGAIKRFNEHLNPCGARTVALEKPTEEEAPQWYFQC
+YIQHLEFMRETPELERMLVNSGVHIIKFWFSVSQREQLNRFAARETDPVRRWKLSPTDLA
+SLDKWDDSTNAKEAMFFYTHTADAPWTVVKSNDEKRARLEAIRHVLHTLPYPDKDERIVH
+RPDPQICGPANELAEYGEVSGGSFPRVCGGGFSRAPPPRTPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001364.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001364.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e802c2c82ffd6bb0beebfe57a98cca663332aa12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001364.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01691
+MSEQHRPDAPTAPGEPPSVRVRLGLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLIRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVQHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVG
+EGAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELHRRAEGTRAKRTL
+>GCF_003691675.1_01398
+MSEQHRPDAPSAPGEPASVRVRLDLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLTRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVTHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVG
+ERAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELHRRAEGTRAKRTL
+>GCF_005280335.1_01187
+MTEQPAPSAPRPSAAGEEPVRVRLDLAYDGGAFRGWARQPGLDSVQGALEDGLERILRRP
+VRTVVAGRTDAGVHARGQVVHLDLAEGEWAGLTRGRPDLEPGASLARRLGGVLSGWDGAV
+VVHGARRAPAGFDARFSALWREYEYRIDDAPDRRDPRTRAFTHWHGAALDERLMALEADA
+VLGLHDFLSFCRPREGATTIREVQDLRVARDEDGSVRVRIRADAFCHNMVRAVVGALLQV
+GEGSREPGWLGLRVATPARDSQVRLAPPRGLTLLAVGYPEDGEGLRRRAEGTRARRTL
+>GCF_020097155.1_01117
+MVGMPDDALPAAPVEPRPEPTTGLPREGEVRLRLDLAYDGSDFRGWAAQPGLATVQGALE
+GALETIVRRPVRTVVAGRTDAGVHARGQVVHCDLTEAEWSALARGRADVDPADALVRRLQ
+GVLRPWQGAVVVRGARRAPDGFDARFSALWRAYEYRISDRPETRDPLARHGVLWHGARVD
+ERLMAVEAGALLGLHDFLSFCRPREGATTVREVQDAEVVRTPDGLVRVRLRADAFCHSMV
+RTIVGALLEVGEGRRTPGWTAARVAGPVRDSAARLAPAHGLTLLEVGYPETGEELRARAE
+GTRARRAPLADLG
+>GCF_023573625.1_01620
+MSEQHRPDAPSAPGEPASVRVRLDLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLIRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVKHLEVRRDEDGVVRIRIRADAFCHNMVRAIVGALLQVG
+EGAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELRRRAEGTRAKRTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001365.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001365.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51fba98052ff156d1d302d8d468294fe1fc239f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001365.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01692
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL
+PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRHGDNAPMAVIEL
+IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP
+TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK
+MA
+>GCF_003691675.1_01399
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL
+PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRQGDNAPMAVIEL
+IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP
+TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK
+MA
+>GCF_005280335.1_01186
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL
+PARRKVQGLIAAKNRTNKSIVHELFTVIGPAMAERNGGYTRITKIGNRQGDNAPMAVIEL
+IMEPISGKQAVVREAEQAAASAPAAETAPVQETAPVEAVDPAAAEDVTVAESQEAAAEID
+GAVATTEDGSAPEGASIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGE
+AAQKMAD
+>GCF_020097155.1_01116
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPHAERLITIAKKGDL
+PARRKVQGIIAAKSRTNKSIVHELFTVIAPAMAERNGGYTRITKIGNRQGDNAPMAVIEL
+VMEPVSGKQAVVREAEQAAASAPAAAPVEETPVEVVDPAATEEVTVAESEETAAEIDGAV
+ATTEDGSAPEGATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQ
+KMA
+>GCF_023573625.1_01621
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL
+PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRHGDNAPMAVIEL
+IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP
+TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK
+MA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001367.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001367.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22e7cdec85aa162fc994ca64cbefe34fdb6b1695
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001367.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01694
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>GCF_003691675.1_01401
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>GCF_005280335.1_01184
+MPPKTRASAARKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>GCF_020097155.1_01114
+MPPKTRSAVRKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGSR
+KSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTPQ
+AHNGARPAKRRRV
+>GCF_023573625.1_01623
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001368.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50b0a4949c8a06095f9adafad464749cbc416937
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001368.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01695
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>GCF_003691675.1_01402
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>GCF_005280335.1_01183
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>GCF_020097155.1_01113
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDRDIRVKDLTDDQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>GCF_023573625.1_01624
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001369.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001369.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71201d907e82fdd1c961a81442cc8b985a3bba31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001369.fa
@@ -0,0 +1,10 @@
+>GCF_002008305.4_01696
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>GCF_003691675.1_01403
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>GCF_005280335.1_01182
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>GCF_020097155.1_01112
+MKVQPSVKRICDKCQVVRRKGRVLVICENPRHKQRQG
+>GCF_023573625.1_01625
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001370.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001370.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6294d4ca77f5d31eb5234e9d0e1ac247947524be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001370.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01697
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK
+>GCF_003691675.1_01404
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK
+>GCF_005280335.1_01181
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK
+>GCF_020097155.1_01111
+MAKKEGVIEVEGTVTEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRVVVELSP
+YDLNRGRIVYRYK
+>GCF_023573625.1_01626
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001371.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001371.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8313be386d869074ca43a5c03d31dadc23c396b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001371.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01698
+MIGRRSLELKTAPQLQAMQRAGVVLSEALDATLAAAAPGVTTAELDAVFAGVLAERGATS
+NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS
+EAGTAGPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVSAQPGEELGILEEYVG
+HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR
+ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE
+>GCF_003691675.1_01405
+MIGRRSLELKTAPQLQAMQRAGVVLSEALDATLTAAAPGVTTAELDAVFAGVLAERGATS
+NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS
+AAGTADPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVSAQPGEELGILEEYVG
+HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR
+ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE
+>GCF_005280335.1_01180
+MVGRRSLELKTTPQLQTMRRAGVVLSEALDATLAAAAPGVTTAELDAVFAGVLAEHGATS
+NFLGYYDFPATICASVNEEVVHGIPGDRVLQAGDVLKVDGGAIVDGWHADSARTLVLGSS
+EAGTADEGDERLSAITREALWVGIAAFATAKHVGDIGDAIDDFVSAQPGEPLGILEEYVG
+HGIGSSMHMPPDVFNYRTGHRGPKVRPGLALAVEPMLVRGGIETRVLEDDWTVVTVDGAR
+ASQWEHSVCRHAGGLWVLTAPDGGASELERFGVVPVPPGE
+>GCF_020097155.1_01110
+MFSRRSIELKTTPQLQTMQRAGVVLSEALDAAVAAAAPGVTTAEVDAVFADVLAQHGATS
+NFLGYYGYPATVCASVNEEVVHGIPGERVLQQGDVLKIDGGAIVDGWHSDSARTLILGSS
+EAGTADPEDERLSEITRQALWVGIAAFAQARHVGEIGDAVDDFVTSQPGAPLGILEDYVG
+HGIGSAMHLAPDVFNYRTGHRGPKVQHGMALAIEPMLVRGGIETRTLEDEWTVVTTDGAR
+ASQWEHTVCRHPGGVWVLTAPDGGAAELAAHGVVPVPPGE
+>GCF_023573625.1_01627
+MIGRRSLELKTAPQLQAMQHAGVVLSEALDATLTAAAPGVTTAELDAVFAGVLAERGATS
+NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS
+AAGTADPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVTAQPGEELGILEEYVG
+HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR
+ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001373.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001373.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5208829b0b09bd8073b043d058c8952c1302d18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001373.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01700
+MLKAIARIVRTPDLLRKIAFTLALIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPSILIQFNTPQDGSAPAPW
+ITWLSRYFGPGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR
+>GCF_003691675.1_01407
+MLKAIARIVRTPDLLRKIAFTLALIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPSILIQFNTPQDGSAPAPW
+ITWLSRYFGPGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR
+>GCF_005280335.1_01178
+MFKAIARIVRTPDLLRKIAFTLGIIAVYRMGAFVPSPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSIFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQSTLTQYTRYL
+TLALSLLQATTMASLARTGALLGCQLPLLRNDSILTVLLVVVVLTAGCIIVMWLGERVTE
+NGVGNGMSLLIFASIAAGFPAGLGQVVQTQGWRVFAIVMLIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTFIPIKVNMANVIPVIFASSVLMLPGILIQFNTPQDGTAPAPW
+IAWLSRYFGNGDHPVYMAVYFLMIIGFTYFYVSITFNPQEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLAGALYLGIVAMIPLIAFVVIGASQNFPFGGTSILIMVGVGLQTVKQ
+VNAQMEQRHYEGLLR
+>GCF_020097155.1_01108
+MFKAIARIVRTQDLRRKILFTLALVAVYRLGAFIPAPGVDYAAVRQCLAAGSAQGGLYSF
+VNMFSGGALLQVSIFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TIALAVLQGTTMASLARTGALLGCRVPLLHDQSIATVLLVVVVLTTGCVIVMWLGERITE
+NGIGNGMSLLIFASIAAGFPAGIGQVLQTQGWRTFAIVMVVGLLTMLAVVFVEESQRRIP
+VQYAKRQIGTRTVGGTSTFIPIKVNMANVIPVIFASSVLMLPGILAQFNTPQDGSAPPAW
+VSFLSTYFVGGDHPLYMALYLLMIIGFTYFYVSITFNPQEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLPGALYLGIVAMIPLIAFVLIGANQNFPFGGTSILIMVGVGLQTVKQ
+ISAQMEQRHYEGLLR
+>GCF_023573625.1_01629
+MLKAIARIVRTPDLLRKIAFTLGLIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPGILIQFNTPQDGSAPAPW
+ITWLSRYFGSGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITFVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001377.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001377.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ab05de98416697103c6d81e63983cb32dabfa67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001377.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01704
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIDAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>GCF_003691675.1_01411
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>GCF_005280335.1_01174
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAWA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLKL
+>GCF_020097155.1_01104
+MSTLKVKGKGKFNARTRRHLRVRKRISGTAVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRAFDGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>GCF_023573625.1_01633
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001380.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001380.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb4bfd9216e3a7492348db1fb97c8272a3331797
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001380.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01707
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
+>GCF_003691675.1_01414
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
+>GCF_005280335.1_01171
+MTEVQQTEKVAPRLKTKYREEIRATLQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVTDLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
+>GCF_020097155.1_01101
+MTEVQQTEKVTPRLKTKYREEIRASLQEQFEYANVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAIADLTAITGQKPMVTKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDK
+>GCF_023573625.1_01636
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001381.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001381.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0194414b912220712b221b4086643c0f4ef647d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001381.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01708
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
+>GCF_003691675.1_01415
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
+>GCF_005280335.1_01170
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGR
+QVAEAPIHISNVAVVDPETKKPTRVGYRFETVEKNGESKTVKVRFAKASGKEL
+>GCF_020097155.1_01100
+MAKIKKDDLVQVLSGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQNNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKNGEQVTVKVRFAKASGKEL
+>GCF_023573625.1_01637
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001382.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001382.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43a072969dd8c42e5770030f78e31932cac32d2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001382.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01709
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>GCF_003691675.1_01416
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>GCF_005280335.1_01169
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>GCF_020097155.1_01099
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIRFDENAAVILKNDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>GCF_023573625.1_01638
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001385.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001385.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b207d6ad9fefcaf068226bc143825ee54c5e242
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001385.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01712
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL
+AIHKLPLKARIIRREGGE
+>GCF_003691675.1_01419
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL
+AIHKLPLKARIIRREGGE
+>GCF_005280335.1_01166
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVSEEVAREALRL
+AIHKLPLKARVIRREGGE
+>GCF_020097155.1_01096
+MLIPRRVKHRKQHHPKRSGMAKGGTTVTFGEWGIQALSPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVSEEVAREALRL
+AIHKLPLKARIIRREGGE
+>GCF_023573625.1_01641
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL
+AIHKLPLKARIIRREGGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001386.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001386.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be09b44f404a4190c23e1a00a072aed747d46578
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001386.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01713
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGVRRSGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA
+>GCF_003691675.1_01420
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA
+>GCF_005280335.1_01165
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCAGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGDRRGGGGGE
+RRRRNDRAERAPRQENAGAGAETPAAAPAEGGNA
+>GCF_020097155.1_01095
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTDGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTYGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGPGGGE
+RRRRNDRAERAPRQENAGAGAEQSAAAPAEGGNA
+>GCF_023573625.1_01642
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001388.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001388.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef710c9d3718d51e5ffaaa9a8c9061da2fdebbf5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001388.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01715
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>GCF_003691675.1_01422
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>GCF_005280335.1_01163
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>GCF_020097155.1_01093
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTFRGHVKDDKKGKRR
+>GCF_023573625.1_01644
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001389.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001389.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba912e7987bd676c4b0538214bb7261f8aa8f060
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001389.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01716
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>GCF_003691675.1_01423
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>GCF_005280335.1_01162
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>GCF_020097155.1_01092
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLIDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLQQGDVVEAG
+PNADIKPGNNLPLRNIPVGTTIHAVELRPGGGAKMARSAGASIQLVAREGKYAQLRLPSG
+EIRNVDVRCRATVGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNPNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>GCF_023573625.1_01645
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001390.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001390.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7140b9b0c28722a52a305a8a712fe1facfa7666f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001390.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01717
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
+>GCF_003691675.1_01424
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
+>GCF_005280335.1_01161
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
+>GCF_020097155.1_01091
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKTEIKQAIERIFDVSVASVN
+TLNRPGKRRRTRFGWGQRKSTKRAIVSLKDGATIDIFGGPLAS
+>GCF_023573625.1_01646
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001391.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001391.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95ecee50d4d35a1374e95171e706176094c284c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001391.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01718
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>GCF_003691675.1_01425
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>GCF_005280335.1_01160
+MAENSVKTVQVDLPAEIFDVQSNVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>GCF_020097155.1_01090
+MAENTVKTVQVELPAEIFDVQANVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLESLNTGRKNVLLVIDRADDLTALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTKVAYEAYVAQASGAKKEDAQ
+>GCF_023573625.1_01647
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001392.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001392.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f42f29e76369002c5ebb4758050e28ab1dbbe18b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001392.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01719
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>GCF_003691675.1_01426
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGQHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>GCF_005280335.1_01159
+MTNTQNIKGLLGTKLGMTQVWDENNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFDKAGVTPRRHLVELRTADAAEYSLGQDLTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVSASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGVDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>GCF_020097155.1_01089
+MTNTQNVKGLMGTKLGMTQVWDEDNKLIPVTVVQADANVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYTLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVSASHGAHKNHRKPGSVGGASTPARVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>GCF_023573625.1_01648
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001393.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001393.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d61534d5107021f9afdc4f477b4dc3a93dcf5f1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001393.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01720
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>GCF_003691675.1_01427
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>GCF_005280335.1_01158
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>GCF_020097155.1_01088
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>GCF_023573625.1_01649
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001395.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001395.fa
new file mode 100644
index 0000000000000000000000000000000000000000..970d70d4cce5f3b3fb2536b44f7f7ece4e1e1d62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001395.fa
@@ -0,0 +1,10 @@
+>GCF_002008305.4_01722
+MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER
+>GCF_003691675.1_01429
+MSDDGAAAAARLGSMPELLILIVVLAVAVVAVRWALRTFRPEIDRARRIRRANRGGELER
+>GCF_005280335.1_01156
+MPELLITLLVLAAAVVAVVWALRTFRPEIDRARRIRRANRNGELRR
+>GCF_020097155.1_01086
+MEWLIALVVIAAVVAGGLWARRAFAPEIERARRIRRAERGGRLER
+>GCF_023573625.1_01651
+MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001397.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f0e0323fc9bc295b7f584ea0f7dd1ee12bd754d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001397.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_01724
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>GCF_003691675.1_01431
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESITFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>GCF_005280335.1_01154
+MAQDVLTDLNKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGASTTDWMEQEKE
+RGITITSAAVTCFWNDNQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVNRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGAEYETREIPAELQEKAEEYRAQLVEAVADTSEELMEKYLEG
+EELTTEEIQAGVRHLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGAVKGHDV
+KDEEVELEREASKDAPFSALAFKIASHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDAAHPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTADGEIYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVKALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>GCF_020097155.1_01084
+MAQDVLTDLNKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGASTTDWMEQEKE
+RGITITSAAVTCFWKNNQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGAKPLVMQLPIGSESDFIGVVDL
+LTMKAFVWPGDAKGDVTMGAEYETQEIPADLQEKAEEYRTQLLEAVADTSEELMEKYLEG
+EEISEEEIVAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGAVKGHAV
+GDEEQVLEREPSKEAPFSALAFKIASHPFFGTLTFIRVYSGRLEGGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPQNPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNDETGQTEIGGMGELHLDVFVDRMRREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPVLLEPLMAVEVRTPEEFMGDVVGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSRTQGRAVYSMTFHSYSEVPKNVADEIIQKSQGE
+>GCF_023573625.1_01653
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001399.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001399.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f41658eee1f50491d6433e6b3563b3da57a36855
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001399.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01726
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVRDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>GCF_003691675.1_01433
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>GCF_005280335.1_01152
+MPTIQQLVRKGRSPKVVKTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVRDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>GCF_020097155.1_01082
+MPTIQQLVRKGRSPKVVKTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+VEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>GCF_023573625.1_01655
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001400.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001400.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0eaaffb59aee826d77a59373b2be5a508f670420
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001400.fa
@@ -0,0 +1,115 @@
+>GCF_002008305.4_01727
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL
+YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN
+LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN
+ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE
+QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTETSVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQSLGENDFHAVSLDDYGRGGDFRA
+>GCF_003691675.1_01434
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL
+YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN
+LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN
+ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE
+QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTEASVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQSLGENDFHAVSLDDYDRGGDFRA
+>GCF_005280335.1_01151
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEGRHRDLANLQAEYDQETRVLADQRDADIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMSQIRKRADAELDRKEQVWDRFKNLKVADLEGDEGL
+YRTMRDKYGQYFEGSMGAEAIQRRLQTFDLAAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDAVGAGN
+AYATVGEAVMAFDGGDLHLNAPVKIGVDGFVPSTAVPAPEGWSEGELAVIETTLGKVLFN
+ELLPADYPWLDTQATKGSLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQALRVQQQYEKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREEDCGTERGLSVTIAVPNADGELVAHE
+QVENSAFARTLAQDVTGEDGSVLASGGADVGDVLIDQLVGAGVSEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTDASVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VAVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGETDLLPGELTDRARFVAANRSAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQQLGESDFHAVSLDDYGRGGDFRS
+>GCF_020097155.1_01080
+MTTENPFGLMRIGLATADDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLPNLQAEHDQETRVLEDQRDADIAAVAADLEKD
+LAKLEAEGAKAAEKKKARDAADKTMAQIRKRADAELDRKAQVWDRFKNLKVADLEGDEGL
+YRAMRDKFGAYFEGSMGAEAIQRRLQTFDLAAESELLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNVKSAKRMVERFR
+PQVWDVLEEVISEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRAEGKGAGR
+QFATVGEAVMAFDNGELHLNAPATIGVEGFVPSAAVAAPEGWTEGEVALIETTLGKVIFN
+DLLPADYPWLDTQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKASIMQGYEDQAQRVQAQYDKGLIADDERRSELIDIWNKATDEVAAAMKAGLS
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTGRGLSVTIAEPNHDGELVVRE
+QVENSAFARTLAQAVTAEDGTVLAEAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGKLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTDASVRLILTPDDGSEEIAYPVLRRARLLVADGEH
+VAVGTQLVAGAVDPKQVLRVLGPRAAQRFLVQEVQDVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGETDLLPGELTDRSRFVAANRAAVAEGKQPAAGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKEDPLLGLKENVIIGKLIPAGTGLDRYTQTTVEPTEEAKANLFA
+APVGFADFDYPGLDQPLGEAEFHAVSLDDYGRGGDFRA
+>GCF_023573625.1_01656
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL
+YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN
+LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN
+ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE
+QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTETSVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQSLGENDFHAVSLDDYGRGGDFRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001402.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001402.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a262ee12f525a6533c51945d0058a5ad99a9c18d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001402.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01729
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRAITSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK
+>GCF_003691675.1_01436
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK
+>GCF_005280335.1_01149
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAAGAAGGDAAAAEEKD
+EFDVVLESAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLEG
+AGATVTLK
+>GCF_020097155.1_01078
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAMAAAGAPAGGDAAAAEEKD
+EFDVILEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLEG
+AGATVTLK
+>GCF_023573625.1_01658
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001403.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001403.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dfdf2ad8dc62ecce03dfeeab91d09dc14a58bab0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001403.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01730
+MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KQLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA
+>GCF_003691675.1_01437
+MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA
+>GCF_005280335.1_01148
+MATSAKESAVAELTDLFRESNAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKEAGVEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KKIADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAQQGEAA
+>GCF_020097155.1_01077
+MATSAKESAVAELTDLFRSSSAAVLTEYRGLTVSELKQLRDSIRQDATYSVAKNTLTEIA
+AKEAGVEGLDAHLAGPTAIAFVTGDPVTVAKALRDFAKDHDKLVLKGGYMDGQPLDEAGI
+EKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTARTVEALRAQQDQAA
+>GCF_023573625.1_01659
+MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001404.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001404.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbea181f1c33693e10034b55a7c6e1bc28780241
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001404.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01731
+MAQRSKAYKAAKAAIGEDLYSPVEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL
+>GCF_003691675.1_01438
+MAQRSKAYKAAKAAIGEDLYSPVEAIRLAKETNPSKIDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL
+>GCF_005280335.1_01147
+MAQRSKAYKAAKAAIGEDVYSPVEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGERAEAARAAGADVVGDDDLIAKISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVTDIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVSMDPNVTSVDSSEL
+>GCF_020097155.1_01076
+MAQRSKAYKAAKAAIGDTVYAPAEAIALAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGERAEAARAAGADHVGDDDLIAKIADGWTDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+ANQLVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVQMDPNAAPPKDEAQA
+>GCF_023573625.1_01660
+MAQRSKAYKAAKAAIGEDLYSPAEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001405.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001405.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e625f7f76cb560c188766d5abd6752bc49d0a982
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001405.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01732
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG
+>GCF_003691675.1_01439
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG
+>GCF_005280335.1_01146
+MAPKKKVSGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFITKTPPAAELIKKAAGVAKGSATPHTAKVGKLTQAQCEEIAQTKMEDLNA
+NDVKAAAKIIAGTARSMGITVEG
+>GCF_020097155.1_01075
+MAPKKKVAGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATEAQRGNVIPVEI
+TVYEDRSFTFITKTPPAVELIKKAAGVQKGSSTPHTAKVGTLTQAQCEEIAQSKMEDLNA
+NDVKAAAKIIAGTARSMGITVEG
+>GCF_023573625.1_01661
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001406.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001406.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6bf2e1223988384fc79d12d0a557d64aab7b063
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001406.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01733
+MSEQELDRQPAEESVPMSEDAVAEETAETAQDAGTPVEDALDEVAGSGDETAEATVQEAD
+LAVAEGEDAPTPVEEQSDDEPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEAR
+ILTQDMEDSIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGV
+TGFVGNDAHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPAAAESGAPAAPAIHVDF
+EVGESVTVNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI
+>GCF_003691675.1_01440
+MSEDAVAEETAETAQDAGTPVEDALDEAAGSGDETAEATVQEADLAVAEGEDAPTPVEEQ
+ADDEPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILTQDMEDSIYEIEVP
+MEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGNDAHHPQPLSL
+DEVYDMLAPSVIQEAARAAEKAGLAVPALVESGAPAAPAIHVDFEVGESVTVNDGPFETL
+PATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI
+>GCF_005280335.1_01145
+MSEQELDRQAAEESVSVQEDGAVEETVETAQDAPAPAEDAAGETAVDGEEAAEATEATAQ
+EADPAAVEQAEEEPAVDPGEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILSQDME
+DAIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGND
+AHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPASAESGAAAAPAIHVDFEVGESVT
+VNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKVI
+>GCF_020097155.1_01074
+MSEQELDRQDVEETAVAEDSTALEAPVEDTAAEEAEQTVQEADLAIAEGDQDAAEAPSAE
+ELDAAGQAPAQPDVEAAEQLRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARIQTQDMEDS
+IYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTSGVTGFVGNDAH
+HPQPLTLDEVYDMLAPSVVQEAVREAEKAGLVPVAVAESGAAGAPAIHVDFEVGESVTVD
+DGPFETLPATISEIKPETQQLVVLVSIFERETPVTLSFNQVTKVI
+>GCF_023573625.1_01662
+MSEDAVAEETAQDAGTPVEDALDEPAGSGDETAEATVQEADLAVAEGEDAPTPVEEQSDD
+EPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILTQDMEDSIYEIEVPMEE
+VVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGNDAHHPQPLSLDEV
+YDMLAPSVIQEAARAAEKAGLAVPAAAESGAPAAPAIHVDFEVGESVTVNDGPFETLPAT
+ISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001407.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001407.fa
new file mode 100644
index 0000000000000000000000000000000000000000..177772815e2a3b5770837fcc6cfb0daf82dd3dd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001407.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01734
+MAANGGGPAPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI
+LLVMGLDWVFGTVAGLLFGAGGL
+>GCF_003691675.1_01441
+MAANGGGPTPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI
+LLVMGLDWVFGTVAGLLFGAGGL
+>GCF_005280335.1_01144
+MTDIAANGGGSTPAPDRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVA
+FMILLVMGLDWVFGTVAGLLFGGGGGL
+>GCF_020097155.1_01073
+MTANHGSSASGPESRRRGPFGRIALFLRQVLDELRKVVTPTGDELLKMTGVVLAFVAVMI
+LLVMGLDWVFGTLAGLLFGAGPA
+>GCF_023573625.1_01663
+MAANGGGPAPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI
+LLVMGLDWVFGTVAGLLFGAGGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001408.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001408.fa
new file mode 100644
index 0000000000000000000000000000000000000000..535d79661df71e873c17481658416f00bd18105e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001408.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_01736
+MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA
+ARDPKNHRYSPASGLPELREAIADKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ
+DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDESVTDRTKVLLFVSPSN
+PTGAVYSPEETAAIGQWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG
+VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT
+AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALAKTYRGGVTPATSAELAAFILD
+EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA
+>GCF_003691675.1_01443
+MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA
+ARDPKNHRYSPAAGLPELREAIAAKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ
+DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDESVTDRTKVLLFVSPSN
+PTGAVYSPEETAAIGQWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG
+VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT
+AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALAKTYRGGVTPATSAELAAFILD
+EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA
+>GCF_005280335.1_01142
+MIGFGAGEPDFPTPAYIVEAAVAAAKDPKNHRYSPAAGLPELREAIAAKTLRDSGVAIDV
+AQVLVTNGGKQAVYNTFAALLDPQDEVLVPSPYWTTYPEAIRLAGGVPVDVFAGPEAGYK
+VSVEQLEAAVTERTKALLFVSPSNPTGAVYSPEETEAVGRWALDRGLWVITDEIYEHLTY
+DGMPFTSILKAVPELAEQAVILNGVAKTYAMTGWRVGWMAGPLDVIKAATNLQSHATSNV
+SNVSQRAALAAVAGPLDAVDEMKVAFDRRRRAMVEAMNAVPGFHCPTPQGAFYAYVDVRE
+ALGRTYRGGVTPTTSAELATFILDEAEVAVVPGEAFGPSGYLRLSYALGDDDLAEGVERI
+RALLSE
+>GCF_020097155.1_01071
+MTRAPSNRAGTSAPDGGSVGWPHGRRVRVRRPPEQMRKVPMATPAHRVSARLSAIAPSAT
+LAVDAKAKALKAAGRPVIGFGAGEPDFPTPDYIVEAAVAAARDPKNHRYSPAAGLPELRE
+AIAAKTLRDSGVELDASQVLVTNGGKQAVYNAFAALLDPQDEVLVPSPFWTTYPEAIRLA
+GGVPVDVFAGPDQGYKVTVDQLEAAHTERTKVLLFVSPSNPTGAVYSPEETRAIGEWALA
+KGLWVVTDEIYEHLTYDGVPFTSILKAVSGLAEQGVILNGVAKTYAMTGWRVGWLAGPLD
+VVKAATNLQSHATSNVANVSQRAALAAVAGPLDAVEEMKTAFDRRRRAMVEALNRVPGFH
+CPTPEGAFYAYVDVREALGRTYTGGVTPATSAELADFILDQAEVAVVPGEAFGPSGYLRL
+SYALGDEDLAEGVERIRALLSA
+>GCF_023573625.1_01665
+MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA
+ARDPKNHRYSPAAGLPELREAIAAKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ
+DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDEAVTDRTKVLLFVSPSN
+PTGAVYSPEETAAIGRWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG
+VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT
+AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALGKTYRGDVTPTTSAELAAFILD
+EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001409.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001409.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8622182018a54c386df488014fb1b2cae993284
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001409.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01737
+MTDPAPRTAVNVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRAVLDLAPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVAD
+AAVRVADGDAVFSPRLAGFVLDAFRGTAPASPPVPAAATSGAAAPDEDLDRLSAREREVM
+RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
+>GCF_003691675.1_01444
+MTDPAPRTAVIVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRTVLDLVPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGVEVAD
+AAVRVADGDAVFSPRLAGFVLDAFRGTAPASPPVPAAATSGAAAPDEDLDRLSAREREVM
+RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
+>GCF_005280335.1_01141
+MSVPAPRTAVIVDDHAIFRSGLRADLDPARLAIVGEAGDVDEAVRAVLELAPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVVD
+AAVRVAGGDAVFSPRLAGFVLDAFRGAAAPAAAPASPAVPDEDVDRLSAREREVMRLIAR
+GYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
+>GCF_020097155.1_01070
+MTVHADPVVPTAVVVDDHAIFRSGLRADLDASRLRIVGEAGDVDEAVRVVLQLAPDVVLL
+DVHLPGGAGGGGAEVASRVLAERPGQRLLALSVSDAAEDVVAVIRAGARGYITKSAAGAE
+VVEAALRVAGGDAVFSPRLAGFVLDAFRGLPTESAPAGPAPSEGDLDRLSAREREVMRLI
+ARGYTYREAGAELFISDRTVESHVSSVLRKLQLSNRHELTRWAARHGWA
+>GCF_023573625.1_01666
+MTDPAPRTAVIVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRTVLDLAPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVAD
+AAVRVADGDAVFSPRLAGFVLDAFRGTAPAPPLVPAAAASGAAAPDEDLDRLSAREREVM
+RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001410.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a7f2db52477f9d2a05a15c3563d7e37accd32ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001410.fa
@@ -0,0 +1,42 @@
+>GCF_002008305.4_01738
+MPTPSAPAPAPRPPLMRHGADRPVSGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALY
+VWLWLLVPEEGPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG
+LAVDWALVGPVAVLVIGLGLAWMQLDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGA
+VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVL
+QSLALIQRRAQDADAVARVARAQERELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGAR
+VEVVAVGRAAGAWLEPLAAAAREAMQNAARHAGDAQVFAEAGEDDRGRTVAEVFVRDRGP
+GFDLPTVPADRLGVRESILGRMGRAGGTARIRSGPGGTEVHLTLAEPEGARARTGQEHP
+>GCF_003691675.1_01445
+MPTPSAPAQAPRPPLMRHGADRPVSGVAAGLARHLGVPVGRVRAALALLSLMGGAGLALY
+VWLWLLMPEEGPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG
+LAVDWALVGPVAVLVIGLGLAWMQLDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGA
+VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQVQRAEIAAHLHDSVL
+QSLALIQRRAHDADAVARVARAQERELRQFLALDSRGGPRSLAEALEEHAAAVEDAHGSR
+VEVVAVGRAAGAWLEPLAAAAREAMQNAARHAGDAQVFAEAGEDDHGRTVAEVFVRDRGP
+GFDLHTVPADRLGVRESILGRMERAGGAARIRSGPGGTEVHLTLTEPEGARARAGQEHP
+>GCF_005280335.1_01140
+MPASAVPPSAPSGRAGPRRAAADDARTRPIGADPRTSEARASGTRAPLMRHRADRPVSGV
+AAGAARHLGLSPRTARAGFAVLALAGGAGLALYVWLWLLMPEEGADGAPTGEAPSLRGRA
+PEVLERVREGGWPVLLAAVVLGVGVITIADGLGLAVDWALVGPVAVLVIGLGLAWMQLDL
+AGGPPAGRVGRVVRLALGTALVLLAVLAIVLGGVTSGDLWLGLLVAVALIAGVAMVAMPY
+ALSWLRRRDAERTAFAVQAQRAEIAAHLHDSVLQSLALIQRRAHDPEAVARAARAQEREL
+RRFLALDDRGGHDSLAATLREHAAAVEDAHGRRVEVVAVGEASGAWLEPLTAAAREAMLN
+AARHAGDAQVFAEVAEDDDGRTVAEVFVRDRGPGFDPGAVPADRLGVRESVVGRMERAGG
+AARIRSGPGGTEVHLTLTRPDRVPPHAAQERP
+>GCF_020097155.1_01069
+MPAPAIPPPADLSARPALLRHAADRPVSGVAGGVARHLGLDPRLARAGFAVLALAGGAGI
+ALYAWLWLLMPEEGPDGAPAGPAPTLRGRAPEVLERLREGGWPILLAVVVLGVGVLTVAD
+GLGVPVDWALVGPVAVLVIGLGLAWMQLGAADGPEGGRWARRARLGLGTALVLLGVLAIV
+VGAVTAGDLWLGLLVAVALLAGGALVAMPFVLARRRRRDEERTGAAVRAQRDEIAAHLHD
+SVLQSLALIQRRADDPETVARVARAQERELRQFLALDSARAHGTLAEAVEDHAAAVEDAF
+GRRVEVVSVGEASGPWLEPLASAAREAMVNAARHAGDVQVFVEVSEDDGGRTLAEVFIRD
+RGTGFDLADVPADRLGVRESILGRMRRAGGTARIRSGPSGTEVQLSLADPGAPGVGLREG
+RGRA
+>GCF_023573625.1_01667
+MPTPSAPAPAPRPPLMRHGADRPVSGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALY
+VWLWLLMPEERPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG
+LAVDWALVGPVAVLVIGLGLAWMQLDLAGGSRAGRSGRLVRLVLGTALVLLAVLAIVLGA
+VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVL
+QSLALIQRRAQDADAVARVARAQERELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGAR
+VEVVAVGRAAGAWLEPLAAAAREAMQNAVRHAGDAQVFAEAGEDERGRTVAEVFVRDRGP
+GFDLHTVPADRLGVRESIVGRMERAGGTARIRSGPGGTEVHLTLTEPEGARARTGQEHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001411.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001411.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbea4efaa805c5c1c3e5a1b33987fcf3f37d86ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001411.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01739
+MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDPDGRVQFGRLRRGEWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG
+RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA
+TRLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
+>GCF_003691675.1_01446
+MTSTHDPFTGPGPHVAPDGAASGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDADGRVQFGRLRRREWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLLGLGALAVLVWWLVTRWDGRAQARVAPG
+RAPDADQPSHAVPRPAWYVGGGPRERAAEVTDPHGFHPEWIDPATGTWRDHVHSRERRAA
+ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
+>GCF_005280335.1_01139
+MRRSDSSWVGGVLAGVAERYRVDPLLARGVFVALCVVSAGFGLLAYAVAWALLPDGDGTV
+HYGRLRRGEWQDATVAIAVIGGIGVLNVVLGAGFTLLAPVVGGPGSLLGLAAVAVLVWWL
+VTRWDGSTQSRVGPAPASEPEASGRAAARPAWYLRRDDARAAASRQDAHGFRADWLDPET
+GTWRSPVHSRELRAAARLAEEEQAAPAGPSGRGSAVVAAPRRLSPAVQAVTYAVAALAAA
+AAVGASLLVGVGSLTLLAVPAIVAALAVIAPVMLAALLTGRRPGSLAPASGILVGAAALQ
+VAVAVAVL
+>GCF_020097155.1_01068
+MDTAHDPFPAPRSSPATRPLPPGPASDARSRSAGTDGPAPDGLEVLPVWLRRPVEGWGVR
+RSRSSWVGGVLAGVAERYRIDPLLSRGVFVALCVVSAGIGLLGYALAWAVLPDADGRVHY
+GRLRRGEWSDAPVAIAAIAAIGALNVVLGAGFTLIAPVLGGPGSLIGLTALAVLVWWLVT
+RWDGEGERRMAPAQPARDAAARPAAEPSWYLRRHRPESATVDAHGFRSDWIDPETGSWRE
+QPHSREHRAAARLAEAQVRAAGQAAGRRPAGTGRGSHSAVKPLLGRGTRIATCVVAAGVA
+LAVSLAMVLGNVSTSATLFPVWPALAALGVMAAVMTAGLLRGRRPGLLAPLSGILVGVVA
+LQVCAHLLFTPLP
+>GCF_023573625.1_01668
+MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMISAGLGLLAYAAAWAVLPDADGRVQFGRLRRGEWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG
+RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA
+ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001415.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ea5a054cfce2eb01a9b4446590101133c38c8cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001415.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01743
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS
+>GCF_003691675.1_01450
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS
+>GCF_005280335.1_01134
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSDGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRERRDGDVGPGMRPADIVPAFRSAEDVESLRAGDEGFG
+ITATITHPGSLAELYYGRIKGPQLQLVTDAVLRGSAAGDYHRATRMAGLVNGQLFWRWDS
+SGSEGAELEAHASAILDRMPSESEGRLAPGAPRPRGAGGAEPGERP
+>GCF_020097155.1_01063
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSEGTDIFYQRVDFVEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARQDGDVGPGMVPADIVPAYRSAEDVEALRSEDGAFR
+ITATITHPGSLAELYYGRIKGPQVQIVMDSLLRGAAAGEYARATRMAGLVNGQLFWRWDS
+SPAVEGPMEVHASAILDRMPDPSEGRLAPGAPRPRGERGRAPEQGA
+>GCF_023573625.1_01672
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001416.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001416.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4d98a823e826c0e7513519dcadc15b1827f2a31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001416.fa
@@ -0,0 +1,10 @@
+>GCF_002008305.4_01744
+MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR
+>GCF_003691675.1_01451
+MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR
+>GCF_005280335.1_01133
+MDTLLALEIFFLALVVLAGLGMAAVAAVVVGGLFKGQR
+>GCF_020097155.1_01062
+MDSIVALEIFFLVLVVLAGLGMAAVAALVVGGLFKGQR
+>GCF_023573625.1_01673
+MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001417.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001417.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e499926858a2d505dbc415df6500c7d04777f24
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001417.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01745
+MAREVRPAVARPGPSRCAPGRMGQVMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI
+LVIAWGWPRQMGAPARLSLSVTLAVAGGAAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW
+STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWTDTPAVAGLVITLAV
+TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL
+VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA
+>GCF_003691675.1_01452
+MAREVRPAVARPGPSRCAPGRMGQVMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI
+LVIAWGWPRQMGAPARLSLSVTLAVAGGAAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW
+STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWTDTPAVAGLVITLAV
+TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL
+VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA
+>GCF_005280335.1_01132
+MMRLSMALSAAVAALVLGGATLLGPVPAAVAAMAVILVIAWGWPRQMGAPARLSLSVTLA
+AVGLVAVLLMLLWPPIEDGRSGAWTLFEPLAVALAWSTMASFVVQLVRGTGRPLRLESTV
+ATMGGGLIAVMTACWVAVSRWTDAPAVAGLVLTLAISVAAFSLIGLIPGVQGRPGVLALV
+VVPLGALLAWPVSALLGVGPQDRAAVVAAVVAVATLVSLTAATAPSARPRPEDRPVGTTL
+RPRRAGYALALAPVGAAGVVAHVMVGFLA
+>GCF_020097155.1_01061
+MMRLSMALSAALAALVLGGAALLGPVPAAVAACLVIAVIAFGWPRQMGAPARLSLTLTML
+VAGVLGVLVMVLWPRGDAGPRGAWALFEPLAVVLAFGTMASFIVQLVRGTGRPLRLESTV
+TTMGGVLVCLLAASWVPLAHHREAPGATGLVVTLAATLIVTSLIGLTPFMQGRPRVLALV
+MVPASGVVAALVSLLLGAPAHTAWVYAAAALGTAGLVSLTAAAAPSSRPLPEDRVVGTTL
+SPRRAGYALAMAPVGAAGVVGHVMLGFLA
+>GCF_023573625.1_01674
+MMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVILVIAWGWPRQMGAPARLSLSVTLA
+VAGGIAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAWSTMASFVVQLVRGTGRPLRLESTV
+ATMGGAFMAVVTACWVAVSRWSDTPAVAGLVITLAVTVAAVSLVGLTPWMQGRPGVLALV
+VIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVLVSLTAATAPSSRPRPEDRPVGTTL
+RPRRAGYALALAPVGAAGVVAHVMVGFLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001418.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001418.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebd33db42a162465698db779d20ce391d53e07c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001418.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01746
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGPDGAIDGAAVLVPEGTAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREETT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVTLY
+ASLGFELFAADAQYRRP
+>GCF_003691675.1_01453
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGPDGAIDGAAVLVPEGTAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREETT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVTLY
+ASLGFELFAADAQYRRP
+>GCF_005280335.1_01131
+MAENPVPATPTDPAAPRVSEPRPDEVDAVLALADRAQAADGHPPLSDQTRVVLARGRQRW
+WGVVREADGSVSGAAVLAPEGGEDSGSVLELVVDPEARRAGRGAALADAAAAAVRERGLE
+STTSVWAHGMLPGSDALARRHGLEPVRELRRMRLPHEALADLPQPQLADGVALRGFVPGR
+DEQAWLDANAAAFADHPEQGGLTRADLEDRMAEDWFEAEGLLLAVREEDDALLGFHWTKV
+EPQAGPGPRVGEVYAVGVTPATQGLGLGRALTLAGLHRMAGQGVDVVDLYVDADNAAAVR
+LYESLGFGLFAADAQHRRP
+>GCF_020097155.1_01059
+MSEQPASPALPPTPGVVSPGTPSDVDAALALADRAHRSDGHPPLNDQTRAVLARDAQRWW
+GLTRDEAGAVTGVAVLAPEGEAAGPGVVELAVDPAHRGAGLGAALAEAAADAVRERGEAR
+RTSAWAHGALPGALALARRHGLEPVRELRRMRLDPAGLGALPPTRLPEGVTLRGFVPGRD
+EDAWLALNAAAFADHPEQGSLTRADLDAREAEDWFEAAGLLLAEDAEGTPVGYHWTKVTP
+AEAGAPSEGEVYAVGISPAAQGRGLGRALTLAGLHHMAGRGVDAVDLYVDADNVPAVRLY
+ESLGFALAAADVQLRPAR
+>GCF_023573625.1_01675
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGTDGAIDGAAVLVPEGAAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREATT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVALY
+ASLGFELFAADAQYRRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001419.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001419.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3e0df3d7344504b94b1c98ab9461a1337282e66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001419.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01747
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLALKTK
+GAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGRTDRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD
+>GCF_003691675.1_01454
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLALKTK
+GAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGRTDRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD
+>GCF_005280335.1_01130
+MPSTPTERVARWSTEDRAADGPRAEVLAAGVVPWRRTPGGRLEVLVIHRPRYDDWSWPKG
+KLDPGETLPQCAVRELREEVGLALRPGIPLCVTEYEVSGKRGARLTKEVWYWAADAGAQR
+AVPDGDEVDEVRWVRPEEAEALLTNETDREPLELLVRADSRGRLRTLPLLVLRHAKAKPR
+SSWSRAEQERPLAATGRRQALAVEGLVAAWAPDRLVSSPWRRCVETLAPLVKSSRLPLKT
+KGAFTETAAKEKPKKTRKAMHELLGRQRAQVVCTHRPVLPVLFEVVEDAARRQERVLRAM
+PREDPWLRPGAVLVVHRSLDGDVVAVEAYDPWDD
+>GCF_020097155.1_01058
+MTRPLSWDGIPDPIPPEDPRTMSAHPDDRAAAWSTPDGAVTAPGAEVLAAGMIPWRPGAE
+GLEVLVIHRPRYDDWSWPKGKVDDGETLPEAAARELAEEVALTLRPGLPLAVTRYDVPDR
+KGKGMLSKEVWYWAGEATGQRPTPDGDEVDEARWVSSARAREMLSNATDLEPLDRLERAD
+ARGHLRTVPLLVLRHAKAKPRSSWSRAEQERPLAATGRRQAHSVARLIAVWRPERVVSSP
+WRRCVETLAPFVKATRLPLKTKSAFTETTAREKPKKTRRAFRDLLARRRPQVLCLHRPVI
+PSILEEVDDAAARPASDVLAALPRRDPHLRPGGVLVLHQGLDAKGAVVAAEVYDPWSD
+>GCF_023573625.1_01676
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLPLKTK
+GAFTETTAREKPKKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGQADRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001422.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001422.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e475070477912d496ee153f246c90b358a79aff2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001422.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01750
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG
+PRHRFERWERD
+>GCF_003691675.1_01457
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG
+PRHRFERWERD
+>GCF_005280335.1_01127
+MRSDPMSRATRPTEPAIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTASEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPVLDPRWRRTAVDPAPDAWLDSASG
+PRHRFERWERD
+>GCF_020097155.1_01052
+MARHHDDGARPRQTIAMIWAQTPDGVIGADGTMPWHLPEDLARFKALTLGHPVIMGRRTW
+DSFPARVRPLPGRTNIVVSRTLTATPEAGEAVRAAGAVVVPDFGAALTAADEADGLDLVW
+VIGGATLYEQALDVATRAEITVVDVDAPGDTHAPALDSRWRLVAADPSPDGWLDSAAGPR
+RRDERWERD
+>GCF_023573625.1_01679
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPLLDARWRRTAVEPAPDAWLDSASG
+PRHRFERWERD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001423.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001423.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4858281df08579c1f2a2ee7211e6afcfb556f0ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001423.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01751
+MAPTDSDQRLLSPQAVSFLALVALPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV
+GGLIAWNRRKRAQQGR
+>GCF_003691675.1_01458
+MAPTDSDQRLLSPQAVSFLALVALPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV
+GGLIAWNRRKRAQQGR
+>GCF_005280335.1_01126
+MAPTDPQDRLFTPQAVTFLALVACPVLAFVCAVMGLILVLQGKTIAGLVFLIVLTQVFAV
+GGLIAWNKRKRAQQGR
+>GCF_020097155.1_01051
+MADLPSDEKAPLLDAQAVTFLTLIAFPVLAFVCAVMGLILVLQGKVVAGVVFLVVLTQVF
+AAGGLITWNRRRRDRSGR
+>GCF_023573625.1_01680
+MAPTDSDQRLLSPQAVSFLALVVLPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV
+GGFIAWNKRKRAQQGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001424.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001424.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3db088e8250537402213a96c3a1c52ba50ad114b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001424.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01752
+MRSRAASLEGMTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARVHPVF
+FSTSNAGGPAPVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWD
+GIWIDAASTLRMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAG
+LVEWGTAMTYQAASGGGARHMRELLTQYAELGGAVRAELADPASAILEIDRKVIELQRGG
+LDSTQFGVPLGGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGA
+MRSHSQALTLKLTQDVPLDEVEQIIAADNEWVQVVPNTKEVTVTDLTPIAATGTLQIPVG
+RLRKLNMGPEYLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>GCF_003691675.1_01459
+MRSRAASLEGMTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARVHPVF
+FSTSNAGGPAPVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWD
+GIWIDAASTLRMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAG
+LVEWGTAMTYQAASGGGARHMRELLTQYAELGGAVRAELADPASAILEIDRKVIELQRGG
+LDSTQFGVPLGGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGA
+MRSHSQALTLKLTQDVPLDEVEQIIAADNEWVQVVPNTKEVTVTDLTPIAATGTLQIPVG
+RLRKLNMGPEYLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>GCF_005280335.1_01125
+MTSAAPPPSPPPDAAAVPTVGLIGWRGMVGSVLMQRMAEEGDFARIRPVFFSTSNAGGPA
+PTFEGLPGDAGPLQDAYDLNVLASLPVIVTAQGGDYTKDVYPRLRAAGWDGIWIDAASTL
+RMEDTSVIALDPVNRSVIDAALASGVKDFIGGNCTVSCMLMGLGGLFKAGLVEWGTAMTY
+QAASGGGARHMRELLTQYADLGGVVRDELADPASAILEIDRKVLELQRDGLDATQFGVPL
+GGSLIPWIDSDLGNGVSREEQKAFDETNKVLGLRGEDRIAFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEVEQIIAEDNEWVRLVANTKEASVAELTPIAATGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>GCF_020097155.1_01050
+MTSAAPAPVSPAAPAAVPTVGIVGWRGMVGSVLMQRMAEEGDFARIHPVFFSTSNAGRPA
+PVFEGMDGDAGTLQDAHDVEALKALPIIVTAQGGDYTKAVYPALRAAGWDGIWIDAASTL
+RMEDSSVIVLDPVNRSVIDAALASGTKDFIGGNCTVSCMLMGLGGLFREGLVEWGTAMTY
+QAASGGGARHMRELLTQYAALGGVVAEELADPSSAILEIDRKVLELQRGGLDASQFGVPL
+GGSLIPWIDSDLGNGVSREEQKAYDETNKVLGLTGDDRIPFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEITEIVADGTEWAQVVPNEKEASLRDLTPIAASGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPIRRMLMIATGNL
+>GCF_023573625.1_01681
+MTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARIHPVFFSTSNAGGPA
+PVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWDGIWIDAASTL
+RMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAGLVEWGTAMTY
+QAASGGGARHMRELLIQYAELGGAVRAELADPASAILEIDRKVIELQRDGLDSTQFGVPL
+GGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEVEQIIAADNEWVQVVPNTKEATVTDLTPIAATGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPVRRMLMIATGNL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001425.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001425.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1cafcc0a68d29e39c896f1b17ec80135b630497
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001425.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01753
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIHVLDGPLPGEGETPPAGDGARSADHEGEAVVVRIAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL
+>GCF_003691675.1_01460
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIHVLDGPLPGEGETPPAGDGARSADHEGEAVVVRIAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL
+>GCF_005280335.1_01124
+MSERLAEHTTTRVGGPARAWETARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIEVRAGDEAHGGDADDQDPAAGGDRAGEAVVVRVAAGHPWDDAVAWTVEH
+GLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVSLRAWDREAGQVVELGAEELEFDYR
+DSIIKRSMLETGAPSPRWIVLSIDLRLRRASGAAEPTAPVRYGQLASALDVAEGTHAPLA
+VVRREVLALRAAKGMVSDPQDPDTWSTGSYFTNPIVPAAVRASLPEGAPAFAAGRAADGT
+ELVKLSAAWLIDHAGFAKGFGLPDVAPREGGPDGRGADGAGLAGGRASVSTKHTLAMTNR
+GDASTEDVLTIARTVRDGVKARFGVDLHPEPMIIGTSL
+>GCF_020097155.1_01049
+MSERLSDHTTTRVGGPARAWVEARTEAEAVAAVRAADAAGEPLFVLGGGSNTLMADAGFE
+GTVVHMGFTGVEVLPAEGAADGAGDVVVRVAAGHVWDEAVAWTVEHGLAGVEALSGIPGS
+AGATPVQNVGAYGADVSQVLVSLRAFDRAAGQVVELSAEDLRFGYRDSVIKRSMFEDGSP
+SPRWIVLSIDLRLRRAEEGAEPTAPVRYAQLARALEVEEGADVSLAQVREHVLALRASKG
+MVSDAADHDTWSTGSYFTNPIVPATVRVTLPEGAPAFAAGTDEDGTPLVKLSAAWLIDHA
+GYGKGFGLPDAPRREGDADGSGPDGRGLAGGRAALSTKHTLAVTNRGGASTEDVLTVARA
+VRDGVKARFGVDLHHEPMIIGTRL
+>GCF_023573625.1_01682
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADSGFP
+GTVVRLAFEGIGVLDGPVPGEGEAPPVGDGARLADHEGEAVVVRVAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001426.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001426.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a9b7163bf6f6c7f7638113644108a2cfe64ba75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001426.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01754
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPSFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA
+>GCF_003691675.1_01461
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPSFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA
+>GCF_005280335.1_01123
+MSTAPRLSELSKGETIGTRTVPLTRADLVAYAGASGDHNPIHWSPSFAERVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGQTGDDGAPVPGATLQVVGKVG
+AVDEAAGTVRIDLDVTNPDAEKPRVLTKAQAVVRLAEPAPAAGESA
+>GCF_020097155.1_01048
+MRAQSARPVLAELAKGQSIGSRTVPLTRAGLVAYAAASGDHNPIHWNQAFAASVGLPGVI
+AHGMLTMGAAVQLVTDWAGDPGAVVDYQTRFTAMVPVADTTGQTDDAGAPVPGAVLEVSG
+AVGAIDAEAGTVRIDLTVNDPAQAKPRVLTKAQALVRLTRAVETPEETA
+>GCF_023573625.1_01683
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPTFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTVRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001427.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001427.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1da5ac4ac12a2bd05c24be5d4d86d3b72227ecc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001427.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01755
+MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA
+VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM
+VTTVTEIADLDGAAVSTVTSTLLVRGEES
+>GCF_003691675.1_01462
+MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA
+VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM
+VTTVTEIADLDGAAVSTVTSTLLVRGEES
+>GCF_005280335.1_01122
+MSVNPDVAGRSYPPAPPFQVGREAVRAFASAVQAQHPAHHDVEAARALGHADLLAPPTFA
+VVIAQRAEAAAVNDPEVGIDFSRVVHADERFVHHRPLVAGDEVVATVRIASVKSLGGNDM
+VTTVTEIADADGAPVSTVTSTLLVRGEES
+>GCF_020097155.1_01047
+MSETESLVGRTYPPAPPYQVGREAVRAFADAVQAAHPAHTDVDAARALGYADVVAPPTFA
+VVVAQRAEAAVVADPEAGIDFSRVVHADERFTHHRPIVAGDELTATVLIEAVKELGGNRM
+VTTVTEIVDAAGAPVSDVASTLLVRGEES
+>GCF_023573625.1_01684
+MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA
+VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM
+VTTVTEIADLDGAPVSTVTSTLLVRGEES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001429.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001429.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0533e3b471ddadcdd51d711cc5b3caf8c2bef426
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001429.fa
@@ -0,0 +1,66 @@
+>GCF_002008305.4_01759
+MSDILDPQTTAEVAPELAEAEQEATGTVPQVDAAPEAPAEPAAPEAPAEPAGPTFLDLGL
+DARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTD
+VTGRADTPQVLVLAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQ
+VVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFS
+ATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDG
+VIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAAR
+GLDVERISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQ
+VEEMAVPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAA
+LGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAA
+GNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEA
+AANAEINGRRLGLRKDTGRPTRAERDGEDRGERRGGFRKDRGERGERGGFRGDRDGGQRG
+GYRKDRDDRGSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR
+>GCF_003691675.1_01466
+MSDILDPQTTAEVAPELAEAEQEATGTVPQVDAAPEAPAEPAAPEAPAEPAGPTFLDLGL
+DARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTD
+VTGRADTPQVLVLAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQ
+VVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFS
+ATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDG
+VIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAAR
+GLDVERISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQ
+VEEMAVPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAA
+LGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAA
+GNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEA
+AANAEINGRRLGLRKDTGRPTRAERDGEDRGERRGGFRKDRGERGERGGFRGDRDGGQRG
+GYRKDRDDRGSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR
+>GCF_005280335.1_01118
+MSDALDPQTTPEAQVDAAELAEARQEAAEAAAPKAETPETAAAATETDSAPEAETAEEPE
+APAEPAGPTFLDLGLDARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTG
+AFALPALARLAETADVNGRADTPQVLVLAPTRELALQVADAFDSYAKHLEDVSVLAVYGG
+SPYGPQLAGLRRGAQVVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDR
+ILASTPDTKQTALFSATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWK
+LEAFTRILETEDHDGVIAFVRTRAGTEELAQKLNRAGFKAVAISGDIAQKQREKTVEDLK
+AGRVDILVATDVAARGLDVERISLVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPR
+ERFLLKQIERTTRQQVEEMAVPAVKDVNAARKRRFADGITRTLERASEEELAVFGEIVAA
+YVEEHDAEPSRVAAALGMMAQGGRPLLAKEQEIPTGPRGRKERDGGRDGGREHGTADGRG
+SRGPAREPAAGNATYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELP
+ADLTPAQLEAAANIEISGRRLGLRKDTGRPTRAERDGDERRGGFRKDRGERGGHGGHRGG
+FRKDRDERGFRGDREERGGFRGDRDDRGDRGGFRKDREDRGGFRKDREDRGDRGGFRKDR
+EDRGGFRKDRDERGGFRGGKAGGRKPRWGAQERSDRGPRR
+>GCF_020097155.1_01043
+MTPHETIPADDQAPVDLTEFDPELAETTAEAPAAEQDADDAEADAEPAGPTFLSLGLDAR
+VLAAVEDLGYQRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETQDVNG
+RSQAPQILALAPTRELALQVAEAFESYAKHLDDVSVLAVYGGAPYGPQLAGLRRGAQVVV
+GTPGRVIDHLERGNLDLSQLQTLVLDEADEMLRMGFAEEVDRILAETPDSKQTALFSATM
+PPAIRRISAQYLNDPEEVAVARQSTTGTNIRQRYLQIAHQWKFEAMTRILETEDHEGVIA
+FVRTRAGTDELAQRLNQAGFSAVAISGDVAQKQREKTVDDLKAGRVDILVATDVAARGLD
+VERISLVVNYDIPQDAESYVHRIGRTGRAGRSGDAVLFMTPRERFLLKQIERTTRQEVEE
+MQVPTVAQVNEARTRGVVAGIGRTLETASEADLDTYARMVAEYVEANDVDPARAAAALAL
+MAQGGRPLLTEADEVPAGGRVRRDRDRDDRRERGDRSERGDRDGRGSRGPRREPAAGNAT
+YWIGVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHALVELPADLTAAQLDAAANT
+EINGRRLNLRKDTGRPTRAERDGDGERGHRGPREDRGGFRRDRGDRGGFRRDRGERPERG
+GFRKDRDDRGPREDRGGFRHDRDDRGGRPGARKPRWGSDDRRDRGPRR
+>GCF_023573625.1_01688
+MSDILDPQTTAEAAPELAEAEQEATGTVPQVDAAEPAAPEAPAGPAGPTFLDLGLDARVL
+AAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTDVTGRA
+DTPQVLALAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQVVVGT
+PGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFSATMPP
+AIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDGVIAFV
+RTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAARGLDVE
+RISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQVEEMA
+VPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAALGMMA
+QGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAAGNATY
+WIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEAAANAE
+INGRRLGLRKDTGRPTRAERDGEDRGGFRKDRGERGERGGFRGDRDGGQRGGYRKDRDDR
+GSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001430.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001430.fa
new file mode 100644
index 0000000000000000000000000000000000000000..508e09144b8738bb3e4ea9ae3b95c537c33bc9ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001430.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01760
+MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
+>GCF_003691675.1_01467
+MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
+>GCF_005280335.1_01117
+MPQNSEDRPLARGLGRAAGRAARSFQESQRADDARLRAERARLAAEDEERLSRRREDRER
+GLAERDAAESDAGLVHPLLRIARMYWLALTVVLAVVAGAFVWNGMRARESGEPVVDPLTG
+IESVGVLGGATGQFTMGVTVALFAAAALWGWIGLLRRRRSAIGTLTFIALLLAAPAFLRA
+NGLLIVLAVIMLVGAALLWLPPVRSRLRR
+>GCF_020097155.1_01042
+MADNSAENSSDRIARAAGRAARAFREGQDAERIRREQARAEAPRTADADGSRATGLRERA
+VRAAAQAAERAEPLKERVGHAAGEAGRSFKENQAQDAARLRGVREQVRADDDAARAERQA
+ERERALDARDETEAGRVHPLLRLTRLWWLAVSLLLLGLATAFVYNGVRADRDGGEVIDPV
+TGLQSIGPLGGATGQYTVGGVLAALALVTLWGWVGLLRRRRASLGTLTTVAVLLAIPAVL
+RPNPLFIVLGAAMAIGAVLLWLPPVRSRVRR
+>GCF_023573625.1_01689
+MPQNSEDRPLARGLGRAAGRATQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLAARDAAESDAGLVHPLLKVARLYWLAVTVVLVGIAGAFIWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001431.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001431.fa
new file mode 100644
index 0000000000000000000000000000000000000000..399c34de2a2f7a6d8d13063aa7d3554e3f465f26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001431.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01761
+MTLTAFVNAHVVPVAAEPFDGALLVEDGRITALGPDVEAPDGAEVVDCEGRWVLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLAGQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
+>GCF_003691675.1_01468
+MTLTAFVNAHVVPVAAEPFDGALLVEDGRITALGPDVEAPDGAEVVDCEGRWVLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLAGQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
+>GCF_005280335.1_01116
+MTVTAFVNAHVVPVESAPFDGALIVEDGRITALGPDVAAPEGADVVDCEGKWLLPGFVDA
+HVHLGMHAEGEVGTTSDVNEMTDPVMAGVRAIDAVDPNEPGWRDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLKAQGYLARQEEAEREGKPFTKDPHMEALGQVLRREIPWRQHCHRTDDIATALRIADEF
+GYELVLDHGTEAHPVADLLAERGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVIPIDFLVYQAALSVKEGLDPETALRAITLNPAKVLGLDDRIGSLAVGKDADLVL
+WSGDPLDVMQRALRVWIGGRCVMEYDLATARPVVASARPVED
+>GCF_020097155.1_01041
+MSITAFTNVHVVPVESDPFDGVLLAEDGRISALGPDVEIPAGADVVDCGGRWLLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRALDAVDPNEPGWRDALAGGITTVNVNPGSG
+NPIGGQAVAMHTHGRTVDEMVLRAPSGVKSALGENPKTVYKEQGRTPSTRLGTALVIRRA
+FMEAQGYMARRTEAEADGKPFTKDPHMEALALVLERRIPWRQHCHRTDDVATALRIADEF
+GYDLVLDHGTEAHPLADVLAERGVPVLIGPLFTTKSKPELRGRSLRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALAVKEGLDRDTALRAITLNPAKVLGLADRIGSLAPGKDADLVL
+WSGDPLDVMQRALRVWIGGRPVMEYDAAAARPVVASARPAED
+>GCF_023573625.1_01690
+MTLTAFVNAHVVPVAAEPFDGTLLVEDGRITALGPDVEAPDGAEVVDCEGRWLLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLADQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001432.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001432.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a44f0e41bbcfeb556c36a3df6c655ba75e8d3c12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001432.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01762
+MTEQNVHEDPHATTPDTGAEDAAAHPQGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAAAGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
+>GCF_003691675.1_01469
+MTEQNVHEDPHATTPDTGAEDAAAHPRGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAAAGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
+>GCF_005280335.1_01115
+MTTHEQRPAGFGTRAVHAGQDLDEVYGAVVPPVHLSSTYAPVRVGELRRGYDYGRGTNPT
+RDALQTQLAALEAGVGEDGTPNALALTFASGLAAETALIMGAAEPGTTIVMGNDVYGGSY
+RLISKVLAKWGIRHAVVDMGDTAKVAAAVESAAAQGPVMVWLETPSNPLMKVSDIAAIAE
+VAHGHDALLVVDNTFATPYLQTPLALGADVVVHSTTKYIGGHSDVIGGALVIKDPELGAQ
+VQFQQFAAGAVNGPWDAYLTTRGLKTLGVRMDRHQANAQAVAEWLAGRPEVTQVLYPGLP
+DHPDHELAARQMRGFGGMVSFRLTGGAAAARTVAESTRLFQLAESLGGIESLMNYPAEMT
+HASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALEALAG
+>GCF_020097155.1_01040
+MTEQNAHEQPHDTAPTGPEATEGPAEGFGTRAVHAGQHLDEVYGAVVPPLHISSTYAPTA
+IGELRRGYDYGRGTNPTRDALQEQLAALEAGVDDAGTPKATGLTFASGLAAETALIMGAG
+QPGMTIVMGNDVYGGSYRLISRVLKPWGVDHAVVDMGEPEQVAAAVEQAAASGPVMVWLE
+TPSNPMMKISDVAAVAEAAHGRGAQLVVDNTFATPYLQNPIALGADVVVHSTTKYIGGHS
+DVIGGALVIPDAELAEKVKFQQFAAGAVNGPVDAYLTTRGLKTLGVRMDRHQANAQALAE
+WLTEQSAVSQVLYPGLPDHPGHELAKRQMRGFGGMVSVRFHGGAAAAKKVAESTRLFQLA
+ESLGGIESLMNYPAEMTHASVAGTELAVPDDLVRLSVGIEDASDLIADLEQAIAGLAG
+>GCF_023573625.1_01691
+MTEQNVHEDPHATTPDTGAEDAAAHPRGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAATGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001433.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001433.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf115e3af90b8552290d9bbf899b24d77b72d2ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001433.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01763
+MQYAENVLELIGHTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL
+LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV
+DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA
+GTGGTITGTGRYLKEVSADRPSGAVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD
+PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD
+SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQTDDDGATGAAGGAGTPV
+EALEHADAEPATRAGAPAEADRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT
+MNRYGVDALPVILEPRHDLRIGEVRGTVSSAALADALAEGRATAQTPVADVMGPVLPCLG
+ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA
+>GCF_003691675.1_01470
+MQYAENVLELIGHTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL
+LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV
+DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA
+GTGGTITGTGRYLKEVSADRPSGPVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD
+PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD
+SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQMDDDGATGAAGGAGTPV
+EVLEHADAEPATRAGAPAEADRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT
+MNRYGVDALPVILEPRHDLRIGEVRGTVSSAALADALAEGRATAQTPVADVMGPVLPCLG
+ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA
+>GCF_005280335.1_01114
+MQYAENVLELIGHTPLVKLNSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEDAEKAGK
+LAPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLTAYGAEIVVTPTSV
+APESEESYYGVANRLERDIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAHRVTHVVIGA
+GTGGTITGTGRYLKEVSADRESGPVRVIGADPSGSVYSGGTGRPYFVEGVGEDMWVDNYD
+PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARDLGPKDVMVIVLPD
+SGRGYLAKIFNDPWMDERGFDYDVQDTVLPEWARGRTRSAAPEADDDGAQGAAGGAGTPV
+EALEQADAAAGADAGQVADAPAEADRWAATAGELLAEKADLFPGSVPTLVTASPTTSVAD
+AVATMNRYGVDALPVVAEPRHDLRIGEVRGTVSAAALGEALAAGRVHPGTPVAEAMGPVL
+PCIGARTPLRAVARRLAQDPTLLVLSAGRVAGVVTLHDVLAHVTA
+>GCF_020097155.1_01039
+MGAVNEINPAPAHGQPRWAENVLDLIGRTPLVKLNRVTEGVEATVLVKVEYLNPGGSVKD
+RIALRMLEEAERDGKLAPGGTVVEPTSGNTGVGLALVAQQKGYRAVFVTPDKVGQEKRDV
+LTAYGAEIVVTPTSVEPSSDESYYGVANRLEKEIPGAFQPNQFFNPAAPASHYETTGPEI
+WEDTAGTVTHVVIGAGTGGTITGTGRYLKEVSADRASSPVRVIGADPEGSVYSGGTGRPY
+FVEGVGEDMWPGNYDPSVPDEVIAVSDDAAFEMTRRLAAEEGLLVGGSSGMAVVAGLQAA
+RELGPDDVMVIVLPDSGRGYLAKIFNDDWMDERGFHYAQEETVLPAWAQGRTRSAVATAP
+SDSREGARGGVGTPVEAPGEGSPQDGAATATPAPGSRWDASLADVLADKEDLFPGSVPTL
+VTASPDTTVADAVATLARYGVDALPVIAEPRHDLRINEVRGTVSAPALAAALAAGRVQPG
+SAVSDVMEPALPSVGAAMTLRAAARRLQEDPILLVMDAGIVQGVVTLHDVLVYATA
+>GCF_023573625.1_01692
+MQYAENVLELIGRTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL
+LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV
+DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA
+GTGGTITGTGRYLKEVSADRPSGPVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD
+PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD
+SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQTDDDGATGAAGGAGTPV
+EVLEHADAELATRAGAPAETDRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT
+MNRYGVDALPVILEPRHDLRIGEVRGTVSTAALADALAEGRATAQTPVADVMGPVLPCLG
+ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001436.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001436.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1c962d1dcdbc3f5bccb2f812abcfbe2ade81cf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001436.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01768
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMRASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR
+>GCF_003691675.1_01475
+MASDSTFDIVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR
+>GCF_005280335.1_01109
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEASMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQEVIAMLKDFEDADLQFVNFR
+>GCF_020097155.1_01035
+MASDSTFDVVSKVDKQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKANSEERVK
+AVLDVFESKLVKRGISLKSLDCGEPFASGKETRMEASIKEGIDQPTAKKITKLIRDEAPK
+SVKAVIQGDELRVSSKSRDDLQETIALLKTFEDADLQFINFR
+>GCF_023573625.1_01697
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001439.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0ee218e1c416d5bda1cfb46cce5c5ce450a1b3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001439.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01772
+MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAV
+LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ
+VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT
+EGPGHFWLMAGLGVLTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA
+ARWAGFGLIWLSLAVFTLDQLNASRLQRRAVRAGQGAHA
+>GCF_003691675.1_01479
+MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAV
+LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ
+VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT
+EGPGHFWLMAGLGVLTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA
+ARWAGFGLIWLSLAVFTLDQLNASRLQRRAVRAGQGAHA
+>GCF_005280335.1_01105
+MARVSPSPASRRPGVPPDAAAPDTGALPAVSPAPANDPRGLALGFTAYFLWGLLPLYMAR
+LAPAGAVEIVVVRVGFALVFCLVLLALMRRLRELRTSLATPARWGATALAAGFIGTNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWAAVGIAVAAVVVMSVAMGQ
+VPWIALGLAFSFGLYGFVKKRFPTPVHAVTTMTAETVVLLPAFAVGMVWLGQAGLLTTFT
+EGPAHFWLMAGLGVLTAVPLILFSAAAKALTLTTLGMLQYTAPILQFIVAVTVLGEQMPV
+ARWAGFGLIWVSLLVFTLDQVRVSRLHRRAARAGHGARA
+>GCF_020097155.1_01031
+MAQVSHSPSPSGPDAPRDGVPVEAAAPDTGALPTITPAPANDPRGLALGFAAYVIWGLLP
+LYMAATAPAGAVEIVVVRVVFALIFCLLLLAVMRRLPELRTALATRARWGSITLAAAFIA
+VNWLLYAHSVTSGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWIAVGIAVVAVVVMS
+VAMGQVPWIALGLAFTFGMYGFVKKRFPVPVHAVTTMTAETVVLLPAFAVGMVFLVQAGL
+LTTVSEGPGHFWMMAGLGVLTAVPLILFSAATQSLTLTTLGMLQYIAPIMQFLVAVAVLG
+EHMPAARWAGFALIWLSLVVFTLDQANASRVQRRAARAAGRART
+>GCF_023573625.1_01701
+MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAM
+LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ
+VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT
+EGPGHFWLMAGLGVFTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA
+ARWAGFGLIWLSLAVFTVDQLNASRLQRRPVRVRRGAHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001440.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001440.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2d35c68a92b5aa96a70e51e114b7bb7a25ab091
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001440.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01773
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDGEGLDR
+>GCF_003691675.1_01480
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDDEGPDR
+>GCF_005280335.1_01104
+MPAKPPAPVHLPAFQRLVPDLLGDAWAEDDGLSPADVEARLGQSPAAGQLGAGFMVPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDAEETVVWGLPVDNLALPDPLVW
+RRSSGAEAEEGDWQDEGGTFSEFITDLLAWTFEDPEDDDGRDER
+>GCF_020097155.1_01029
+MPAKPPAPVYLPGFQRLVPDLLGDTWAKDDGLAPADVEARLAESPAAEQLGTGFMVPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDEGETVVWGLPVDNLALPDPLVW
+RRDTGADAEEGDWQDEGGTFSEFITDLLVWTFEDPEDDAAEDAR
+>GCF_023573625.1_01702
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWAFEDPEDDDEGPDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001443.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001443.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24e403c1edcb414cb0aebea21b510af8ceec6474
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001443.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01776
+MTDTPTSPAPDSTSAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVVGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAADLAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR
+>GCF_003691675.1_01483
+MTGTPTSPAPASTPAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVVGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAAELAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR
+>GCF_005280335.1_01101
+MTAAPSSSPSESAPPPVVRRADVLISGGGPAGATAAAHLAAAGLDVVVLEKTAHPREKVC
+GDGLTPQAVRELQLLGVPHRGEPGDDGGWQVIRGLRLRAGERSVDVPWPETRSWPDYALT
+RTRRDFDALLADLARERGAEVRERHAVTSVVRDDAGRVCGLDAELIAPNGRKTGETARFE
+APVVLSCDGVSARAAVSAGIHRREDRPMGVAVRAYYTAGPAADGAVPAPPGDRGEWMESW
+LRLPDAQGRPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWSGALTPDWGI
+SEQTRVSKILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARIAADLA
+VQAHAAGSDAAADTVLSRYPVITQHLWGRHFALGARFARLIGDPRVMRASLGAGMAVPPL
+LRAVVKVMGNTVDPERGDAVDRAVRVLEALTPALTTADSAPLGRLAR
+>GCF_020097155.1_01025
+MTEHPTPAAAPVVRRADVLISGAGPAGATAAAHLAAAGLDVVVLEKSAFPREKVCGDGLT
+PQAVQEIRNLGIEHQGGPGDDGGWHAVRGLRLRAGERSVDVPWPATQSWPDYALTRTRKD
+LDALLADTARARGAEVRERHAVTGVTRDDAGRVDGLEAELIAENGRKTGERVRFAAPLVL
+ACDGVSARAAVSMDVHRRTDRPMGVAVRAYYTAGPVGADGAVPRPPGDRVDWMESWLRLP
+DEHGNPLPGYGWLFPLADGTVNVGLGILDTSPLFGKLDYRALLKQWSGALSEDWGISEET
+RTSKILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARIAADLAVQAH
+AAPNTPAADAVLARYPVITQHLWGRHFRLGTVFARLIGEPRVMRAALATGMAVPPLLRTV
+ARVMGNVVDPSGGDAVDRAVRILESVTPSLTTADAPGVGRLAR
+>GCF_023573625.1_01705
+MTGTPTSPAPASTPAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVIGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLRSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAADLAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001445.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001445.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f347d534875f0c3f600e0637a038169e4d40fdd2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001445.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01781
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVTSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLAGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLATGAAVAALLLVPARWRPLTTVLGAVVSSCTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLDTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD
+>GCF_003691675.1_01488
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVTSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLVGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLAMGAAVAALLLVPARWRPLTTVLGAVVSACTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLGTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD
+>GCF_005280335.1_01097
+MVAMPRTARPPLRVPSWPWWAALAACVAGVVLLYAALVWSSAGQVLEYQVFRAVEERYAD
+TVPDLASRVVRLLPLTLAAGVALASLGALAVPRWRRRGLLALAALIGANLTTQLLKAVLP
+RPEHAAGVPFSGGNSLPSGHMTLAAGAAVAALLLVPARWRPVTAVLGTAVSALTGAVAYT
+EAWHRPSDMAAAALVAAGWGLLAVPLALHEDGPRPAPRGARAAEIGMWTVGAVGMAAGLV
+LLWLTLEAPAAAGASPHPAAEPAGILLSAAPVVLCWGALATAFRRSRTA
+>GCF_020097155.1_01020
+MVGMTVTPPPGSPADAAARPVASSRRPRGSRWAWLLGLAAAAGVVALVHAVFVGTSGGQL
+LEYQVFHAVEDRWGTRSTGPAQRILTVLPVVLAGAATLAALACLIPRRTRRRGVVALVAL
+AGANVGTQALKESLGRPSFANHVPWAGGNSLPSGHTTLAASAAVAALLLVPARWRPAVAV
+VGAGATALTGSAAYLEAWHRPSDMAAAFGVAAFWAVLVAPWRRAADHRPRHASRAALAVE
+RMLWTLGVAGVLVGLGLAVATLGSPAVSADPHPLAAPAGALLSGTPALVLCAALLTGLRR
+AEQH
+>GCF_023573625.1_01710
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVSSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLAGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLATGAAVAALLLVPARWRPLTTVLGAVVSSCTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLDTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001446.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001446.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fcac9f86493dde34a6e9a90d803470758d822ee0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001446.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01782
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH
+GAEGETMDVGSPLITIGAAGESGEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGAARPTPAP
+TAGAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPL
+VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT
+ALLELRASLKAKDSENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHL
+GLAVQTDRGLMVPSVEHAEKLSADELTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPL
+GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASAFLT
+FVADCLHDPTAALARI
+>GCF_003691675.1_01489
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH
+GAEGETMDVGSPLITIGAAGESGEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGAARPTPAP
+TAGAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPL
+VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT
+ALLELRAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGQDEIVEVDGVHL
+GLAVQTDRGLMVPSVEHAEKLSADELTAAINDTVSRARAGRAAPAELTRGTFTLNNYGPL
+GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASAFLT
+FVADCLHDPTAALARI
+>GCF_005280335.1_01096
+MSNTFLLPDLGEGLTEADIVRWLVAEGDEVVVDQPIVEVETAKALVEVPSPYAGTVLTLH
+GAEGQTMEVGRPLITVGAAGESGEGSAPVAGTEAQAVPPATGEDAAEADRPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDEEASGAVLIGYGTSGHSATSRTRPSKRGRRGAGTTTAG
+GSGAASGQGEQAGQARAPRVTSPIVRKLAREQGVDVAALTGTGPDGLITRADVLSAAQGG
+DAPQAAAAPAAQPAATAGAASTVGAGSADARTGLAVVARTPISGVRKVIADQLSRSRREV
+PEVTAWLDVDVTALLELRAALKAKDAENAPSLLGLIARFTLAGLRRYPVMNARIEAGADG
+KDEIVEVDGVHLGLAVQTDRGLMVPSVEHAERLSADELTAAINETVTRAREGKAAPAELT
+RGTFTLNNYGPLGTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHR
+VTDGATASAFLTFVADCLNDPQSALARI
+>GCF_020097155.1_01019
+MSNTFLLPDLGEGLTEADIVRWLVAEGDEVAVDQPMVEVETAKALVEVPSPFAGTVLTLH
+GAEGETMEVGAPLITVGAVGESAGDAPPPSSAADAGTAPAADGAVPGALSYREEERAGVQ
+PKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHTATSRSRPSKRARGGAGTTQAAAGAAP
+AASGRAPRVTSPIVRKLARERGVDVATLTGTGPDGLITRADVLGAAGGASAPQDAQAPAP
+VQTAPSAAAQAPAVAAGATDARTGLAVVARTPISGVRKVIADQLSRSRREVPDVTAWLDV
+DVTALLELRAQLKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDG
+VHLGLAVQTDRGLMVPSVEHAEKMSADELTRAINDTVSRAREGRAAPAELTRGTFTLNNY
+GPLGTDGATPILNIPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASA
+FLTFVADCLNDPQAALARI
+>GCF_023573625.1_01711
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH
+GAEGETMDVGSPLITIGAAGESGEGSAPVAGTEALAVPPSTGADAAEAARPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGATRPTPAP
+TAWAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPS
+VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT
+ALLELRAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHL
+GLAVQTDRGLMVPSVEHAEKLSADELTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPL
+GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIMVRKVTEMTVTFDHRVTDGATASAFLT
+FVADCLHDPTAALARI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001447.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001447.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b81eb0d259287f33a0cf85017d0caa3c310f6f26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001447.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01783
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA
+>GCF_003691675.1_01490
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITLRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA
+>GCF_005280335.1_01095
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTKRFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPMTIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRAAIRLDDPVVFMEPKKMYWTK
+AELDLEDLRAEFEERWGRVEEKKEHGEAWARAAVVRAGSDVTLVSYGPSVPTCLAAARAA
+EEEGLSVEVVDLRTVNPLDEDTMVASVSKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA
+>GCF_020097155.1_01018
+MANLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTQRFGDERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQVASHVAKMRNRTKGGAPMPIVIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYLMLRSAIRLDDPVVFMEPKKMYWTK
+ADLDLDELRAEFDEQWARAQEKTAQGEAWARAAVVRQGADVTLVSYGPSVPTCLAAAQAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNVDRILDAIDDLNWDLDAEEARA
+>GCF_023573625.1_01712
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLREEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMTASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLGAEEARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001448.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4c4e7347e100a8568deade182e2d4f20714c9a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001448.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01784
+MSDPTPAVPGAARTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+EDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
+>GCF_003691675.1_01491
+MSDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+EHDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQITRDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
+>GCF_005280335.1_01094
+MSDPTPAVSGSARTDQAEARPNAGAAFGISLEEYLLPATRRIQLIGEDGTLLSPEEQGAE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+KQDWLFPTYRDTVAVIARGVPPLEVMVSYQGTWHQGYDPNEHHVSVQSTPLTTQLLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVDLCRQGQGPFLVEADTYRMQAHTN
+TDDPTRYREDAEVQEWEARDPLRRMTAYLESTGALTEEVSAEIAQAAEDVAKDLRDAMNA
+EAELDPLELFDHVYSVQTPQLAAQRAQLTEELSRSENQEA
+>GCF_020097155.1_01017
+MTSTRPGPATPDTRTEAAAAFGITLEEYLLPAARRIQLISPEGELLPAEEQGTAPGHEYP
+LPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLGQDDWLF
+PTYRDTVAVIARGVAPLDVMVSFQGTWHQGYDPKEHRVSVQSTPLTTQLLHAVGMAKAAR
+LRGEDVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFLVQNNKFAISVPFAKQSAAPSL
+AHKAVGYGLAGERVDGNDLAALLAVLGRAVDLCREGKGPFLVEADTYRMQAHTNTDDPTR
+YREDSEVKEWEVRDPLRRMTAYLESTGALTAEVSTSIAKDAEDVAQQLRDAMNADVELDP
+LELFDHVYSVQTPQLAAQRAQLAEELSRSENKEA
+>GCF_023573625.1_01713
+MSDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVSLG
+EDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001449.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001449.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1f391ec05fff9c8a87b530fe5960246e21508d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001449.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01785
+MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDTADLRR
+VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD
+>GCF_003691675.1_01492
+MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDTADLRR
+VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD
+>GCF_005280335.1_01093
+MPTEALDRVDRAIVRALTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTLKLRQHNWRELRATLLAIPEVWHVSLVGGNVDVILLVRARDTADLRR
+VIFDELQTLPGVVDTQTYMVFDDHASGQTLPPEDPAA
+>GCF_020097155.1_01016
+MSTSSPLDRVDRAIVRELSQDGRLSVAALAERVHVSRAHCYSRLNRLQNSGVITGFSARV
+DPVKTGFTASAHVMLKLRQHDWRELRAALLAIPEVWHVSLVGGNMDVVLLVRARDTADLR
+HVIFEKLQSLPAVVDTQTYMIFDDHASGQTMPPEEGADAPRTPTAFG
+>GCF_023573625.1_01714
+MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDPADLRR
+VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001450.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001450.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acecfa0ef6a10ea4d2e5444438b358d080dd90fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001450.fa
@@ -0,0 +1,49 @@
+>GCF_002008305.4_01787
+MASRTASPPPSPAPSPAAPRGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPESLKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVVATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVAVGGAASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN
+>GCF_003691675.1_01494
+MASRTASPPPSPAPSPAAARGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPEALKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVAATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVTVGGGASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN
+>GCF_005280335.1_01089
+MGQEFRGGLATFLAMSYIVVLNPLILSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWA
+RHPFAVAAGLGVSAFVSITIATTPGLTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPE
+ALKSGIVVGIGLFIALIGLVNAGFVRRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLL
+TAVLVIRKVRGAILIGIVAATILANVLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTA
+PDLHLLGSVDLFGAFTSVGGLMASLLVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPD
+LNRVLAADALAVAVGGGASGSAHQIFVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLI
+HLVPFEAVAPALVVVGFMMCQHVVQIDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVA
+YAVIRTGQGRGREVHPLLWFVALAFVAYFGLGVVRASLGLN
+>GCF_020097155.1_01015
+MSSRTTGATPPGTAPSNPASPAGPRSGLDRFFGISALGSSVGQEVRGGIATFLAMSYIVV
+LNPLILSGPDSTGAVLGIPRVAAATALVAAVATLAMGLWARHPFALASGLGVNAFLAITV
+ATTPGLTWPDVMGLVVIAGLVMVVLVATGFRTAVFNAVPEALKTAIVVGIGLFIALIGLV
+NAGFVRRLPDAAGTTVPVGLGTGGELAGWPVLVFIVGLLVTAILVIRNVRGAILVGIVTA
+TVLANILEAVFHIGPSVGADGSHNPTGWALVAPSLPEWAAPDLSLLGSARPFGAFEAVGG
+LMGALLVFAILLSVFFDAMGSTVGLAREAGSMDEHGNVPRLNRVLMVDALAVTGGGAASA
+SAGQIYVESGTGIGEGARTGLASVVTGLMFVATIFLTPLIHLVPFEAVAPALVVVGFMMC
+SQVVRIDWTDWGAALPAFLTFILMPFTYSIANGIGAGMIAYAVIRTGQGRAREVHPLLWV
+VAAAFVLYFGMGVFRGILGLA
+>GCF_023573625.1_01716
+MASRTASPPPSPAPSPAAPRGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPEALKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVAATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVTVGGGASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001451.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001451.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c59ae7cf59aef2987bb3cf534fa77e94fdcd7f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001451.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_01798
+MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVRAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQAAHWREPAFDEELYACHLSATAAES
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVGLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYAAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATARIV
+>GCF_003691675.1_01495
+MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REISTGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQAAHWREPAFEEELYACHLSATAAQS
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYEAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATARID
+>GCF_005280335.1_01078
+MPQTTSHAPVPPSVSAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLRAAIFGEIKARTVETDRSVPSRRDGWWYFARTKEGAEYPVHCRVPAADTGDLEADW
+TPPVVTPDAPLEGEQVILDGNAEAEGHPFFALGGLHISPDSTRVAYAVDHTGDERFTLRV
+REIATGEDLPDVVENIAHGVRFDRSGARVLYTVWDDSWRPYQVKAHVLGTDPAQDQLLYE
+ESDPGMWTGFTGTADRTQLLIGVGNSEVSETHVVDLPESPDAPLPAPRLLIPRAWGMLAD
+VEPVTGADGVRRLLVVHDRTVARQDAADAGADAPAPNGMLSLVAEADVADRGAWRTVVPH
+REDVKVDGVMVTLTHAALAVRRETTPRVVVAPLDSVLAGEAADWREPAFEEELYACHLAS
+TAAESPFLRLAYTSWISPARVLDVSAATGEVHLRRETEVPGYDPSLYVAERVWAPASEPS
+SVTGEPVRIPVTVIRRKDVAADGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVYAVA
+HVRGGGELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACTGGSAGGLLMGA
+VLNLAPELYRACLAVVPFVDALTSILDPELPLSALEWEEWGNPIEDPEVYAAMRDYTPYE
+NVRAVDYPTIAAVTSLHDTRVLYVEPAKWVARLRRTVTSDQATPLAEGGAPVLLRTEMDG
+GHGGASGRYQGWEDTAWEYAFLLTALGATQRVD
+>GCF_020097155.1_01013
+MYETSLPTPPRAAARPTARTVHGETFTDDFEWMRAKTEQEVLDHLQAENAYTEAATADQA
+DLRAAIYGEIKAHTVETDQSVPARRDGWWYFVRTVEGKDYAVHCRVPAQDTGDALADWTP
+PVVPADAALPGEQVILDGNAEAAGHPFFSLGGMHISPDGALAAYAVDLAGDERYTLRVRE
+IATGTDLPDVVRNIAPGVRFDRSGTRLIYTVWDETWRPYQVRVHTLGTDAAEDAVLYEES
+DPGMWTGFDASADRTQLLIGVGNSEVSETWAVDLPVDASPLPAPRVLVPRTARMLADVEP
+FDMDGRRRLLIVHDRLADGTTAPNGMLSIVDEADVADRDAWRPVVPHADDVRVDGVLVTR
+THVGLAVRRDTTPRVLIAPLEGLREGSAPAWTEPSFDEELYMCRLAGVNLDSPFLRLSYA
+SWTTPARVLDVVAATGEVRLRREVEVPGFDREDYVAERWWAPASEPSSLTGEQVRIPLTV
+IRRRDVAQDGTAPAVVYGYGSYEMSMDPVFGVARLSLLDRGVVYVVAHVRGGGELGRAWY
+EDGKKAAKRHSFTDFVDATRFVADSGWVDPARIACTGGSAGGLLMGAVLNLAPELYRACL
+AVVPFVDALTSILDPDLPLSALEWEEWGNPIEDPEVYATMKAYTPYENVRAVDYPAIAAV
+TSLNDTRVLYVEPAKWVAQLRRTVTSDQTTPIAAGGSPILLRTEMDGGHGGASGRYQGWE
+DTAWEYAFLLTALGATARVD
+>GCF_023573625.1_01717
+MPQTTTHAPVPPSVAAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARETGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVTELDAVLAGQAAHWREPAFDEELYACHLSATAAES
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYAAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQARPLADGGAPVLLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATRRVV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001452.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001452.fa
new file mode 100644
index 0000000000000000000000000000000000000000..650fd3a2cc7b3aee760e6377cdb791df9a406a78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001452.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01799
+MSTPQPDAARPDRDRLPEQVSDLFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
+>GCF_003691675.1_01496
+MSTPQPDAARPDRDRLPEQVSDVFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
+>GCF_005280335.1_01074
+MTETTPAAARDRLPEKVSDLFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPTVRI
+AFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQRIR
+GRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHVVAD
+LTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVALGAV
+NEAVDHERLEEVALEYAADINAQSPQALRMLKFAFNLADDGMAGQQVFAGEATRMAYMTD
+EAVEGRDAFLQKRDPDWSAFPYHF
+>GCF_020097155.1_01010
+MPAVRFSNDSIPGGIHVTNENAVVATTVLSMTESTPHHDRDRLPEKVSDVFDPTRWRVVE
+GFEFEDMTYHRQVERDADGRWVRDLPTVRIAFDRPEVRNAFRPGTVDELYRALDHARMTP
+DVGTVLLTGNGPSPKDGGHAFCSGGDQRIRGRDGYRYAEGETAETIDPARAGRLHILEVQ
+RLMRNSPKVVIAVVNGWAAGGGHSLHVVADLTLASRQHGKFKQTDATVGSFDAGYGSALL
+AREVGQKRAREIFFTAREYSAEEMVAMGAVNEAVDHERLEEVALEYAADINRQSPQAIRM
+LKFAFNLPDDGMAGQQVFAGEATRMAYMTDEAVEGRDAFLQKRDPDWSAFSYYF
+>GCF_023573625.1_01720
+MSTPQPDAARPDRDRLPEQVSDIFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYHALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEKMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001454.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001454.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33dcf1abbf53625b21721c55717282e285d6dd0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001454.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01801
+MPATADALARATDALAAAFDGGAPVELTADGAVLPRPEARDSRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDDAGPRLISLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVTAAVAPDGPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVPAADGARAFLTEDTGILSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAALEAHPGVAAAHVAGVPDPEWGARLCAAVVPVRPAAAPDEAVLRAHVRAALGA
+AAVPKTWLLLEALPLLSTGKTDRQALAARFTAG
+>GCF_003691675.1_01498
+MPATADALARATDALAAAFDGGDPVELTADGAVLPRPEARDSRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDNAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVTAAVAPDGPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVTAVDGARAFLTEDTGILSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVADPEWGQRLCAAVVPADPASPVGENALRAHIRDALGA
+AAVPKTWLALDALPLLSTGKTDRQALAARFTAAG
+>GCF_005280335.1_01072
+MPATADALARATDALAAAFDGGDPVELTADGAVLPRPEARDPRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGIAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDHAGPRLVSLVPTQLARLLAADTDPAGRTALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAVAVAPDGPDAPPRVRLAGPMV
+AVGYLDDPARTAAHFVPAADGARAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVADPEWGQRLCAAVVPADPASPVGENALRAHIRDALGA
+AAVPKTWLALDALPLLSTGKTDRQALAARFAAAG
+>GCF_020097155.1_01008
+MPATADALARATDALAAAFDGGAPVELTADGAVLPRPEARDPRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDDAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAVAVAPDGPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVPAADGARAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVPDPEWGARLCAAVVPAHPAAAPDEAVLRAHVRAALGA
+VAVPKTWLVLDALPLLSTGKTDRQALAARFTAG
+>GCF_023573625.1_01722
+MPATADALARATDALAAAFDGGAPVELTADGAALPRPEARDPRRCGDPDAVAVVRSSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDDAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAAAVAPDDPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVTAADGTRAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVPDPEWGARLCAAVVPAHEAAAPDEAVLRAHVRAALGA
+AAVPKTWLVLEALPLLSTGKTDRQALAARFTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001455.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001455.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9424f4e9e01dc6a8ce40bcc95e6bf098098e5946
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001455.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01802
+MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAARVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG
+LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGIVYAITFTLGALL
+>GCF_003691675.1_01499
+MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGRFHLGAALLALVVSLALQVGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFASFGLAGLAGLGLILLSGHWWFLLV
+GVACVVAAWYYTGGKKPYGYLGLGEVFVFVFFGLVAVLGTTYTQAGQVSGLAWAGAIGCG
+LISTALLMANNIRDIPTDRAVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPWL
+LLVPLGGLLAIRPVRTVLRAQDRRALIPVLRATGVIGIVYALTFTLGVLL
+>GCF_005280335.1_01071
+MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSRLAWAGAIGCG
+LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRTLIPVLRATGVIGIVYALTFTLGVLL
+>GCF_020097155.1_01007
+MAATLSQWVAAARLRTLPMAVAPVIVGSAAAHALDQFRPGRALLALVVSLALQIGVNYAN
+DYSDGIRGTDDARVGPFRLTVSGLVPAKTVKHAAFACFGVAAVAGLALVALSGTWWLLIV
+GVASIVAAWYYTGGKKPYGYMGLGEVFVFVFFGLVAVLGTTYTQALAVNGLAWAGAVGCG
+LISTALLMANNIRDIPTDREVGKMTLAARIGDGPARASYVAMLAVAVVLPLLFTGAHPWL
+WLVLAAGAVAVKPCLTVLHAHERAALIPVLKATGIVGVVYAAAFALGVAL
+>GCF_023573625.1_01723
+MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG
+LISTALLMVNNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGLVYAITFTLGVLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001456.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001456.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82d2c05deade502c22b1b6f675322a86f18a80c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001456.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01803
+MRIFFYGLVRVVLFVALWALFYYVMDLWMIFAVIAAAILAFAVSYLFLDRLRTGATEDLS
+AAWEGRPGRRGRTETADADAEDAYTEGRFRE
+>GCF_003691675.1_01500
+MRILYYGLLRVALFFVLWWVGLQLGLGMVMATLAAAILTFAVSYLFLGRLRRGATQDLSA
+AWEGRPGRRGRTEAADAEAEDAYTQGRFRE
+>GCF_005280335.1_01070
+MRILYYGLLRVALFFVLWWVGLQLGLGMVMATLAAAILTFAVSYLFLGRLRRGATQDLSA
+AWEGRPGRRGRTEAADAEAEDAYTEGRFRE
+>GCF_020097155.1_01006
+MRLFLYGLVRVVLFFVIWALCYYVFGLGMLFSTLAAVILTFAVSYLFLTRLRLDASTDLQ
+NAWEGRPSRRGRTEAADAAAEDAYTDGRFPG
+>GCF_023573625.1_01724
+MRIFFYGLVRVVVFVALWALFYYVMDLGMIFGVIAATILTFAVSYLFLGRLRAGATEDLS
+AAWEGRPGRRGRTETADADAEDAYTEGRFRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001457.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001457.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f31714f70f31898fba6c43ac0f8fa2ed359068c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001457.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01804
+MGRFIIPAAIILAGLTLYALFEALLTPAREVRSLPKAAWVAVIVLVPLVGPLLWLLLGRA
+RPAGAGGRPAPRPTGAPDDDEAFLRSLRVQRRQVAREQDLDRREAELRAREEELRRRREQ
+GDDDADPDGDGPRA
+>GCF_003691675.1_01501
+MGRYIIPAAIVLVGLTLYALFEALMTPAHEVRSLPKWGWVAVVVLLPLVGPLLWLVLGRA
+RVARGTARPAPRGPGAPDDDEAFLRSLRVQRRQAEREQELDRRDAELKAREEELRRRRER
+GEEPDADDPDAPTP
+>GCF_005280335.1_01069
+MGRYIIPAAIVLVGLTLYALFEALMTPAHEVRSLPKWGWVAVVVLLPLVGPLLWLVLGRA
+RVARGTARPAPRGPGAPDDDEAFLRSLRVQRCQAEREQELDRRDAELKAREEELRRRRER
+GEEPDADDPDAPTP
+>GCF_020097155.1_01005
+MARILVPTAILLVALTLFALFDALLTPAGRHRGMPKWAWIPTVLLLPLAGPLLWLFLGRP
+VPLFSGRTAAPASRPASPDDDDEFLRTLRVQRAQTERARNLDRREAELRAREEELRRRRE
+RGEDDATGEPDADA
+>GCF_023573625.1_01725
+MGRFIIPAAIILAGLTLYALFEALLTPAREVRSLPKAAWVAVIVLVPLVGPLLWLLLGRA
+RPAGAGGRTAPRPSGAPDDDEAFLRSLRVQRRQDAREQDLDRREAELRAREEELRRRREQ
+GDDDADPDGDGPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001458.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23990ecfa6ce9edd52a3aee092c1f5d5e97c277d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001458.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01807
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRAVGFFTRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>GCF_003691675.1_01504
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFLRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>GCF_005280335.1_01067
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLAGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>GCF_020097155.1_01002
+MQDNRFAEIALDGSLLAAAPVAFLAGLISFLSPCVLPLVPGYLGYVSGLGGAALDGARRG
+RVALGAALFVLGFTVVFMVMNILFAQVAFRILRDLSWVMQLLGVLVILMGVVFMGGLRWF
+QTERKVHVKPAAGLTGAPLLGMTFGLGWAPCIGPTLAAVFALSYTQDSSSVARAALLAFV
+YCLGLGLPFVLISFGVERGMRALGFFRRHRRGVMVFGGAVLILLGAVMVTGLWTQWMVQL
+QTWFQNEWVMPL
+>GCF_023573625.1_01728
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001460.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001460.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e8a62bc5c408abd86870b25ec386952a155ee4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001460.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01811
+MTADLPAATARVQLLVKPGCHLCAEAEATVVQVCDARGEAWEAVDGAAHPDLLERFVDEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRA
+>GCF_003691675.1_01508
+MTADLPAATARVQLLVKPGCHLCAEAEATVAQVCDARGEAWEAVDGAAHPALLERFADEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRA
+>GCF_005280335.1_01063
+MSTLLPASAARVQLLVKPGCHLCEDAAATVAQVCGARGEAWEAVDGAAHPDLLERFVDEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRP
+>GCF_020097155.1_00998
+MAAMMTPPASAARVQLLVKPGCHLCAEAEAVVAEVCDARGTAWERVDGPAHPDLLETYAE
+EVPVLFVDGVQRDFWRVDAQRLGRLLDGPAA
+>GCF_023573625.1_01732
+MTADLPAATARVQLLVKPGCHLCAEAEAAVAQVCDARGEAWEAVDGAAHPALLERFADEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001461.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..531ca2103a161846ce4e7266ab7906be4c9f90cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001461.fa
@@ -0,0 +1,10 @@
+>GCF_002008305.4_01812
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>GCF_003691675.1_01509
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>GCF_005280335.1_01062
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>GCF_020097155.1_00997
+MGSVIKKRRKRMAKKKHRKLLRKTRHQRRNKK
+>GCF_023573625.1_01733
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001462.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001462.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c851c03b6e0a68a22b3949490c9a83d6cf23049
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001462.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01813
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLV
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANEIGGSAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLEAFAPDVLVSQHGCDGHLTDPLADLRLSVDGQRQLAFDVGDWADRFAY
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVRSEIPAAWIEHVRALTADELTGDMS
+VHEGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
+>GCF_003691675.1_01510
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLV
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANEIGGSAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLQAFAPDVLVSQHGCDGHRTDPLADLRLSVDGQRQLAFDVGDWADRFAH
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVKSEIPAAWIEHVRTLTADELTGDMS
+VHEGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
+>GCF_005280335.1_01061
+MSTTSQRPAPTPAAVVWDPSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVSIIEP
+PVATDAQLALVHDPDYIAAVRRASEAASDEDAPFGLGTEDCPVFPDLHEASARIAGGTLA
+AAEAVWSGQVRRAVNFAGGMHHAARAKASGFCIYNDCALAIQRLLDLGAERVVYLDVDAH
+HGDGTQAIFYDDPRVMTISVHETGISLFPGTGFANEIGGPDAQGTAVNVAVPPRTGDAGF
+LRAVHAVVPQLLQGFDPDVIVSQHGCDGHHADPLADLRLSVDGQRQLAFDIGDWAEKFAD
+GRWVATGGGGYNPLRVVPRVWTHLTAAVLQTPIPVKAEIPQSWIEHARTLTAEELTGDMS
+LHEGDESERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRRELFPLHGLDPWFD
+>GCF_020097155.1_00996
+MTSATSDCSQPAPSAVVWDPSLLKYRFSAQHPMAPLRLDLTHRLASSLGLLDAEHVRILQ
+PPVATDEQLATVHDPAFIAAVRAASREDAEADEPHGLGSEDCPTFPDLHESAARIAGGSL
+VAAEAVWSGEVSRAVNVAGGMHHAARAKASGFCIYNDCAVAIQRLLDLGAERVAYVDVDA
+HHGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANETGGPGAEGTAVNVALPPGTGDAG
+FLRAVHAVVPQLLGAFQPDVLVTQHGADAHRGDPLADLRLSVDGQRQLAFDLGDWADRYA
+HGRWLATGGGGYNHVRVVPRAWTHLIGAVTGQPVPSSTPVPESWLEHVRSLTPDDLEGDM
+SLFEGAEEDRYPLTMTEDADVWWRSWEVGYDPADPVDQTIMATRREVFPIHGLDPWFD
+>GCF_023573625.1_01734
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLA
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSVFYDDPRVLTISLHETGISLFPGTGFANEIGGAAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLEAFAPDVLVSQHGCDGHRTDPLADLRLTVDGQRQLAFDVGDWADRFAH
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVKSEIPAAWIEHVRALTADELTGDMS
+VHVGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001464.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001464.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3fed1dc0d9904064d962e72b423501344139dc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001464.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01815
+MADTPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA
+DATDSEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR
+IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESHVRSKY
+GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP
+>GCF_003691675.1_01512
+MADTPQRTDPNAPVLLVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA
+DATDSEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR
+IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESKVRSKY
+GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP
+>GCF_005280335.1_01059
+MADPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAIERDPVLVQRFAPSLTHVVEAD
+ATDPEALRQLGAQDFSTAVVGVGTSIEASVLITANLVDLEIQHIWVKAISEAHGTILKRI
+GANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLGESNVRSKYG
+VTVVGVKTPGEDFTYAQPDTRVGARDTLIVSGHTDLIDRFAARP
+>GCF_020097155.1_00994
+MADQPRTDPNAPVLVIGLGRFGAATAEELVTQGREVLAIERDPVLAQRFAPTLTHVVEAD
+ATDAEALRQLGAQDFDVAVVGVGTSIEASVLITANLVDLEIPHIWVKAISDAHGTILKRI
+GAQHIIFPEKDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPTETVGFTLEESNVRQKYG
+VTIVGVKTPGEDFTYAQPHTRVGPRDTLIVSGHTDLIDRFAARP
+>GCF_023573625.1_01736
+MADTPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA
+DATDPEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR
+IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESHVRSKY
+GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001465.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001465.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12546bb3c9b38d2eb951acc28dbef98d403c9849
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001465.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01816
+MKLTILGLGTMTGAILAGALDAGAVRAEDVTATTRSAASAEKAAAQHGVTVTSQERDERA
+NHAAVAEADIVLVGVKPKDMVATLTDLASSLRPETVVVSVAAGVTAATMAAVLPAGQPIV
+RTMPNTPLTVGSGVVGVAPGPGVTEEQATAVRALFEGSGLVVPVAEEQLSAVVATAGSAP
+AYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQQEGARAGALRKAVMSPNGTT
+EKAVEAFLDGGMGDLVNRAMDAAAQRDREMAEEFGA
+>GCF_003691675.1_01513
+MKLTILGLGTMTGAILAGALEAGAVRAEDVTATTRSAASAEKAAAQHGVTVTSQERDERA
+NHAAVAEADIVLVGVKPKGMVATLTDLAPSLRPETVVVSVAAGVTAATMAAVLPAGQPIV
+RTMPNTPLTVGSGVVGVAPGPGVTEEQTTAVRALFEGSGLVVPVAEEQLSAVVATAGSAP
+AYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQQEGARAEALRKAVMSPNGTT
+EKAVEAFLDGGMGDLVNRAMDAAAQRDKEMAEEFGA
+>GCF_005280335.1_01054
+MKLTILGLGTMTGAILTGAIEAGAVRAEDVRATTRSAASAERARGRHPGVEVLAAEEDAH
+ANKRAVEGADVVLLGVKPKDIAATAAEVAQALGTDTTVVSVAAGVRAETIAAALREGQPL
+VRTMPNTPLTVGSGVVGVAPARGVTDAQTQAVEALFAGSGLVVRVAEEQLAAVVAAAGSA
+PAYVFLLAESIAKHAEQLGLDRANAEAMAAATVKGAGLMLQNGIREGDQTAEDLRRGVMS
+PGGTTEQAIRTFQEGGFERLVADAMDAAARRDEEMGRELAG
+>GCF_020097155.1_00992
+MTAQPRIAILGLGSMTGAILTGLLAASVTTPERVVATTRTAASAQAKGNRFPGVRVLSGE
+QDVDANLTAVAEADVVLLGVKPKDIVVTARQIAPALRPEAVVVSVAAGVRAETLAGALPE
+GQPLVRTMPNTPLTVGSGVVGVAPAAGVTADQRALVESLFSGSGVVVPVSEEQLPAVVAA
+SGSAPAYVFLLAEAIAAHAVELGLSAEAAEAMAAATVKGAGAMLVDAVTSGEQTAEGLRR
+AVMSPNGTTERAIAAFEDGGFAGLVADAMDAAARRDEEMGREFGA
+>GCF_023573625.1_01737
+MKLTILGLGTMTGAILAGALDAGAVRAEDVTATTRSAASAEKAAAQHGVTVTSQERDERA
+NHAAVAEADIVLVGVKPKDMVATLTDLAPSLRPETVVVSVAAGVTAATMAAVLPAGQPIV
+RTMPNTPLTVGSGVVGVAPGPGVTEEQATAVRALFEGSGLVVPVAEEQLSAVVATAGSAP
+AYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQQEGARAEALRKAVMSPNGTT
+EKAVEAFLDGGMGDLVNRAMDAAAQRDKEMAEEFGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001466.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001466.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7f4f5589356c260409945965fa899fb0fbfe252
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001466.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01817
+MADATAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGREAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGNDSGKDDHLVPGEGTQRVAETLRHLAAEGLAGA
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTDHHDDDGVPRPTTKETDRP
+>GCF_003691675.1_01514
+MPDSTAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGRKAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGDDSGKDDHLVPGEGTQPVAETLRHLATAGLAGT
+VCVEVGTRGVEYAGQREEMLAASLAFAREHLAAGGTDHHHDGGVLRPTTKEMDRP
+>GCF_005280335.1_01053
+MAGSTAHLAPAPRFGSDIPVTLSSSSVFPLGTQDVFATAQDLGYDGVEVMVTHNAWSQDA
+DRLKRLSARHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAPVVVAHPPFRWQ
+GTYASGFAEGIHEIMADTGVVIAVENMYPWRAHGREATMYLPHWDPMPEPYEHVCWDFSH
+AAIAREDSLEALRRLGSRVRHIHLTDGNDSGKDDHLVPGEGTQKVAESVRHLAADGFAGT
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTKDDDGAPGA
+>GCF_020097155.1_00991
+MTGPSGAGSRPWDPHGRHLEPPLVSTAHLAPAPRFGAEIPVTLSSSSVFPLGTQDVFATA
+ADLGYDGVEVMVTHNATSQDARALARLSERTGMRIDSIHAPTLLFTQQVWGSAWSKIVRS
+VELARAVGAVTVVAHPPFRWQGSYASQFARRTAEIMEATGVVIAVENMYPWRAHGRDLTM
+YLPHWDPVPEPYEHVTWDFSHAAIAREDSLANIRGLGGRLRHVHLTDGVDGTKDAHLVPG
+EGTQNVAESLRFLGREGLAGTVCVEVGTRGVEYAGQREEKLSASLAFAREHLGQNDQSGR
+HES
+>GCF_023573625.1_01738
+MPDSTAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGREAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGNDSGKDDHLVPGEGTQRVAETLRHLAAEGLAGA
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTDHHDDDGVPRPTTKETDRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001467.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001467.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c267fd72c604c346e87bcacd06beb4579e14f4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001467.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01818
+MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV
+REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV
+RRWQGWDAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVPEDPPSPKAVK
+KLRKHVEKRLEEAYTVFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL
+HLWVNRLAAMTIAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTRDGLPGVGHVNLNPDTLLPGLSLGVR
+>GCF_003691675.1_01515
+MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV
+REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV
+RRWQGWGAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVLEDPPSPKAVK
+KLRKHVEKRLEEAYTAFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL
+HLWVNRLAAMTVAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTRDGRPGVGHVNLNPDTLLPGLSLGVR
+>GCF_005280335.1_01052
+MRLGVLDIGSNTVHLLLVDAHPGARPSAYAEHKRSLPLIRYQDAEGAITEEGQHELVDFI
+REAVAFAEEHRAEDMISFCTSAIRESANGAEVLARVDREAGVHLAELSGDQESAMTYFAV
+RRWQGWDAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWLPEDPPSPKAVK
+KLRKHVEKRLEEAFAAFPPVEAPVAVTATSKTFRSLARLTGAAPSAAGPYVKRHLRADDL
+HLWVNRLAAMTAAERADLPGVSEVRAPQVLAGAIVALAAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTHDGLPGVGHVNLNTDTLLPGLRLGVR
+>GCF_020097155.1_00990
+MRLGVLDIGSNTVHLLLVEARAGARPTPYAEHKRSLPLIRYLDESGAINEEGQDELVGFI
+GEAVAFAEEHRAEDMISFCTSAIREAENGPAVLARVEAETGVHLSELSGEQEASMTYFAV
+RRWQGWGVGSILNFDIGGGSFEIAYGQDELPSHAVSLPLGAGRLTRERLPDDPPSPKAVK
+KLHKHVSREIEAVFADFPPLEAPYVVTATSKTFRSLARLTGAAPSAAGPYVKRHLRADDL
+QLWVNRLAAMTWEQRAELPGVSEVRAPQVLAGALVALAAMRTFGVAQLEICPWALREGLI
+LNRLDALMLEGHLTREDGLGVGHVNLNTDSLLPGLSLGVR
+>GCF_023573625.1_01739
+MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV
+REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV
+RRWQGWGAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVLEDPPSPKAVN
+KLRKHVEKRLEEAYTAFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL
+HLWVNRLAAMTVAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTRDGRPGVGHVNLNPDTLLPGLSLGVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001468.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001468.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4564804243cca0ae9a71cad4a6a11fc1018167e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001468.fa
@@ -0,0 +1,85 @@
+>GCF_002008305.4_01819
+MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA
+WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS
+FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED
+KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE
+VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY
+APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE
+LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY
+LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTIVA
+KDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV
+DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ
+ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYITDGVTNITVPRGRRPE
+ELTAEEAYQLLADKRAKGPATRGGAKKPAARKAPAKKTTARKKA
+>GCF_003691675.1_01516
+MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA
+WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS
+FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED
+KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE
+VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY
+APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE
+LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY
+LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTVVA
+RDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV
+DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ
+ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRQPE
+ELTAEEAYQLLADKRAKGPATRGGAKKPAARKAPAKKTTARKKA
+>GCF_005280335.1_01051
+MPTTPASVTASVPEGKKLVIVESPAKSKSIAKYLNAVGEGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPFGKFAVDTENGFAPYYVVHPDKKKKVTELKRELKDAVALYLATDADREGEAIA
+WHLLDTLKPKVPVYRMTFGEITKEGVRRGLENIRELDTHLVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAAYWGVEGTFTVAPGAQAADAVGSS
+FTARLSTVDGERVATGRDFDDAGALKASAGKKVTHLDEAAASSLAQGLRGADFTVDAVED
+KPYTRRPAAPFTTSTLQQEASRKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGQDAVPAQPRVYAKRNESAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRFSATAQDGRAAQFSASGTVITFKGFLDAYEEGKDAE
+TEDEKAEAKDRRLPQVAEGERLVGEPIEATGHETSPPARYTEASIVAELERREIGRPSTY
+APTISTIMDRGYVSKRGNALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE
+LGREAWLQTFYFGAPASETGKGVEGLQQVVENLGEIDARAVNSLPITDEITLRVGQYGPY
+LEKPLPADAEAGSTPPRANVPEELAPDELTPAKAEELFATAKPSERELGTDPETGRAVVA
+KDGRYGPYVTEVIPEMTEEQLQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFSSMSV
+DTVTLEEALRLMSLPRVVGADAEGEVITAQNGRFGPYLKKGTDSRSLESEDQIFTITQEQ
+ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRQPE
+ELTAEEAYQLLADKRAKGPATRKAPARKPAARKAPAKKSAPKKKA
+>GCF_020097155.1_00989
+MPTASASTSSSVPQGKKLVIVESPAKSKSIAKYLNAVGEGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPYGKFAVDTEHGFTPYYVVHPDKKKKVTELKRELKDAEALYLATDADREGEAIA
+WHLLDTLKPKVPVYRMTFGEITKEGVRRGLENIRELDTHLVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVAAQYWGVEGTFTVGPDAKADGAAGSS
+FTARLSTVDGARVATGRDFDDAGRLKESAGKKVAHLDEAAAASLAEGLDGKDFTVDSVED
+KPYTRRPAAPFTTSTLQQEASRKLRMSARVTMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGQESVPTQPRVYAKRTENAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRFSAQAEDGRTAQFAASGTVITFKGFLDAYEEGRDAE
+PEEEKDAKDRRLPQVAEGETLTGAPIQPTGHETTPPARYTEASIVAELERREIGRPSTYA
+PTISTIMDRGYVSKRGSALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGEL
+AREAWLQTFYFGADSADTQKGVEGLKHVVENLGEIDARQVNSLPVTEDITLRVGQYGPYL
+ERRLPEGAAEGTAPERANVPEDLAPDELTPAKAEELMAAGGADERELGVDPETGRTVVAK
+DGRYGPYVTEVIPEMGEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFKTMSVD
+TVTLEQALQLMSLPRIVGADAEGEVITAQNGRFGPYLKKGTDSRSLESEDQIFTVTQEQA
+LEIYAQPKQRGRGTAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRAPEE
+LTAEEAYQLLADKRAKGSAKKPAAKKPAARKPAAKKTTTSTTTRKKA
+>GCF_023573625.1_01740
+MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA
+WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS
+FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED
+KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE
+VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY
+APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE
+LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY
+LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTVVA
+RDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV
+DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ
+ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRDRQPE
+ELTAEEAYQLLADKRAKGPATRGGAKKPATRKAPAKKTTARKKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001469.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001469.fa
new file mode 100644
index 0000000000000000000000000000000000000000..569084e9ace6c41c6a44ec772dd47ddbf9c91336
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001469.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01820
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRER
+LEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTADADTAPWDARPRSWVASGMQAWFIQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVA
+EELTQAVDEALGTAWAAAVARRDRLTAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG
+>GCF_003691675.1_01517
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATRALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRHGTRGLAAAVGAWLLGDSVPAADLDAALPRLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRDR
+LEDRVRLAAGDLLAPVTGERFDLVVSNPPFVITPRTDPGAPVLIYRDGGREGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTANADTAPWDARPRSWVAPGMQAWFLQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVA
+EELTQPVDEALGAAWAAAVARRDRLAAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG
+>GCF_005280335.1_01049
+MKPPAPSPSSPSLPAPRLTPATAAALDADLAALPYTTAAVEELLGPVATAALDREHAEPA
+RRVVARVLTAAPGDHTQALYDDGALGSGARPLEAGIGSPAARRALAALVSVWMLGDAADA
+ADVAAALPALGLDGAREAGLVAEEGGGTVRGTVDLSPYEADEPGRMWVASDQTALQRRGP
+LPEDHVLGIGRASLTLAGATQRRPVACALDVGVGCGIQTLHLLAHAEHVTATDLSERALE
+FTRFNLLLNADVLGLDRERLEDRVRLAAGDMLAPVAGERFDLVVSNPPFVITPRTDPDAP
+VLTYRDGGREGDRIVAELVAALPAHLTEGGTAQLLANWEIPAGAAAIPAAAAASADGDLA
+DTAGPAPWDARPRSWIAPGMQGWIIQRDAQDPAGYAETWLQDSSLELDPHRYEAAYRGYL
+EDFAARGVAGVGFGHVWLRRPVDDGAQGRAWTVAEELTQPVDEALGAAWAAAVARRDRLA
+AGAPDGAGDPALAALRGLHLRVAEDVSEERHGRFGAEHPEVILARQGAGFRRTARLDTAT
+AGVLSASDGELSVGQLVGAVAALLELDDAGRAGLLAAIRELYEDGFLVERAED
+>GCF_020097155.1_00988
+MSLPAPHLSPAAAAALAADLTALPYTTDVVETLLGPVATAALDREHAVAARRVVAGVLAA
+PAARDAAAASRPLAAVVGAFMLGEPVPAADLAAALPALGLDGAVEAGLVVLDGADTGAER
+ARATVDLSPYAADEPGPMWVASDQTALQRRGPLPEDHVLGIGRASLTLAGATQRRPVARA
+LDLGVGCGVQTLHLLAHAEHVTATDLSERALDFTRFNLLLNADVLRLDRERLEDRVRLAA
+GDLLGPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRLVAELIAALPEHLVE
+GGTAQLLANWEIPAGAAEIPAGAAEVPAGDDAPPAWDARPRSWVGPGMQAWFVQRDRQDP
+AGYAETWLQDSSLELDPAAYEAAYRGYLDDFAARGVTGVGFGHVWLRRPAADRSQGRAWT
+VAEELTQPLDEALGTAWAAAVARRDRLAAGPEAGATDAVVTGDPALAALRGLHLRVAEDV
+TEERHSRFGAEHPEVILARQGAGFRRTARLDTATAGVLSASDGELSVGQLVGAVAALLEL
+DDAGRAGLLAAVRELHEDGFLLEA
+>GCF_023573625.1_01741
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRER
+LEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGGEGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTADADTAPWDARPRSWVAPGMQAWLLQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRAWVVA
+EELTQPVDEALGTAWAAAVARRDRLAAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001470.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001470.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38d08857d9267c22b24b7ce536e1ca8f4819c3c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001470.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01821
+MSTAALSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYVRGTREHPAFRDLEVKWSDGSAADFPRLSVKLKPELVAFGAPERVTVDADGVVGTGER
+LTPAQVDALVAERAGSANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCEAPTSALRNCADPACTTLEVRCAACAVDDPERRCPVCVHH
+PHPAERTEA
+>GCF_003691675.1_01518
+MSTAPLSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYMRGTREHPAFRDLEVKWSDGSAADFPRLSVKVKPELVAFGAPERVTVDADGIVGTGER
+LTPVQVDALVAERAGTANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCHAPTSALRNCADPACTTLEVRCAACAVDDLEHRCPFCAHR
+PHPAERTEA
+>GCF_005280335.1_01048
+MSPAPVSRIALYYRFAPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+QYVKGTREHPALKDLEVKWSDGSAADFPRLSVKVRPELVAFGVPERITVDEHGVVGTGER
+LTPERLEALVAERAGTENPVRFLDGRNTVEAQIGRFDGAVVPAAHTTRDLLAAVDSGSLD
+HLRDAPLVTYCTGGVRCEVLSALLKDRGFREVYQLDGGIVRYGEAFGDAGLWRGELAVFD
+RRIALRFSEDAETIGRCVTCEAPTSALRNCSDPACTTLEVRCAACAAADPDRRCPVCTER
+SAA
+>GCF_020097155.1_00987
+MTAAAPAAPTPLPAPGGPGRIALYYRFTPLADPEAVRLWQRTLAVSLGLAGRIIVSPQGI
+NGTVGGPAEAVKRYVRGTREHPAFRGLEVTWSDGSAADFPRLSVKVRPELVAFGAPERIR
+VDEHGVVGTGEHLPADQLHALVAERAAQGRPVRFLDGRNSVEAAIGRFEDAVIPAAHTTR
+DLLEAVDSGSLDHLKDQPVVTYCTGGVRCEVLSALLKDRGFSEVYQLDGGIVRYGEAHGD
+AGLWHGRLAVFDRRLSLAFTDGAETLGRCVTCGGATSHLANCADPACTTLQVRCPDCVAA
+HPDHVCPRCLERTPA
+>GCF_023573625.1_01742
+MSTAALSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYVRGTREHPAFRDLEVKWSDGSAADFPRLSVKLKPELVAFGAPERVTVDADGVVGTGER
+LTPAQVDALVAERAGSANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCEAPTSALRNCADPACTTLEVRCAACAVDDPERRCPVCVHH
+PHPAERTEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001473.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001473.fa
new file mode 100644
index 0000000000000000000000000000000000000000..733b56b53408f600c631cb06be94ed3f54756c2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001473.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01824
+MTRGRAPARGERGSGTVSVLGTAALGAGLLLAVAALGQASATGSRAAGAADLAALAASDA
+RRGLSDHEPCVLAGRTAERNGAAVVACEVREDGTVRVAVELARAPLPAATADAVAGPPRS
+QAPGAASVAPPEDPPEAPPPEPSVEASAGTR
+>GCF_003691675.1_01521
+MTRGRAPVRGERGSGTVSVLGTAALGAGLLLAVAALGQASVTGARAAGAADLAALAASDA
+RRGLSDHEPCVLAGRTAERNGAAVVACEAREDGTVRVAVELARAPLPAATADAVAGPPRS
+QAPGAGSADPPEAPPPEPSVEASAGTR
+>GCF_005280335.1_01045
+MTGRAPGGVPRGAASETGSGTVSVLGTAALGAGLLLAVAALGQASVAGAQAAGAADLAAL
+AASDARRGLSAGEPCLVAGQTAARNRAVVVECEVRENGTVRVSVERGRAPLPPALAAAVA
+GPPRLQAPQAVPEDPLPDASSPSTPTPSSVPPSVSPDPSATTGTR
+>GCF_020097155.1_00984
+MSGTATALGTALLGAGLLTGVLAVGHASATAARASGAADLAALAASDARRGLGAVPDAGV
+LEPCPLAEESARRNGAEVTECVLLPDGSVRVAVVIAADPLPASTAVAVAGPPVGPRGPVA
+GPGRDDAPEDAPDTPGAPPEAATP
+>GCF_023573625.1_01745
+MTRGRAPARGERGSGTVSVLGTAALGAGLLLAVAALGQASVTGSRAAGAADLAALAASDA
+RRGLSDHEPCVLAGRTAERNGAAVVACEVREDGTVRVAVELARAPLPAATADAVAGPPRS
+QAPGAASVAPPEAPPEPSLEASAGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001474.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001474.fa
new file mode 100644
index 0000000000000000000000000000000000000000..989c99f950c54db311a1497b25a886c784272515
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001474.fa
@@ -0,0 +1,19 @@
+>GCF_002008305.4_01825
+MTEHPTSASPSGRRTGARTAGRPRALRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV
+QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTVEGGWVTVEVVQPGPGPL
+AWAEVLTLTAHAAAPDQRPGTPAAGPEDRS
+>GCF_003691675.1_01522
+MTEHPTSAPPSARRTGARTAGRPRGLRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV
+QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTVEGGWVTVEVVQPGPGPL
+AWAEALTLTAHAAAPEQRPGTPAAGPEDRS
+>GCF_005280335.1_01044
+MTAEYAVLLPVIAFVLAAVLLAGAAAVQQVRGQDAATAAARILARGDGEAEARRAVARMA
+GDDAALAHTADGGWVAVEVSQPGPGPLAWAEALTLTARAAAPQQHPGAAVDPDGGRT
+>GCF_020097155.1_00983
+MADLPAEAPRPGRLRGARAGASGTVAFRDAERGEGERGAVTAEYAVLLPAAVAVLVAVLL
+AGVAAVHQVRAQDAAASAARILARGDAESLARDAVGRMAGGDAALEARTAEGWVTVTVTR
+PGPGPLAAVTLSAEAVAPVQATSPTPPGRTPGITAPTGEAAP
+>GCF_023573625.1_01746
+MTEHPTSASPSGRRTGARTAGWPRALRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV
+QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTIKGGWVTVEVVQPGPGPL
+AWAEALTLTAHAAAPDQRPGTPAAGPEDRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001476.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98ed88c6346f16bf140fcb250d93589ca0e740c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001476.fa
@@ -0,0 +1,37 @@
+>GCF_002008305.4_01827
+MLVGALRRWAALVAAGLTEEQAWRETACTLPACGSGPGEAGAACCAHHRARRRAEALAWD
+VPASHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEAD
+VDAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWL
+AGRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATA
+ALLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADER
+AAEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG
+>GCF_003691675.1_01524
+MSPTTATGPARRSHAGRAVALLPWRAGRVPPEEETEVLIGVLRRWAALVAAGLTEEQAWR
+ETACTLPACGSEPSEAGTACCAHHHARRRAEALAWDVPAAHAPTGEAARRGGTLPWRTPA
+RDPGWALVDAALAAGARAGAAPAAVARRLAHSLEADVDAARARRSAAAGPGATSRLLQWL
+PLGGLGLAWLLGTSPGDLVRSPFGAVVAAVGLLFWLAGRSWTRLLLRAAAREPAAVGAAV
+VLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATAALLLWGRDWDEAWVGLDTDPVWAE
+TAARLRPLHRSGMAGARTLAETAAAVRQQTRRADERAAEELAVRLVMPLGLCLLPAFVCW
+GVVPVVMALLGAGPG
+>GCF_005280335.1_01042
+MSTAAPEDATEELVVVLRRWAALVSAGLTEEAAWRETVRMLPDDDGHARHAARLRAERLA
+WDAAGDLSTGRDAPDVRGLRRDEHPPGDTHDASPDRSRRRWCPPWRTPPPDPGWALVDAA
+LAAGARAGAAPAVVVRRLAESLEADVDAARARRSAAAGPAATARLLQWLPLGGVGLAWLL
+GSSPWETVSTPFGAVVAAVGLLFWLAGRSWTRLLLRSAAREPAALTAPVVLDVLAALLGA
+GRSLPAALDDLARTLPGARGLRVTSALLLWGRGWDEAWAGIGEETVWAEAAARLRPLHRS
+GMAGARTLAESAAAARQQGRRADERAAEELAVRLVMPLGLCLLPAFVCWGVIPVVMALLG
+AGA
+>GCF_020097155.1_00981
+MIALPGRAEERAEERAQEVVEALRRWAGLTAAGMTPAEAWTAVAQASSPCGRPTPGCCPR
+HEALRRAALARWGGPGRGAEGGQPRPGERSPWDLADAALAAAARAGASFSRTAARLADAL
+EADVDASRARRTAAAGPRATARLLSWLPVGGLGLAWLLGMGPADLLATGFGWVLLVLGGV
+LTAAGRAWTRLALRRGARPLGEASPGVVVDVAAVLLGAGRSLPAALDDVSAHLPGAADLR
+VVAVLLRWGADWDEAWAPVTEEPRWAALGERLRPLHRTGMAGEAVLHQTAAALRQETRRA
+DERGAEELAVRLVVPLGLCQLPAFVCWGVAPMALALLGAR
+>GCF_023573625.1_01748
+MLVGVLRRWAALVSAGLTEEQAWRETACTLPACGPGPSEAGTACCAHHRARRRAEALAWD
+VPASHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEAD
+VDAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWL
+AGRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRTTA
+TLLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADER
+AAEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001477.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001477.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4df0abb2771cc9d9ddc40620647a9a611f398e23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001477.fa
@@ -0,0 +1,44 @@
+>GCF_002008305.4_01828
+MRPFVPAAPARPPRGRRRRPAPPEGGRRFPWPRTGPAEPERTQVAAPPLAAPAAGPDGLD
+AAVVRRRVAEARASAADGAEPPLAPLIAEALDVPIDDPRVAALVDELDGFGPLAPWVRTP
+GVTDVLVDGAGAVWTDGDGGLVRRPDRLDPETARALAVRLLHRAGRRLDAAVPLADARVG
+GVRVHAVLPPVSGGGTLLSLRIPAAATPSLAALADGWPDGALWADALEALVRDRATVLVS
+GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVVALQCRAANAEGAGEVGLAE
+LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA
+GWRPETVAAQARAGVDAVLHIARDGHGRHPVELAVPDLRADGFALLPALTWRPGTEATGG
+RTVEGPGMPALAARLAGRSGR
+>GCF_003691675.1_01525
+MRPFVPAAPARPPRGRRRRPAPPEGSRRFPWPRTDPAEPERTQVAAPPLAAPAAGPGGLD
+AAVVRRRVAEARASAADGAEPPLAPLIAEALDAPIDDPRVAALVDELDGFGPLAPWVRTP
+GVTDVLVDGAGAVWTDGDEGLVRRPGRLDPETARALAVRMLHRAGRRLDAAVPLADARVG
+GVRVHAVLPPVSGGGTLLSLRIPAATTPSLAALADGWPDGALWADALEALVRDRATVLVS
+GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVIALQCRAANAEGAGEVGLAE
+LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA
+GWRPETVAAQARAGVDAVLHVARDGHGRHPVELAVPDPRADGFALLPALTWRPGTEATGG
+RTVEGPGVPALAARLAGRSGR
+>GCF_005280335.1_01041
+MRRRVAEARAAAAEGQEPALAPLVAEAIGVSATDPRVAALVDELDGFGPLAGWVRAPGVT
+DVLVDGSGAVWTDGAEGLLRRPQRLDPHAAQALAMRLVHRAGRRLDAAVPLADARVDGVR
+VHAVLPPVSGGGTLLSLRIPAARTPSLAELAAGWPDGDLWGEALEALVRDRASVLVSGAT
+GTGKTTLLAAALGCVPGDERILTVEDTAEAAPEHPHVVALQCRAANAEGAGAVGLAELIR
+HALRMRPDRLVVGECRGAEVADFLTALNTGHQGAWGTLHANGAADVPARLTAMGSLAGWG
+PDTVAAQARAGVDAVVHLVRDRHGRHPVELAVPDPDARGFALLPALTWTPGPGPGDGSTA
+EGPGLRALAARLAGRGSR
+>GCF_020097155.1_00980
+MPAWVPDAPRPARRPALLPAGLSLPAPLLPDLRRVGRRRPGSDRGEPAHVGPDPDARLRR
+AVAEAQARADPHAPPPLRETVSRALADLAAEDGDTPPSGCPRPAGLRDPDAVLEELVGFG
+PLAPWVRRTGVTDVLVDAAGSVWTDGVEGLVRRPLILPEPTARALAVRLIGLAGRRLDPA
+CPVADARVDGVRVHAVLPPVSGGGTVLSLRVPAAEPPSLDALAADWPDGERWRDAVVALV
+RGRASVLVSGATGTGKTTLLAAALGLAGADERIVLVEDTAEAAPAHPHVISLQARAPTAD
+GAGEVTLAELIRQALRMRPDRLVVGECRGPEVADLLTALNTGHQGAWGTLHANAAADVPA
+RLAAMGALAGWSASAVAAQARAGVDAVLHVRRDGRGRHPVELAVPAPAAHPDAPLSVLPA
+LTWDGGGTRAGPGLEVLEARLSGRGHG
+>GCF_023573625.1_01749
+MRPFVPAAPARPPRGRRSRLAPPEVGRRFPWPRTGAAEPERTQVAAPPLAAPAAGPCGLD
+VAAVRRRVAEARASAADGAEPPLAPLIAEALDAPIDDPRVAALVDELDGFGPLAPWVRTP
+GVTDVLVDGVGAVWTDGDEGLVRRPGRLDPETAGALAVRLLHRAGRRLDAAVPLADARVG
+GVRVHAVLPPVSGGGTLLSLRIPAATTPSLAALADGWPDGALWADALEALVRDRATVLVS
+GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVVALQCRAANAEGAGEVGLAE
+LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA
+GWRPETVAAQARAGVDAVLHLARDGHGRHPVELAVPDPRADGFALLPALTWRPGTEAAGG
+RTIEGPGVPALAARLAGRSGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001478.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001478.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8daac9abc9432cc2ce6bba7dacb451c2af5375d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001478.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01829
+MPETPASPRPTSRDAVGTSDASLAGARDQLADLVARWGAAPADAPGHHDPVSLTTVPPEA
+VPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAERVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLGLLGWDVPWDDSRVRDARTHEILRD
+>GCF_003691675.1_01526
+MPETPASPHPTSRDAAGTSDASLAGAREQLADLVARWGAPPAEAPGHHDPASLTTVPPEA
+VPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAGRVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLALLGWDVPWDDSRVRDARTHRILRD
+>GCF_005280335.1_01040
+MAAVRDRLAALVERHGVPADQAPRDALTEIPASAVSTWGFDWPRAQRARPSAVLILFGSL
+DDVPAHHADDRVHPDVDVLLTQRAATLRTHAGQIAFPGGRVDPEDADVVATALREAEEET
+DLDPDGVEVLGVLPPVPVVVSGHVVHPVIGWWRDPSRVAVVDQAEAAAVFRMPVGDLVDP
+ANRCRVARPGGRRGETPGFLVGERLVWGFTAALLDRILTLLDWDTPWDSGRVIDAHTHAP
+LRG
+>GCF_020097155.1_00979
+MSIPPLPPSSPSSARADLQRIVAEHGVAPVAGDDEAGLTTIPASSVRVWGFDWPQAARPR
+ASAVLILVGELDDVPAAHDGRACGVSPAVDVLLTQRAAGLRTHAGQVAFPGGGVEAQDAD
+VVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGYVVHPVIGWWRDPSRVAVVDHNEAT
+AVFRVPVADLAAPANRVRVRRPGGRRGETPGFLAGDRLVWGFTAALLSRVLELAGWDEPW
+AGAPLIDAGSRAVLEG
+>GCF_023573625.1_01750
+MPETPASPRPTSRDAAGTSEASLTGARDQLADLVARWGTAPADAPGHHDPASLTTIPPEA
+VPMWGFEWPRSGDPRPSAVLILFGALDDVPARHDAERVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDADVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLALLGWDVPWDDSRVRDARTHEILRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001479.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001479.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84217a23cf8e8f09678f8aae02bad4c80c3fd68d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001479.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01831
+METEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTEFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
+>GCF_003691675.1_01528
+MEPEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
+>GCF_005280335.1_01037
+MDAEQADTPTGESRLALVRRARRIDRELAATYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAAAMAGASEAELQGLVRSTGFYRNKASAILRLSQELVERHGGEVP
+GRLEDLVALPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTQDTDPVKVEHAVAE
+LFPRRDWTMLSHRLIFHGRRICHARRPACGACPIARWCPSYGEGETDPEKARALLSYELK
+PGREELLALMRAGLSRRELRARGHGLDA
+>GCF_020097155.1_00977
+MAPADTTTPTGETPLALTRRARRIDRALAEAYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAVTPALFARFPDAVAMAGADEVELQELVRPTGFYKNKASAVLRLSRELVERFDGEVP
+DRLEDLVTLPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTEETDPVKVEHAVAA
+LFPPRDWTMLSHHLVFHGRRVCHARKPACGACPIARWCPSYGAGETEPEAARALLSYELK
+PGREELLARMRAGATRRQLRDEGWTLEA
+>GCF_023573625.1_01752
+METESTGTPTGETRPALVRRARRINRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGAGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001480.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001480.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b019ea8379de46bb05d47d7b998c7f3e37aed50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001480.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01832
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTDVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDAQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAATHHDTFDLHPESDVFWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM
+KWGRHIPDEYDLSSLRVLGSVGEAINPEAWRWYHEVIGAGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA
+>GCF_003691675.1_01529
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTDVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDGQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAVTHHDTFDLHPESDVFWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM
+KWGRHIPDEYDLSSLRVLGSVGEAINPEAWRWYHEVIGAGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA
+>GCF_005280335.1_01036
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTEVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGNGDRVAVHFEGEPGDTRTYTYAELASEVRRTANAFE
+SLGVAKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSADALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDEALSAPGHSVQHVLVVRRNEAEVSLVEGRDLWWHDVVPAQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQTAATHHDTFDLHPETDVYWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTCM
+KWGRQIPDEYDLSSLRVLGTVGEAINPEAWRWYHEVIGGGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQTPVPGVTLEVVDEIGEPMKDTSAGFLVAREPWPSMLRGIWGNPERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAADETTGEAVVAFVLLTEEAAAAGRDVAEVEEELRQHVGRDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDATTLADPTVMQRIVETLAPGA
+>GCF_020097155.1_00976
+MDETRATYPPSEQFAAQAVAGADLYEEAAADRLAYWARRAREHLHWEQDFTQVLDWSDAP
+FARWFADGTTNAAYNALDRHVEAGRGDRTAIVFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVAKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSADALRSRVDDAEAKLVVT
+ADGSFRRGRPSMLKPAVDQALSAEGHTVEHVVVVRRNEADVDWTEGRDLWWHDVVPTASD
+EHEVVWHEAEHPLFILYTSGTTGKPKGILHTTGGYLVQTAATHHDTFDLHADTDVYWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKHGVTILYTAPTAIRTFM
+KWGRQIPDGYDLSSLRVLGTVGEAINPEAWRWFHDVIGGGRCPIVDTWWQTETGAHMLTP
+LPGVTELKPGSAQRPVPGVVLEVVDELGEPMEGSTAPGFLVAREPWPSMLRGIWGDPERF
+KETYWSRFPGMYFAGDGAQYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPKVAE
+SAVVGAADETTGEAVVAFVLLTEEATAAGEDVEAVQEELRQHVGKDIGPIAKPKRVLVVP
+ELPKTRSGKIMRRLLKDVAEGRRPGDATTLADPTVMDRITEAVGS
+>GCF_023573625.1_01753
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAKDRLAYWARRAREVLHWEQDFTDVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDGQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAVTHHDTFDLHPESDVFWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM
+KWGRHIPDEYDLSSLRVLGSVGEAINPEAWLWYHEVIGAGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001483.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001483.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82f76a3d2e136de788faa7d159a046e604eb9bf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001483.fa
@@ -0,0 +1,54 @@
+>GCF_002008305.4_01835
+MSSTVSAPATAPKRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGDDPETFLMGDYLQVADDPSPSFDVVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPV
+ATTRKEL
+>GCF_003691675.1_01532
+MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPT
+AATRKEL
+>GCF_005280335.1_01033
+MSSTVSAPAAAPTRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTESVGWWQVLICVVIAVYYAAIIGWA
+IMYTWFSVDQRWGADPETFMMGEFLQVSETPNPTFDVVSGVFWPMLAVWVITLLIMGFGV
+RRGVAMASMIGIPLLVVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLKKRTNLTSSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VADVAGSGIGLAFIAFPTLISQAPVGALIGVLFFGSLVLAGFTSLISILEVVISAVKDKL
+GWGRWTATIIVVGLAGVVSMALFSTTSGLHMLDTMDAFANNFGIVGAALVSVLLVTGVLG
+SARRVTAHLNAVSSFKLGRGYVLLIGVLMPIVLAYIWLSWIMKVISEGYGGYPGDFLGVY
+GWGVAIGSVVLAVVLSLIPWSRKSNLYAEEMETEIHGDLIPHNAVPEGTTPTGAIPLVPA
+DHTRKEL
+>GCF_020097155.1_00974
+MSTSTGATAAPSRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYEHGGGAFVIPYLVA
+LLTAGIPLLFLDYAIGHRFRGSAPMAFRRMSRWTEAIGWWQVLICAVIGVYYAAIIAWSI
+MYTWFSLDQRWGDDPEGFLFSTYLQQVKDPNPSFDIVPGVFWPMVAVWGVLLLIMGLGIR
+RGVALASMIGIPLLVVMFVVLVIISLTLPGAMQGLDALFTPNWAALKEPGVWIAAYGQIF
+FSLSVGFGIMITYASYLKKRTNLTASGLVVGFSNSGFEILAGIGVFSALGFMAQASGVQV
+SEVAGSGIGLAFIAFPTLITQAPAGALIGVLFFASLVIAGFTSLISILEVVVSAVKDKLG
+WGRWTAVLVVVGISAVISISLFSTTTGVAMLDTMDAFANNFGIVGAALVAVIAVMWIARR
+GGELVAHLNSVSSFRVGRVYRILVGVVMPVLLGWMWIEWIRENAATPYGGYPTDFLAVYG
+WGLAIGSVVLAVLLSLIPWSHKSSLHAEESVNEIDHTAPVASKES
+>GCF_023573625.1_01756
+MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPA
+ATTRKEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001485.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001485.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25f132587d942bc9019bd7c384035bd65dffc815
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001485.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01838
+MSADPAGLLLPVPGQEEDLTRQWLDRRFRQVRPARPGSSVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADSCPWYGPEPSQWARTFGTTDRRRARQHVVAAVRELHDEAGV
+LLAGRSDTDVVSTARIETWGGGRSSLEEGSESLPHLLAARGLGVRADLLRPVMRWRSAPH
+VHRRFDTAVFATMTPPLQSAPASEEPGPELQAWVSARRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVKRATRD
+>GCF_003691675.1_01535
+MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV
+LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH
+VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVERATRD
+>GCF_005280335.1_01030
+MVLVRDGEDGPEVFLRHRPGRTPLGRVGLPGGALSEADADACAWFGPDPAHWARVLGTTD
+RRCARQQVVAAVRELHDEAGVLLAGRTDADVVLDARGETWGGGGSSLEEGAESLPRMLAA
+RGLGLRTDLLRPVARWHSAPHAHRRFDTAVFAAAVPPLQRPLERPETAPALQAWVSARRA
+VAGPVPLPGPAGEEGVAPLDQVATPLTQVLVRRVAAHRTAAAFLLSLTQGAGHGPVPEYR
+LVTEAGDDGAPRMRVERVTRD
+>GCF_020097155.1_00971
+MSAEPDAPRVRVPGHEEELTRQWLAQRHRQVRPARPASAVVLVRDGADGVEVLLRHRSGR
+TPLGRIGLPGGSLVDSDADPCTWYGPAPDEWARALGLADRRRVRQHVVAAVRELFEESGV
+LLAGPADMDLVQDARGETWGASRSSLEEGDESLPRLLGDRGLGLRTDLLRGVGRWLSAPH
+SPRRFDTVVFAAALPPQQELVHRPEGPVLQGWFSARRLLSEPAALPGPDGWLGESGVVAL
+EEVSTPMTQLVLRRVAEHRTAAGFLLSPAGCRGPVPVVKLRTEAEHDDLATGTLYTVAER
+VDPVG
+>GCF_023573625.1_01759
+MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV
+LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH
+VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVERATRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001486.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001486.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8605bbc52ab56a69f6c37a58855e9975886c2ed3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001486.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01839
+MTEQSSAPTWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARACAVNAVAAVHELVGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEAGRHARSAVGVAVLPMDAPVEVEITVRVR
+>GCF_003691675.1_01536
+MTAQSSAPAWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARVCAVNAVAAVHELLGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEVGRHARSAVGVAVLPMDAPVEVEITVRVR
+>GCF_005280335.1_01029
+MAEKAQAPTWGEGAVADRLAELGLERPAVAAPVGSYVPAIRDGDLVLTSGQLPFVAGSLP
+ATGKVGAEVSAERAQELARVCAVNAVAAVHELIGDLDRVAQVVKVVGFVASDPSFTGQPG
+VLNGASDVLAEIFGEAGRHARSAVGVAVLPLDAPVEVEITVRVR
+>GCF_020097155.1_00970
+MAGQNAWGGGPAAERLAALGIERPAVAAPVGSYVPAVRDGDLVLTSGQLPFVAGALPRTG
+KVGAEVTLEQAQELARTAAVNAVAAVHELVGDLEAVVQVVKVVGFVASAPDFTAQPAVVN
+GASDVLAEIFGEAGRHARSAVGVAVLPLDSPVEVEITVRVR
+>GCF_023573625.1_01760
+MTAQSSAPAWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARVCAVNAVAAVHELLGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEVGRHARSAVGVAVLPMDAPVEVEITVRVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001487.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001487.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87e6fe1524f9929f664873852f75f976d792edac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001487.fa
@@ -0,0 +1,10 @@
+>GCF_002008305.4_01840
+MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA
+>GCF_003691675.1_01537
+MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA
+>GCF_005280335.1_01028
+MTEQTKWEYATIPLLIHATKQILDQWGEDGWELVAVVPGPDGPNPVAYLKRPKAA
+>GCF_020097155.1_00969
+MTQRIQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGANPVAYLKRPKDA
+>GCF_023573625.1_01761
+MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001489.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001489.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88dca89380cd90e45bf57a7604ebacce8a088f6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001489.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01842
+MPPAASPTRRMLRSAAPAAVGMAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL
+HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV
+PGSNDYYAPKAANPLRYFAGPSRMDEDRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR
+AGTTLEVLAAGTDDPHLGLDAWAGFPGAAPDENAGRPGDDGRFRLGVTHAPYRRVLDAMT
+ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWTAAGRTVPLEVSAGLGTA
+PSAPVRFACRPEAVVLDLVPRG
+>GCF_003691675.1_01539
+MPPAASPTRRMLRSAAPAAVGMAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL
+HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV
+PGSNDYYAPKAANPLRYFAGPSRMDEDRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR
+AGTTLEVLAAGTDDPHLGLDAWAGFPGAAPDENAGRPGDDGRFRLGVTHAPYRRVLDAMT
+ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWTAAGRTVPLEVSAGLGTA
+PSAPVRFACRPEAVVLDLVPRG
+>GCF_005280335.1_01026
+MRPSATAPRRLVRAGSRAAVGMGTAAALGLAWGLVEAEARVVRTHRLAVLPAGADPVRVL
+HLSDIHLLPRNRSRMAWLRGLDALEPDLVVNTGDNISAAASVPLVLDALGPLLRRPGVFV
+PGSNDYYEPKPANPFRYFAGPSRMDEDRARLPTEALFGAFRAAGWADLTNRGSVLSVPTR
+AGTVLEVLAAGTDDPHLGLDAWGGFPAPAPAPAPAPGDAAASGPASAHDDGAARPGGDGR
+FRLGVTHAPYRRVLDAMTVDGADLLLAGHTHGGQVCLPGFGALVTNCDLPRAQASGVSTW
+TAAGRTVPLEVSAGLGTAPSAPVRFACRPEAVVLELLPCA
+>GCF_020097155.1_00967
+MTDAPGPRLRRLTHTAAWAAGGASALGAGALVWGRVEAEARVVRTHTVPVLPAGARPLRV
+LHLSDIHLLPRHRRRLEWLCSLADLEPDLVVDTGDNISSAASIPLLLDALAPLLAVPGVF
+VPGSNDYFTPKPANPLRYLRGPSELEASRSRLPTEDLFSAFRAAGWTDLTDRAADVVVGS
+GPDAVRIRAAGTDDPHLGLDRWPGFDLADEGAAGDAPLLRLGVTHAPYRRVLDAMTADGA
+DLLLAGHTHGGQVCLPFAGALVTNCDLPRSQASGLSSWTAAGRTVPLEVSAGIGTAPSAP
+VRTFCRPEAVVLDLVPRA
+>GCF_023573625.1_01763
+MRPAASPARRMFCAAAPAAAGLAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL
+HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV
+PGSNDYYAPKAANPLRYFAGPSRMDADRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR
+AGTTLEVLAAGTDDPHLGLDAWAGFPGSAPDGGAGRPGDDGRFRLGVTHAPYRRVLDAMT
+ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWMAAGRTVPLEVSAGLGTA
+PSAPVRFACRPEAVVLDLVPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001490.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001490.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6beb66ba0f063b2afd8571c47421e3ce96e73c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001490.fa
@@ -0,0 +1,61 @@
+>GCF_002008305.4_01843
+MTRATSPDASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEETVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA
+>GCF_003691675.1_01540
+MTRATSPDASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEETVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA
+>GCF_005280335.1_01025
+MTRTATRPLPLREALQVVAPYLQGVRGRWVLGLLSAMAAGLVALAIPQVVQVLVNTVFAE
+AAPGTAGTADPAAGVWWAAGALALFGLAEALFIWLRRFFILPPAADVENRARISIYRRLQ
+RLPVAFHDAWASGQLLSRAQGDLALLRRWIAFGSVMLVVETVTIVVGLVLLFVMSWQLAL
+LYLVAAVPIMIRSFRFRTDFRAASRLSQDQAGDLATTVEESVHGIRVLKAFGRGPDALDG
+FRGEAETLQGTEVHKASVLAKFISLTVSLPELVLGVALGLGLYLVAVGDLTVGALAAYFA
+TTAVLARPVEGVGQLMGMTLSAKTAIDRHLEVMRVPVAVASPAGTDAAEEEATSRAVASS
+AAEDSPVVTDGLPPSSGRLAFRDVVFRYPDAPEDSRPLLAGVDLELTPGETMALVGVTGS
+GKSTLVQLVPRLLDVTAGVVEVDGTDVRAYPLDELRRRVSIAFEDATLFSDTVRANVLLG
+APAEVTADGLDSPRAQALLDLALDTAQAGFARDLPAGVDTEIGEEGLSLSGGQRQRIALA
+RAIAARPDVLVLDDPLSALDVRTEEAVTGRLREVLAGTTTLIVAHRPSTVALADRVAVLQ
+DGAIHDVGTHAELLARSAAYREIITTGAAEDRSLAGLADAAHDDAALAAATDAARPPAGA
+ARPPAGRTAGREETR
+>GCF_020097155.1_00966
+MTRTTTAAAPLPLRDAVRGIAPYLEGVRTRWVLGLLSALAAGLVALAIPQVIRLLVNTVF
+AAPTTPGAPAAEDATASVWWAVGGLALLGAAEALFIWLRRFFILPPAADVENRARIAVYR
+RLQRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVETVTLVVGVGLLFWLSWP
+LALVYLAAALPIMWRSYGFRNDFRTASRLSQDQAGDLATTVEESVHGIRVLKAFGRGPHA
+LEGFRGEAQTLQGTEVHKAGVLASFIAFTVSLAEVMLGVALALGVWLVATGQMTVGALAA
+YFATTAVLARPVEGIGQLLGMTLSAKTAIDRHLEVMRQPVSIASPPGTDPAEEAATGASV
+GEDPDPAVADAPVDVSALPPSRGGLAFRGARFRHPDTPDDAPDLLAGVDLELVPGETMAL
+VGLTGSGKSTLLQLVPRLRDVTGGVVEVDGVDVRDYPLEELRRRVSIAFEDATLFSDTVR
+ANVLLGAPAAEVADGPDSPAAEALLELALDTAQAGFVADLPQGVDTPIGEEGLSLSGGQR
+QRLALARAIAARPDVLVLDDPLSALDVRTEEAVTARLREVLAGTTTLIVAHRPSTVALAD
+RVAVLQDGRIADVGTHADLLARSGAYRQIITTDREDAR
+>GCF_023573625.1_01764
+MTRATSPAASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEEAVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001491.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001491.fa
new file mode 100644
index 0000000000000000000000000000000000000000..990b2c0fae478d0a298d710858bd15ac14559bd3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001491.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01847
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK
+>GCF_003691675.1_01543
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK
+>GCF_005280335.1_01021
+MKTLVLGNGGREHALLAALSRDPQVGELHAAPGNAGMAALAALHAVEATDPDAVVALARE
+LAADLVVVGPEAPLAAGVSDALREAGFAVFGPSRAAAQLEASKAFAKEVMAAAGVPTAGS
+RTCATAEEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAQACFDAGGTVVIED
+FLDGPEVSLFVVCDGTDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFAEEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLTTPLGG
+LLADAAAGRLGADRALEWSDDVAVDVVMASAGYPATSSQGDVITGLTDAEALEGVHVIHA
+GTATSGDDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+AVPAAVGQAGQAGEDAR
+>GCF_020097155.1_00963
+MKILVLGNGGREHALLRALSRDPQVGELHAAPGNAGMADAAVLHPVTATDPEAVVALARD
+LAVDLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGA
+RVCATEAEVDAALTAFGAPHVVKDDGLAAGKGVVVTSDRAAALDHARACLSAGGTVVVED
+FLDGPEVSLFVLCDGEHAVPLTPAQDFKRIHDGDAGPNTGGMGAYTPLQWLPEGFVDEVM
+ERVARPVLAEMSRRDTPFAGVLFIGLAVTENGPEVIEFNVRFGDPETQSVLARLETPLGQ
+LLADAAAGRLGADRELRWSDDVAVDVVLASAGYPASSHSGDVIAGLEDALALEGVDVLHA
+GTARTEDGDVVTAGGRVLAVVGRGATLEQARERAYAGVAKIRFDGAQHRTDIAIKAERGE
+ITVPERRRGYAGAEALELPGWRHVYSGKVRDLYEPADAEPGTSETLLVVASDRISAYDFV
+LEPPIPGKGAVLTRLSLWWFEQLAGVANHVVSTDVPAEVAGRAMVVKRLDMHPIECIARG
+YLTGSGLAEYREHATVTGIPLPDGLVDGSRLEPPIFTPSAKAEVGEHDENITFEQTVERV
+GAPTAEALRAATLEVYTRAEAIARKAGIILADTKVEFGADPVTGELVLGDEVLTPDSSRF
+WDAEAYEPGRAQASFDKQFVRDWLTSPESGWDRTSGEEPPALPADVVERTRARYVEAYER
+LTGRRFEA
+>GCF_023573625.1_01767
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001494.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..480b6521dcf8919345bdde2ddf2b8a4590aaa026
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001494.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01850
+MSVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPAT
+TLVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWVA
+FPLFFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAGGVRVPAVIGPLVGAA
+VAVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQG
+LASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLIEAL
+ERAVAGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGARRAR
+VTLGYLGDELTVDVADDGAGFDPAVVAARPRAGAAGADPGAGTGVGLASVRERLAAVGGE
+ATVESAPGEGTVVALRVPLVAAGAGRSADPEQTESEETA
+>GCF_003691675.1_01546
+MSVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPDASGPFPATT
+LVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVGHHGDFAWVAF
+PLFFVVLHVVDRVARQAWVRHVVGPALVVAMAAVVVAGMAAGAGGVRVPAVIGPLVGAAV
+AVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQGL
+ASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLVEALE
+RAVTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGARRARV
+TLGYLGDELTVDVADDGAGFDPAVVVARARAGAAGADPGAGTGVGLASVRERLAAVGGEA
+TVESAPGEGTVVALRVPLAAAGAGRSADPEQTESEETA
+>GCF_005280335.1_01018
+MPTTRPSADTAGAPAETGAAAVLAGLRVALHVAFAVLLAVGLGRALADLSRTGAPAPAVL
+ALTGCTALLAGVYLAGTLVERRRWGRGEDVGRGPALLWLALVLALWGLLVAQHRDFAWVA
+FPLFFVALHVVARTARTAMARRIAGPVLVAAMAAVVVAGMAAGVDEGVRPAAVIGPLVGA
+AVAVVLSGAYRALHQESERQRDVAEQLRAAQAELARTQHRAGVGEERERLAREIHDTLTQ
+GLASIVLVSRAAQDALDAQDPALARTRMETVRTTAAENLDESRRFVRDLRATGGASLVAA
+VERAVAGFAERQAAAGTPVAADVEVVGTPVPLAEAVEAALLRAVQASLANVAAHARATRA
+RVTLAWMPGELAVDVADDGVGFRPEAVVTGDAGTQGTGAGTQGARAGRASRPGAGTGVGL
+ASVRERLAGVGGHASVESAPGEGTVVALRVPLPAAAGRAEEDEGRERG
+>GCF_020097155.1_00960
+MRTSDPADGPRGANGTAALLSGLRVAVHVGFAVLLALALVRALAGPDAGARLTGRPALAL
+VGLTVVLAGVYLTGTVAERRLHAAGRAPGRTAAGTWLAVLLGVWALAVLRHPDMMWVAFP
+LFFVALHAVHVILGRPRLALACVAAMTVVVVVASLERGTAPGAVLGPAVGAAVAVVVFHA
+CRLLVVESERQRSVAEQLRATRAELAASERHAGVLAERERLAREIHDTLTQGLASIVLVS
+RAAQDAVRAGDAALADERLETVRTTAAENLAESRAFVRGLRAPVDGVQGGADRAGSALEA
+ALGAAVRGFRARRQALGRPVEAELAVVGEPVAVGEAVETVLVRAAQSSLANVDQHARTDR
+CRVTLTWMDGEVALDVADDGVGFDPEAARARASRAAVSDPAAPRPAEEGTGVGLAGLAER
+VAGVGGRVDVESAPGQGCVVAVRIPVPRQHERRGA
+>GCF_023573625.1_01770
+MSVAPRAAAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPVTTLV
+LLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWVAFPL
+FFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAGGVRVPAVIGPLVGAAVAV
+VLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQGLAS
+IVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLIEALERA
+VTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGAHRARVTL
+GYLGDELTVDVADDGAGFDPAVVAARPRAGAAGADPGAGTGVGLASVRERLAAVGGEATV
+ESAPGEGTVVALRVPLVAAGAGRSADPEQTESEETA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001496.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001496.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3fe4e25df0d785848bdea0e95db2ed01cc78ee11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001496.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01853
+MTHATVAPAGETLALSDAVELVETVRNGFVESRTAGAAVVTGPDGRVLAGLGPADALIYP
+RSTLKPFQAVASLRHGAALEGEALSIACGSHRGTLRHQALAERMLADAGLDASALQCPPA
+WPADTSEVVAQVRRDGESAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV
+DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML
+EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA
+LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPAFEARA
+>GCF_003691675.1_01549
+MTHATIAPAGETFALSDAVELVETVRNGFVESRTAGAAVVTSPDGRVLAGLGPADALIYP
+RSTLKPFQAVASLRHGAALEGEALSIACGSHRGTLRHQALAERMLADAGLDASALRCPPA
+WPADTSEVVAQVRRDGESAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV
+DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML
+EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA
+LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPTFEARA
+>GCF_005280335.1_01015
+MTQTPSATFALADAVELVHVVRNGFVESRTPGAAVVTGPDGTVLAALGPVDALIYPRSTL
+KPFQAIASLRHGARLEGQEVAIACGSHRGTAAHRELAARILAEAGLSAADLQCPPDYPAD
+AAEIVRFAQDLEHGAEKTPLAYNCSGKHAGFLAACVAAGHEVGTYLEPDHPLQAEVERVI
+EEYCGEPVAHTGTDGCGAPAAVLSLTALARGIGKVASAPSRRDAEIHAATVANAMLEHPW
+AVHGQSSSNTVVMRELGLLAKLGADGVMVMAAPDGTAVAVKALDGGTRAGNLVALALLAQ
+FAPDHVDADRLPAVLETVAPKILGKGEPVGAVRLARPVLDLLD
+>GCF_020097155.1_00957
+MTQTSAAPAGQTFALADAVELVEVVRGGFVESRTAGAAVVTGPDGEVLAALGPADALVYP
+RSTLKPFQAIASLRHGARLEGEALAIACGSHTGSEAHQQLAARVLADHGLAPEALQCPSA
+LPEVAGEVARLAAQAGTAEIATPLAYNCSGKHAGFLAACAASGHDVGTYLDPEHPLQREV
+DAVIAEYCGEPVAHTGVDGCGAPAAVVSLAGLARGIGAVSKAPGREGAEPHAAAVARAML
+AHPWAVQGPGKANTVVMEELGLVAKLGADGVMVMGAPDGTAVAVKALDGGTRAGNLVALA
+LLGRFAADQVDAGRLAEVSARVAPSILGRGAPVGEVRLAAPVRQLVGA
+>GCF_023573625.1_01773
+MTHATVAPAGETFALSDAVELVETVRNGFVESRTAGAAVVTGPDGRVLAGLGPADALIYP
+RSTLKPFQAIASLRHGAALAGEALSIACGSHRGTLRHQALAERMLADAGLDASALRCPPA
+WPADTSEVVAQVRRDGEAAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV
+DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML
+EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA
+LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPAFEARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001497.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001497.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f3149821e286911c902be13115b02cbb7f2cee9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001497.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01854
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRATAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV
+RADLGAHLPLVRP
+>GCF_003691675.1_01550
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTSWDEATAAGGVRASGV
+RADLGAHLPLVRP
+>GCF_005280335.1_01014
+MTTGSVPRRRIPVPEGHAALTSWARTHAQDPAAAAALPRSTRATAVRFALEELATRVPGN
+AVEVRVPPFGVAQAIPGPRHTRGTPPNVVEMDAVTWLSLATGLLGWADAVGTGAVRASGT
+RADLGAHLPLIRP
+>GCF_020097155.1_00956
+MTTGSVPKRRVPVVEGHAALTAWARAHAEDPAAAAALPRSTRATAVRFALEELATRAPGN
+SVEVRVPPFGVAQCIPGPRHTRGTPPNVVETDPVTWLSLATGLTRWNDAVASGAVRASGV
+RADLAGHLPLVRP
+>GCF_023573625.1_01774
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV
+RADLGAHLPLVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001498.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001498.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b265277dee07918748b7563ae64d0e2552e56f3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001498.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01855
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+APPARTTPTERTPEQ
+>GCF_003691675.1_01551
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFAALLSMLGTGVLGLIVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+TPPARTTSTERTPEQ
+>GCF_005280335.1_01009
+MTTGPERSQHQHAYTVRRAPRLAAVLAVALALGLVIALVITTAVHGSPTPPADPYSGIPL
+SFSETFGFAALLSMLGTGVLGLVVWLLLDRRSRATTRTVVLERTDDPAAADIRLDRSAAD
+ALRSRTAPTERTPEQ
+>GCF_020097155.1_00953
+MTSGPERSTPSAPQQQEYVLRRAPRLSAAVIVSALVGVVLALLGTAAVHAGPQPPADPYS
+GMPLSFASTFGYMVVAAVLACLVLGLLVWLLLDRRSRRTQRTVLLERTDDPAAADVALPR
+PEAVAPAARPAADPSDGRTPEQ
+>GCF_023573625.1_01775
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+APPARTTPTERTPEQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001500.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001500.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9887193f297249a23b396ba5685f030e48b9e618
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001500.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01857
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAADEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHEGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLNFVQGAKGVDGGAVLMRGQYAA
+>GCF_003691675.1_01553
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAVDEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHEGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLDFVHGAKGVDGGAVLMRGQYAA
+>GCF_005280335.1_01007
+MTENQNTAHDAPITYASAGVDVEAGDRAVELMKDAVKATHSPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGATPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLGVDEYDVAGAATGVVDADMVLGA
+DRVQTGDVLIGMASSGIHSNGYSLVRRVVNAAGWSLDREVSELGRTLGEELLEPTRIYAR
+SCLDLVQRLNGHDGGSGLPVRAFSHVTGGGLAANLARVLPQGLMATVERETWSLPPVFRL
+LAEAGRVPQPDLERTLNLGVGMVAVVDPEIAAKSISVLVDAGIDAWEMGTIGHVTDEAAG
+AGLDFVQGAKGVDGGAVLMRGAYAA
+>GCF_020097155.1_00951
+MTDAPRTETQTADALDAPLTYAAAGVDVEAGDRAVELMKDAVKATHTAEVLGGVGGFAGM
+WDASALTGYRKPLLATSTDGVGTKVAIAQALDRHDTIGQDLVGMVVDDIVVVGAKPLFMT
+DYIACGKVVPERVADIVRGVAEGCRLAGTALVGGETAEHPGLLAVDEYDVAGAATGVVEA
+DRVLGAERVRSGDVVIGMASSGIHSNGYSLVRRVINAAGWQLDRDVDELGRTLGEELLEP
+TRIYTRACLDLMDSLNGTEGGADLSLRGFSHVTGGGLAANLARVLPQGMMATVDRGTWAL
+PPVFRLVGELGRVPLADLERTLNLGVGMVAVVAADAADRAVAAIEAAGIPAWVMGGIDEV
+TEQAQAAGEDYVQGAKGVDGGAVLMTGTYAD
+>GCF_023573625.1_01777
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+RVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAAEEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHDGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLDFVQGAKGVDGGAVLMRGQYAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001501.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001501.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e4c47647d19c1c9d7ec396464f2f1a442eeb5e7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001501.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01858
+MATSSLPLSDIVETGRPFTRGDLRAAGVSERLVRGGDVRRVTHGVHRLRSDHLGSWADLG
+YVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRVFAS
+>GCF_003691675.1_01554
+MVTSSLPLSDIAEAGRPFTRGDLRAAGVSERLVRGADVRRVTHGVHRLRSDHLGSWADLG
+YVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRIFAS
+>GCF_005280335.1_01006
+MSMSTSTSTSLPCPQDRRPPVPARPLDVVAAGGPLFTRADLSAAGLPADRLRAADVRRVT
+HGVHRRADDVPGDWGALGYAEPPVAFAPEETAAIVTASRGVASHLSALLLHGIPVPPFLV
+DDGRVHVSRPHSRGASERPEVRSHARSVPEADAVVLHGIRVTSVERTWADLAALVRPGHL
+DPVVAAGDAVVTGIWTPQGRLPPRATILRLRAGLARSGRFKGARTARAALELIRAGADSP
+PETALRLALLHAGLPEPELQLVLHRGRRRSPDADLGWRAWRLVVHYDGDPHLDPAQQAVD
+AWRNGGWARAGWSQIVATVDDARDDFRRVVAEVLAHRARLGGRAYVA
+>GCF_020097155.1_00950
+MALESLADVLGSAPLPIRAEGPPPLGLFTRSDLRAAGLGGHRVHGRDVRRVTHGVHRLAT
+DPAGDWAVLGHRCPPAPFAPEETAAIVEAAGGVASHLTALLLHGVPLPPFLAEDGTVHVS
+RPHARGASGRLEVTSHARSVPAADVTSLHGIRVTSLERTWADLASLVPPGLVDPVVAAGD
+AVVRHPWTPQGRSAPRTTPARLAAALDRAGRFKGVRTARRALEAVRVGSDSPQETALRLA
+LVHAGIPEPELQLVLHPGRERSPDADLGWRMWRLVVHYDGASHLEPAQRAVDARRHEGWE
+RAGWAQIVATVDDARDDFRRVVAEVQAHRRRLGGRVYVC
+>GCF_023573625.1_01778
+MATSSLPLPDIVETGRPFTRGDLRAAGVSERLVRGGDVRRVTHGVHRLRTDHLGSWADLG
+YAEAPAPFAPEETAAVVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRIFAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001502.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001502.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b20df045f484fa628b1df836db7e8f17683da85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001502.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01859
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEESRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA
+AEGRIAGVLTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE
+AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPPA
+RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR
+APVADALAWLDARL
+>GCF_003691675.1_01555
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEESRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA
+AEGRIAGILTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE
+AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPAA
+RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR
+APVADALAWLDARL
+>GCF_005280335.1_01004
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLLEETRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNAAHRILAGWA
+VRGLVSGILTQNVDGLHAQAAAEAGAPEDRLIELHGDLARVVCLHCGATESRRDLDVRLE
+AANLGYLERVSIDPEAVNPDGDVTLDRHWVDEFAMVGCLRCGSVELKPDVVYFGESVPVA
+RREAAEAMADDGGAVLAVGTSLAVMSGYRFVLRAERAGKDTGLINLGSTRADPKASWRWR
+APVADALAWLDSRL
+>GCF_020097155.1_00947
+MTPVRHPSQDGHQAALRSIARVVGETAPLQDPETASRGLLRMLEAGRPLVITGAGVSTDS
+GIPDYRGPNGTLHRHRPMTYQEFRDDPAARHRYWARSFVGWRHMDEAAPNAAHHVLADWV
+RRDVVAGIVTQNVDGLHAQAFAAAGAAPSRLIALHGDLARVVCLQCGAMEDRTSLDARLA
+AANPGYLEAVTVDPDAVNPDGDVTLDQRWVDAFTMVGCRVCGSVQLKPDVVYFGENVPPA
+RRDAARALAEEADSVLAVGTSLAVMSGFRFVLDAERAGKEVGVITLGPTRADPKAQWRWR
+TRVAEALAWLDARL
+>GCF_023573625.1_01779
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEEFRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA
+AEGRIAGILTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE
+AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPAA
+RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR
+APVADALAWLDARL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001505.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001505.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0aaf308ca7b74b9d37dc03d781f0c9c4435cad8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001505.fa
@@ -0,0 +1,80 @@
+>GCF_002008305.4_01862
+MDAKFTTKSQEALSAAAMNASTAGNPQVEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIRRLPSTQGSTVAQPQFSRAALQVVQNARTQAEQRSDEFVSTEHLLLGVAADSG
+EAGEALRSNGASLEALAAALTLVRGDSRVTTQDPETTFQSLEKYGTDLTEIARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVFVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPASIERLDALRAEKADREEELTALTARWDAEKATLNQAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSATEPMVSEEVTADD
+IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRGAFKPEFLNRLDEIVQFDALTVAELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAATGFDPAYGARPLRRLVQREIGDRLARGILAGE
+IADGDTVVVDRVEGENGLTVTRKG
+>GCF_003691675.1_01558
+MDAKFTTKSQEALSAAAMNASTAGNPQIEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIQRLPSTQGSTVAQAQLSRAALQVVQNARTQAEQRSDQFVSTEHLLLGVAADPG
+EAGEALRSNGASLEALAAALTQVRGDSRVTTQDPETTFQSLEKYGTDLTELARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAAALSDRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPASVERLEALRAEKADREEELTALTARWDAEKATLNEAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSSTEPMVSEEVTADD
+IAEVVSAWTGIPSGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRAAFKPEFLNRLDEIVLFDALTVDELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAETGFDPAYGARPLRRLVQREIGDQLARGILAGE
+IADGDTVVVDRVEGENGLTVTRKG
+>GCF_005280335.1_00998
+MDAKFTTKSQEALSAAAMNASTAGNPQIEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIRRLPSTQGSTVAQAQLSRAALQVVQNARTQAEQRSDQFVSTEHLLLGVAADPG
+EAGEALRSNGASLEALAAALTQVRGDSRVTTQDPENTFQSLEKYGTDLTEVARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPSSVERLEALRAEKADREEELTALTARWDAEKATLNEAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSTTEPMVSEEVTADD
+IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRAAFKPEFLNRLDEIVQFDALTVAELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAETGFDPAYGARPLRRLVQREIGDRLARGILAGE
+IADGDTVVVDRAEGEEGLTVASA
+>GCF_020097155.1_00945
+MNPSPQFTTKSQEALSAAAMNASTASNPAVEPAHLLKALMDQRDSVAVAVLKAAGADPDV
+VSVAASTAIHGLPKASGATVSEARLSPAAGAVVKAAQQQASAHGDEYVSTEHLLLGLAAD
+GGEAGRALTDAGASLAALQAAFTQVRGDERVTTPDPEATFQSLEKYGTDLTAVARSGKLD
+PVIGRDQEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLI
+SLDLGAMIAGAKYRGEFEERLKSVLEEIKKSDGQIVTFIDEIHTVVGAGASEGAMDAGNM
+LKPMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYE
+AHHKVAIADSALVAAATLSDRYISGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDALRRQ
+VDRITMEELALDGESDPGSVERLAGLRAEKADKEEELRALTARWEAEKASLNEAGDLRAR
+VDELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAQEGQQGDVEAMVSENVTA
+DDIAEVISAWTGIPAGRMLASETEKLLSMEEHLGDRLIGQKDAVRAVSDAVRRARAGIAD
+PNRPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHAVSRLVGAPPGY
+VGYDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVI
+LILTSNLGSQFLVDQTMPEQARKDAVMDVVRAAFKPEFLNRLDEIVTFDALGVEDLARIV
+DLQVASLGERLQQRRLTLDVTDAAREWLALTGYDPAYGARPLRRLVQREIGDQLARALLS
+GAVQDGDTVVVDRAGEDTADGLTVAARRA
+>GCF_023573625.1_01782
+MDAKFTTKSQEALSAAAMNASTAGNPQVEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIRRLPSTQGSTVAQPQFSRAALQVVQNARTQAEQRSDEFVSTEHLLLGVAADSG
+EAGEALRSNGASLEALAAALTLVRGDSRVTTQDPETTFQSLEKYGTDLTEIARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVFVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPASIERLDALRAEKADREEELTALTARWDAEKATLNQAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSATEPMVSEEVTADD
+IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRGAFKPEFLNRLDEIVQFDALTVAELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAATGFDPAYGARPLRRLVQREIGDRLARGILAGE
+IADGDTVVVDRVEGENGLTVTRKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001508.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001508.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a55f3f0a8d213d3a23a54bfb319fa81c700e5b87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001508.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01865
+MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV
+PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
+>GCF_003691675.1_01561
+MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDI
+PYPPFEFEEKGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
+>GCF_005280335.1_00995
+MGLTASAALLTGCAVLGGDSGVAGVVSDDDLSTTYNLVQPGVLTVCSDIPYPPFEFELDG
+ELTGYDIQLVHAIAEELELGVNVIDSSFEAIESGASLTGCDLNASSISITEQRQRAMAFT
+LPYLDDDLVLVAATDSGITDVESAKGRRVGVQAATTGDAYAKENGLNPIEFEDGGMQVQA
+LQAGTVDALLGNQSVILYSLKDDERFEVVENLPTGEQLGMAVAPQNAQLGSAVNRALQQL
+RNDGTVAELQERWFGLAQEDYR
+>GCF_020097155.1_00933
+MPRTPSRALGAVGAGLSAALLSGCAVIGGDAGTTGPLAEDDLRATYRLHEPGVLTVCADV
+PYPPFEFEQDGQLTGYDIDLTRKLAETMDLQLKVVDTSFEAIESGASLTGCDLNASAISI
+TEPRQHVMAFTLPYLDDDLVLVARKDSGITDVASAQGKRVGVQTATTGEEYAQSQGLDTV
+QFEDGGMQVQALQAGTVDALLGNQSVLLYSLKDDPRFGVVESLPTGEQLGMGVAPDNALL
+GSAVNRALQTLRNDGTVAELQQKWFGTAQKDYQ
+>GCF_023573625.1_01785
+MTRIHSRLLGTVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV
+PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVELLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001510.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001510.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48e32eaac12423a296685afd800185b43ea514ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001510.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01867
+MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK
+STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV
+AQLKVLKRGKAEAVDIARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF
+DEPTSALDPETVGDVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA
+AAVISDPQQPRTQDFLRRVLHPTEIDL
+>GCF_003691675.1_01563
+MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK
+STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV
+AQLKVLKRGKAEAVDVARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF
+DEPTSALDPETVGDVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA
+AAVISDPQQPRTQDFLRRVLHPTEIDL
+>GCF_005280335.1_00993
+MAQQTPQPAASAVDAAGVHVADLNKSYGSNHVLRGIDLDVAPGEVVCLIGPSGSGKSTLL
+RCVNLLEKPDSGRITVGEFDVTDEDVDLDALRRHVGMVFQQFNLFPHLSVLENCTVAQVK
+VLKRSKAEAAEVARRQLARVGLAELEDRFPDQLSGGQQQRVAIARALAMDPQLMLFDEPT
+SALDPETVGEVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVSMDAGVVVETGPAAALI
+ADPQQPRTQDFLRRVLHPTEIDL
+>GCF_020097155.1_00931
+MTEQTASPRPSDAGTAAGVHIAGLHKSYGSNHVLRGIDLDVAPGEVVCLIGPSGSGKSTL
+LRCVNLLEVPDSGGVQVGEFTVTDPDVDLDRLRQHVGMVFQQFNLFPHLTVLENCTVAQV
+KVLKRSAAEAADTARRQLARVGLGELEGRYPDQLSGGQQQRVAIARALSMDPRLMLFDEP
+TSALDPETVGDVLAIMRKLAREGMTMLVVTHEMGFAREVADRVVFMDGGVVVEQGPASAV
+ITDPQEPRTQDFLRRVLNPAGVDI
+>GCF_023573625.1_01787
+MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK
+STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV
+AQLKVLKRGKAEAVDVARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF
+DEPTSALDPETVGDVLGIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA
+AAVISDPQQPRTQDFLRRVLHPTEIDL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001511.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001511.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c59f99b190d7f6afde68a717923fa5f2ce179684
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001511.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01868
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMGARGLPALANLSPEQFKKFLVTT
+EIGVGSALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTGVAKDIFL
+VGSGLAIAADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA
+>GCF_003691675.1_01564
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMGARGLPALANLSPEQFKKFLVTT
+EVGVGAALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTGVAKDIFL
+VGSGLAITADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA
+>GCF_005280335.1_00992
+MSIVQIPLRLASGAFILNSGLNKRNISEEQAAGMRDMGAQGVPYLAKLTPAQFKNFIVAT
+EVGTGAALLAPFVPGWLAGSALTAFSGGLMSMYLNTPAMTEKDGVRPSQEGTGVAKDVFL
+VGSGLAIAADSVANRSGKRRKAAKKRAARIGNARDAKVQAIRDAQDEKVAAIHAARDEQV
+AALREAREELKKLRQKA
+>GCF_020097155.1_00930
+MSIIQIPLRLTSGAFILNSGLGKRKLGEEQAAYLQNMAAKGVPSLAKLSPSQFKNFITAT
+EIGTGAALLAPFVPGWLAGSALTAFSGGLMSMYLNTPEMTEADGVRPSQDGTAVAKDVFL
+LGAGLAVTADSVVNRPGKRKKAAKKRAARISDARDAKVDAIRAAQDEKVAAIHEAREQQV
+AALREARQELAKLRKKA
+>GCF_023573625.1_01788
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMSARGLPALANLSPEQFKKFLVTT
+EIGVGSALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTAVAKDIFL
+VGSGLAIAADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001512.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001512.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3598cbdb985e7364839eb8264526cd2a3debcc1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001512.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01869
+MLPLVAPLTVAAAAPTDYGWLGNIVVDIMEAVGPIGVGLAVFAENIFPPIPSEVILPLAG
+FTAAGGAFSPHAALVWATVGSIVGALALYGLGAWLGRHRMYRLADRMPLVDMEDVAKTER
+WFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLAKFTLFTALGSLIWNAIFVYGGYALG
+ERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRRDARRRNDPDWRPPTADEMAARVEAI
+LESSDHRK
+>GCF_003691675.1_01565
+MLPLVAPLTVAAAAPTDYGWLGNIVVDIMEAVGPIGVGLAVFAENIFPPIPSEVILPLAG
+FTAAGGAFSPHAALVWATVGSIVGALALYGLGAWLGRHRMYRLADRMPLVDMEDVAKTER
+WFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLAKFTLFTALGSLIWNAIFVYGGYALG
+ERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRRDARRRNDPDWRPPTADEMAARVEAI
+LESSDHRK
+>GCF_005280335.1_00991
+MLPAVTPLTLAASTVTADTDYGWLGNVVVDIMEAVGPVGVALAVFAENIFPPIPSELILP
+LAGFTAAGGAFSPLAALLWATVGSVTGALALYGIGALLGRRRMYRIADRMPLVDVEDVAK
+TERWFARYGYWTVFLGRMVPVFRSLISIPAGIERMHLGMFTLFTTLGSLIWNAIFVYGGY
+ALGERFHLVSDYADVFSNVVVVLVLAFLVVWVVLRLRRNARRAKDPDWHQPTADEMAARV
+DALLESSDHRK
+>GCF_020097155.1_00929
+MIRRGRTTSDAAAVVVVENGGMSALSTLPLLAAAGTPDYGWLGNTIVAIMEAIGPVGVGL
+AVFAENIFPPIPSEVILPLAGFTAAGGAFSPHAALIWATVGSVVGALALYGLGAWLGRRR
+LYRIAAWMPLVDVSDVERTEKWFARYGYWTVFVGRMVPVFRSLISIPAGIERMNVAKFTL
+FTALGSLLWNAIFVYGGYALGENFHVISDYADMFSNIVMVLILVFLAVWVVLRLRRNRGR
+AADPAVDHEDPEAAAARVEAEIKALQHRK
+>GCF_023573625.1_01789
+MLPLVAPLTVAAAAPTDYGWLGNIVVDIMEAVGPIGVGLAVFAENIFPPIPSEVILPLAG
+FTAAGGAFSPHAALVWATVGSILGALALYGLGAWLGRHRMYRLADRMPLVDMEDVAKTER
+WFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLAKFTLFTALGSLIWNAIFVYGGYALG
+ERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRRDARRRNDPDWRPPTADEMAARVEAI
+LESSDHRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001513.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001513.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6296b80d5294bddf945e6695c43c7b0aa8f4500
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001513.fa
@@ -0,0 +1,47 @@
+>GCF_002008305.4_01870
+MHPVLPSPRRGRAALGLAAVALVALSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP
+SHDLERVPEASVAVLEGEDPDHHGAWLQVSGAPAWTDAMAGAVRDQIDQYRRDTDPSADP
+RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA
+FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA
+AGVLTVRIPRDTATAWLSDLGHVAADAASAPADLRLPDRSTPTPEEQQPEPAPEPEPETS
+SWTEEATGAPVPPPSAPADTAAPTPSVTTPVPSSTAPSSSAPAPTRSATPSSPSSPPTSS
+SPSGTGSGSPTPSTPDPTPTSATPTPTSPTPTSPSPSGPSTSASGPSTSAPATDPAPDPT
+ESAPEPTATTASASASPTSGDRSSSTP
+>GCF_003691675.1_01566
+MHPVLPSPRRGRAALGLAAVALVTLSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP
+SHDLERVPEASVAVLEGEDPDHHGAWLQVPGAPAWTEAMAEAVRAQIDQYRRDTDPSADP
+RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA
+FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA
+AGVLTVRIPRDTATAWLSDLGHVAADAASAPADLRLPDRSTPTPEEQQPEPAPEPEPETS
+SWTEEATGAPVPPPSAPADTAAPTPSVTTPVPSSTAPSSSAPAPTRSATPSSPSSPPTSS
+SPSGTGSGSPTPSTPDPTPTSATPTPTSPTPTSPSPSGPSTSASGPSTSAPATDPAPDPT
+ESAPEPTATTASASASPTSGDRSSSTP
+>GCF_005280335.1_00990
+MSTPASPSARRARAALGLAAVALVALSACARTEPAPEPAPSTASATALPPMDMAPFTVDV
+PSLDLDRVPGASIAVLEGTDPDHRGAWLQVPEAPAWTEAMAGSVRGQIDAYRRDTDRGAD
+PRLEVQPRLAVVGEDIAAARLLSTETRGTDSVSSSHVVWYSAREDRVLETRDLFTDEGWD
+AFRTEVRQRMKNDPDVVRERLASAVDSPELVENRRIWDAVVLLPDGSVMLEADQASMAPA
+AAGVLTVRIPRDTAAPWLSDLGDAATDAARTPADLRLPDRSTPSPSTSAPEPAESSWTPE
+ATGAPVPPRVPVPDPTTTAPSVDPGGDRDPSTSSAPPSSRPGTTAPSPVAGPQHPGPHHP
+GPHHLRADRPGARPLDDDGAPAPGADQPDAHADADPVDSHADADAHDAHPDPDRDGDHGP
+ADRPGAGARAGADDAAAERHERLRPRDPGRAGLSRPTPGCPGRPRTGACPARRRPAPPPH
+GLT
+>GCF_020097155.1_00928
+MHRLSPASTVRLRAGAGLLALGMLGLTACGSGDDAASSSPAPSSAAATQELPSMDMAPFT
+LDVPSLDLDKVPGASLAVIQGQDPEYHAAWLQVPGAPAWTQAMDESVRGLVAQYQRDTDR
+TASPVLDVQPRLAVAGRDVAAARLLSTERRGDRSVSAVHVVWYAAREDRVLSTEDLFTAD
+GWAAFRREVGARMAGDPAVVQDRLRSAVDAPAQVENVRVWDALTFLPDGSALLEVDQAAM
+SPADAGVLTARIPADTVRPWLSALGVSAQDAARSPEALVLPERPSAAPASEGGDAAVPAP
+GQPSSDGATTSAPGQGSVPPAPGLPGAPAPGTPGTASQGGGSPGTAPQDTGSQHTGSQGT
+GSQGTGASAPGASPSATRGDAGPAPTSSSAAPAPTGTGAPAPAPLPMPAPTTSSATPSGP
+APAPTGGTPAPSPTTVAPTEPSPSADPTTSEPAPSSDPAPAPTDTASPAPTASSPSTPAD
+VTGTATASGPLPATGGSTDPVTPTPAA
+>GCF_023573625.1_01790
+MHPVLPSPRRGRAALGLAAVALVTLSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP
+SHDLERVPEASVAVLEGEDPDHHGAWLQVPGAPAWTEAMAEAVRAQIDQYRRDTDPSADP
+RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA
+FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA
+AGVLTVRIPRDTAAPWLSDLGHVAADAASAPADLRLPDRSTPTLEEQQPEPETSSRTQEA
+TDAPVPPPSAPADTAAPTPSATTPVPSSTVPSSTAPSSSVPTSTGSATPSSPTSPASSSS
+PSGTGSGSPTPSTPDPSPTSATPTPTSPSPSGPSTSAPATAPAPDPTESAPEPTATTASA
+PAPPTSGDRSSGTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001515.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001515.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5fbf7a87178754ad2282bf3033bb874596aabbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001515.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01872
+MQERLRADMARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLEGPDGPRAVVA
+AGDPATATHLTWLVSGMGIRPQTALWGTAREAAHLAAAQRAAGAPRPVVIGWLGYPAPTP
+WRVVLDGPGRRGGAMLAADVRAWWEFLRHGPGEDDDVAPALRARGTAVHGAVEAHSYGSL
+VAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGTVGLPAALAARSAHLGLRSGRTFR
+ALAPGDLLARVGRAVGRRRDWTDAAVLPVAPRPGLAGAAVRGHRTARWSPTAPEDAPRGY
+RDAGSVTLAATARVTAGLPLSPVPDGADPAGPVAPA
+>GCF_003691675.1_01568
+MQERLRADMARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLEGPDGPRAVVA
+AGDPATATHLTWLVSGMGIRPQTAMWGTAREAAHLAAAQRAAGAPRPVVIGWLGYPAPTP
+WRVVLDGPGRRGGAMLAADVWAWWEFLRHGPGEDDDATLALRARGTAVHGAVEAHSYGSL
+VAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGAVGLPAALATRAAHLGLRSGRTFR
+ALAPGDLLARVGRAVGRRRDWTDAAALPVAPRPGLAGAAVRGHHTARWSPTASEDAPRGY
+RDAGSVTLAATARVTAGLPLSPAPDGADPAGPVAPV
+>GCF_005280335.1_00988
+MARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLDGPDGPRAVVAAGDPATAT
+HLTWLVSGMGIRPHTAMWGTAREAAQLAAAQRAAGAPRPAVLAWLGYAAPTPWRILLDGP
+GRRGGERLADDVAAWWDFARTGAGETEDRAGEPDDDRPSLRARGTALHGAVEAHSYGSLV
+AAHALRLLAERGLQPDDVEVLDDTDGGADADAGAQDTARPAERPVEALVVSGAVGLPAAF
+AARAGRLGLPPGRVFRAQAPGDVLARVGRALGRRRDWTDAVLLPVTPRPGLEGGAVHGHR
+TARWSPAAGTDAPRGYRDPGTVTLAATARVTAGLPLPPEPA
+>GCF_020097155.1_00925
+MDLPEQARAAAARLDADRARARDGRLSARQLAALDGAEHALRRDSMDAAIPERVLVDWDL
+DAPDGPVAAVAVGELERPTHLTWQVSGMGIAASTAAWGSAREAGQLLLAQRAAGAPRPCV
+VAWLGYPAPPWWRTLDDGLARRGGARLAEAVRETRPGPSHGAGTAVHTAIEAHSYGTLVA
+THALEGLAAGDPPLTVDALALSGALGLPRRLAGRLEALGLAAGRVFEARAPGDRLAWLGR
+TLAGRAPWPEAVALPVAADPAAGLAGVRGHNTARWRPEDGDDGAPRGYRDPGSVTLAALA
+RVTAGLPVAGGGPRSGQRRA
+>GCF_023573625.1_01792
+MAARSRVRERLRADMARRDGLGRRARSALDGIVHALKPEGMDPHLPARHLLDYVLDGPDG
+PRAVVAAGDPATATHLTWLVSGMGIRPQTAMWGTAREAAHLAAAQRAAGAPRPVVIAWLG
+YPAPTPWRVVLDGPGRRGGAMLAADVRAWWEFMRHGPGEDDAAAPALRARGTAVHGAMEA
+HSYGSLVAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGAVGLPAALAARAAHLGLR
+SGRVFRALAPGDLLARVGRAVGRRRDWTDAAVLPVAPRPGLAGAGVRGHHTARWSPTAPG
+DAPRGYRDAGSVTLAATARVTAGLPLPPVPDGADPAGPVAPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001517.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001517.fa
new file mode 100644
index 0000000000000000000000000000000000000000..001c1b0abb3c7e6527b62763446444959bcafadf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001517.fa
@@ -0,0 +1,32 @@
+>GCF_002008305.4_01874
+MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARMYHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRATQSEPDLSDL
+FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG
+ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF
+PEAALGATIEVPTLERPVKVKVPAGSQCGRVLRLKGRGVERGKTTGDLLVELRVTVPTTL
+NDDARAAVEALQSATAGDDPRRELARKAAW
+>GCF_003691675.1_01570
+MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSEPDLSDL
+FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG
+ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF
+PEAALGATIEVPTLDRSVKVKVPAGSQCGRVLRLKGRGVERGTTTGDLLVELRVTVPTTL
+NDDARAAVEALQSATAGDYPRRELARKAAW
+>GCF_005280335.1_00986
+MSLRAADGETIEVKIPKGIRDGQKVRARGKGAPGAAGRGDLLVTVHVREHEFFRRDGDDL
+RITVPVTFPEAALGATIEVPTLERPVKMKVPAGSQSGRVLRLKGRGVERGTTKGDLLVEL
+HVTVPTELNDDARAAVEALQSALAGDDPRRELARKAAW
+>GCF_020097155.1_00923
+MASQDWLEKDFYQVLGVSKDASESDIKKAYRTLARKHHPDQNPGDAAAEQRFKEISEAYD
+VLSDPKDRQEYDAIRSMGGGARFGAPGGFGGAGGGAGAGGFEDVFGGMFGGGGGSRTFRT
+GGAQGGPDLSDLLGAFTGGGAGGFGGGQGFGGGGFGQPAPTKGADRTATTTISFRGAVEG
+TTVSLRAADGETVDVRIPKGVKDGQKVRARGKGSPGTAGRGDLIVTVQVREHPFFQRDGD
+DLRITVPVTFAEAALGATVEVPTLDRPVKVKVPAGSQSGRVLRLKGRGVAGAKHTGDLLV
+ELQVAVPAELSAEARGAVEAYAAATAGDDVREGLAGKAQW
+>GCF_023573625.1_01794
+MASQDWMDKDFYATLGVSKDASESDVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSGPDLSDL
+FSGMFGGAAGQTGGFGDAGYPRPRPTKGADRTATTTISFRGSIQGTTVSLRAPDGETIEV
+KIPKGIRDGQKVRARGKGSPGAAGRGDLLVTVHVREHEFFHRDGDDLRITVPVTFPEAAL
+GATIEVPTLERPVKVKVPAGSQSGRVLRLKGRGVERGTTTGDLLVELHVTVPTELDDDAR
+AAIEALQSALAGDDPRRELARKAAW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001518.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001518.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c298fdb793c6fb088fb726c61cdd90705284e91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001518.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01875
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALAQAER
+ILDEAGAQAGTEAPQPEASDREAELEADLRRLQAEYVNYKRRVDRDRDLARDAGVLKAVT
+ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPAVHEAV
+MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE
+>GCF_003691675.1_01571
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALAQAER
+ILDEAGAEAGTQAPQPAASDREAELETDLRRLQAEFVNYKRRVDRDRDLARDAGVLKAVT
+ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTVLAGLGLERHDQAALAGVEFDPALHEAV
+MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE
+>GCF_005280335.1_00984
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALTQAER
+ILDEAGAQAGTEAPQPAASDREAELETDLRRLQAEYVNYKRRVDRDRALAQDLGVLKAVT
+ALLPVLDDLDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPSVHEAV
+MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE
+>GCF_020097155.1_00922
+MSENQNETPSPEEPVIRDRRRIDPETGQARTPGAGEDTVPAQEQGQAPQDSGDALSQAEQ
+ILDEAGAAAEAEALPAAGSDREAELLEDLRRLQAEYVNYKRRVDRDRDVAKEQGVLKAVT
+ALLPVLDDLDAARAAGDLEDGPFAAIAAKLMTALEGLGLEREDQEALAGVEFDPVRHEAV
+MRQPHAEVPADHVVQVFRNGYARDGRVLRAAQVMVSAGQD
+>GCF_023573625.1_01795
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETDEPRVSAESAAEQAEDGDALAQAER
+ILDEAGAQAGTEAPQPEASDREAELEADLRRLQAEFVNYKRRVDRDRDLARDAGVVKAVT
+ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPAVHEAV
+MRQPHAEVPADHVVQVFRNGYLRDGRVLRAAQVMVSAGDE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001519.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001519.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e981da0294bc5eaa3e5f5ea528e1680bb1bdc6d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001519.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01876
+MSRAVGIDLGTTNSVVAALEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTFASVKRHMGTDWTAEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVTRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSDLVKELTGGKEPNKGVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAEAHADEDRKRREAADRRNQAEQSAYSVERLLQDNADKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>GCF_003691675.1_01572
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTSISLQYLSVTPEGPVHLDEHLSRAKFEDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSDLVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSQEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVERLLQDNGDKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>GCF_005280335.1_00983
+MSRAVGIDLGTTNSVVAALEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVTRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTSISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVVLVGGSTRMPAVSDLVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVDKLLQDNADKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>GCF_020097155.1_00921
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGEVLVGEVAKRQAVN
+NPDRTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATSGDNRLGGDDWDQRIVDWLLQQAKSKGADLSNDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFNDVI
+KEAGVKVSDIDHVVLVGGSTRMPAVSELVKELTGGKEPNKGVNPDEVVAIGASVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAESHAEEDKARREAAERRNQAEQSAYSVDKLLADNADKLPEDVTT
+EVQADVDALKAALEKQDNDDEVKAAFEKLQASQVKIGEALYAQQSAEGAQPDAESGSAQA
+DEDIVDAEVVEDEDEKKN
+>GCF_023573625.1_01796
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTFASIKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSELVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSQEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVEKLLQDNGDKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001521.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001521.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa35d71d261cc5406d53dc9ee6152976b60783c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001521.fa
@@ -0,0 +1,99 @@
+>GCF_002008305.4_01881
+MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK
+EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVNPFEAQAQQDDA
+RTRLDEGRTELADGEQRLADGRQEIEDGRAELERRTAEADAAEQRLAEAAAQLEEGQAKL
+DAARADLEERGLDALPAEALAPLREAEQQVAEGQEQLDAGRAELEEQAERLEAGQAKLDA
+QRQELEAAQAELDARWAELEAGQAELDARAEQLAAGRAELEQARDAALAEAEAAGIPAEQ
+VTEQFADQEAQLAAAEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR
+LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED
+GRAQLAAGAERLDQAEADLADGRAELEDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV
+TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATAPSLLGPGEVVGLVVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRQELRRGTGLHESIALANGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP
+AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRDLRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERAHAPAQ
+PSVPAPDGGAHRA
+>GCF_003691675.1_01577
+MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK
+EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVNPFEAQAQQDDA
+RTRLDEGRTELADGEQRLADGRQEIEDGRAELERRTAEADAAEQRLAEAAAQLEEGQAKL
+DAARADLEERGLDALPAEALAPLREAEQQVAEGQEQLDAGRAELEEQAERLEAGQAKLDA
+QRQELEAAQAELDARWAELEAGQAELDARAEQLAAGRAELEQARDAALAEAEAAGIPAEQ
+VTEQFADQEAQLAAAEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR
+LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED
+GRAQLAAGAERLDQAEADLADGRAELEDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV
+TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATVSSLLGPGEVVGLVVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRHELRRGTSLHESIALATGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP
+AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRELRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERGHAPAA
+EAASAPAPEAGRTPAVDGGAHRA
+>GCF_005280335.1_00977
+MAKLLYRLGLGAARRPLTVILAWVLALALAVGGFLAFGGTLSTNVTIPGTPTAQVTDRLQ
+DEFPEASRGMGQVVFTTEDGQPFTDAQRDAVAALLDEVAGQDAVDAVVDPFEVQAQQDDA
+RTALADGRQEIADGEQALVDGREQVDAGRAEIEEGRAQADAGEQELADAAAQLEDGQVQL
+DAARADIEARGLDALPAEALAPLREAEQQIADGQAELDAGRAEIEEQAARLAAGQAEIDA
+NREQLEAGQAELDARWGELDAAQAQLDAQREELEAGRAQLEQALAAALEQAEAAGIPAEQ
+VTAQFAEQQAQLEAGQAQLDAAQEQADAGREQLVAAQAEADAGAEQLAEAQAQADAGAEQ
+LAAGREQLEAAEAELESGREQLAAGRQQALDAAAAELDAQQARIDEGRAQHEQGVADLEA
+GRAELAAGAERLDQAEADLATGRTELEDGRVAAERGERSLALVGGYRSVSEDGSTAVGIV
+SFSQPSLDVTAEEKEAVTGALTGADIDGVAVHPSQELNATVPSILGPGEVVGLIVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSVVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRQELKRGTALHEAIALANGTSGNAVVFAGITVIIALVALNVTGIGFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGTRILSRKERARLADEGPASAAEGSAAVRRAGRRSTMSTP
+AAIASALAAIALLVLVALPFGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRELRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSVFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPI
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERGHAPAA
+EAASAPAPEAGRTPAVDGGAHRA
+>GCF_020097155.1_00915
+MATLLHRLGLASARRPWAAILAWLIALALAVGAFLAFSGTLTTAVTIPGTPTAQVTDRLK
+EQFPDAAKGTGQVVFATEDGSAFTEAQRRAVSDALRGVEGQDAVDSVVDPFDVARQQDEA
+RTALEDGRRQIAEGEQKIAENEKALEDGRAQLAEAKDKAEAGQKELDAAAAQLDAGQEKL
+DAARADLEARGLDALPAEATAPLTEAQQKLDAGQAEYDAGVAALEEQRPALEAAEAEIAK
+QEAALEQAQARFEAGRAQAIAQAEAAGATPEQAAAAVDARLAPEREKLDAGAAQLEEARA
+RTEAGRAEFDAGEEKLAAAAAELEQGRAQLAAGREKALTAARAELDAQQQKIDAGRAEHE
+QGVRELEAGRAEIAQNEAKLADGPAQLEQARKDLAAGREKADRGQRMLTLTDGYRVVSED
+GSAALGTVAFDRPSLDVTTEQKTAVIDALADADIPGVRAIPTQALNATMPSLIGPGEVVG
+LAVAALVLVLMLGTLVGAGLPLVNALIGVGVGAAGALAFSGVVEMMSVTPVLGIMLGLAV
+GIDYALFIVNRHRLELKRGTPLHASIALANGTSGNAVVFAGITVVIALVALNVTGIPFLG
+LMGTVGAVCVAVAVLVAVTLTPALLSLAGMRILSRKERARRAAEAAPVADDAAAPSGSHA
+AAPVSRSAARAVRDARRRRRMSTPAAVATVLASAAALIVVAIPFGSMRLGLPDGASEPVG
+SDSQVSYELIADEFGEGYNGPLVVTVDLPSGLDETTAEDAQVQVGEQLKGLEHVAAVVPA
+GFNQDRTTAMFQVLPEEGPNAISTGDLVHTLRDTEPAGEASNLGVAGVTSGFIDVSEKLS
+AALPLYLGVVVGLSLLIMILVFRSILVPLIATGGFVLSVFAAMGGVVAIYQWGWLGGLFN
+VHAPGPVLSFLPTIMIGVLFGLAMDYQLFIASGMREAYAHGQPARDAVMTGLRAGRAVVT
+AAAIIMISVLGGFVFSHDAMIRPIGFGLAFGVLLDAFVVRLLLMPALMHLLGDAAWWLPK
+WLDRILPDVDVEGAGLERHGAAGEAADAAPVGADRA
+>GCF_023573625.1_01801
+MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK
+EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVDPFEAQAQRDDA
+RTRLDEGRAELADGEQRLADGRQEIEDGRAELERRTAEADAGEQRLAEAAAQLDEGQAAL
+DAARADLEERGLEALPADALAPLREAEQKVADGQEQLDAGRAELEEQAERLEAGQAEIDA
+QRQELEAGQAELGDRWTELEAGQAELDAQAEQLAAGRAELEQARDAALAEAEAAGIPAEQ
+VAAQFADQEAQLAAGEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR
+LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED
+GRAQLAAGAERLDQAEADLADGRAELDDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV
+TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATAPSLLGPGEVVGLVVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRQELRRGTGLHESIALANGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP
+AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRDLRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERAHAPAQ
+PSVPAPDGGAHRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001524.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001524.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54edf9e694ac21af415bb575047355fb863d8b01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001524.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01884
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLAI
+EWRSWVWLPVLLLAWVTQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVVRRAEPPA
+DPGPRRAGARPRGRR
+>GCF_003691675.1_01580
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLGI
+VWRSWVWLPVLFLAWITQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVGRRAEPPA
+DPGPRRAGARPRGRR
+>GCF_005280335.1_00974
+MTETATFLDWLSAALLVSGAFFTLVAGVGLLLLPDLLARMHASAKPQVLGLMLMLAGLAI
+AWESWPWVPVLFLAWVTQMVTAPVASHLVGRTAYRTKHARRELLHRDELAAIARRVEPAP
+ELDPRSPESRRRRRR
+>GCF_020097155.1_00912
+MDAAWTDWLAAALLVGGAFFSLVAGVGMTLLPDLLSRMHASAKPQVLGLLLMACGVAVLW
+QAWAWVPVLVLAWVTQMITAPVASHLISRTGYRTKHVRRDLLHRDDLAAQAEPGPREDPD
+AR
+>GCF_023573625.1_01804
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLAI
+EWRSWVWLPVLLLAWVTQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVVRRAEPPA
+DPGPRRAGARPRGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001525.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001525.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa40960ddca41c6363032642d2720e710c418c68
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001525.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01885
+MDPMDLATWAGGALLVVGAVGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAVHRHT
+HHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR
+>GCF_003691675.1_01581
+MTDPFHLAAWIAGTLLFVGALGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAAHRH
+THHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR
+>GCF_005280335.1_00973
+MTDPFHLAAWIAGTLLFVGALGALYRIVRGPSLLDRAIATDVLLVVLSSGLILDMAVRRH
+TDNVVLVVLAATVGFVGSVTVARFVEDRRPDHSMEDQARVPGTSDVPGGEEGR
+>GCF_020097155.1_00911
+MSLPLTLAAWIGGAMLFVGAVGALYRIARGPSLLDRAAATDVLLVVLSGALLLDMGVHRR
+TDTVVLVLLAAAVGFMGSVMVSRFVEDRRPEHPQEHEALVPGTSDVPAPREDA
+>GCF_023573625.1_01805
+MDPMDLATWAGGALLVVGAVGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAVHRHT
+HHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001526.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001526.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6353f5eeb8f75daeda6e3a4b823137e726bdeb2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001526.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01886
+MPGSDSARRGVVRPDRIRGIVAQWPLILVMVAVWCALWQDFAPHVALTGLAFALLIIGLF
+PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVAGTVLLRGRRARGSIVGVPLRSHDDL
+IITLVSHALALVPGSIVLDVDRVRSVLYLHVLDATTDEDVAGFRAKALDVEAGIIRAVGT
+REDLELVRRFPSSAPPAARPPKEEA
+>GCF_003691675.1_01582
+MPGSDSARRDVVRPDRVRGIVAQWPLILVMVAVWCALWQDFAPHVALAGLAFALLILGLF
+PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVTGVVLLRGRRARGSIVGVPLRSHDDL
+IITLVSHALVLVPGSIVLDVDRVRSVLYLHVLDATTDEDVEGFRAKALDVEAGIIRAVGT
+REDLELVHRYPDTAPPEEESAERRRPAAPRPGGTAPIGSTADHAKEGT
+>GCF_005280335.1_00972
+MPGTDPARDAAGAERPARPHRVRDMVGQWPLIAVLVLLWCAVWEDYSLHVALAGLAFSLL
+VMVLFPMPRIPFSGRLNPWWFLVFTAQFLGDVVRSSVEVSKVVLLRGRAARSSIVGVRLR
+SHDDLVITLVSHALALVPGSIVLDVDRARSILYLHVLDATTDEDIEDFRAKALRVEAGII
+KAVGTREDLELVHRYPDTAPPEEESAERRRPAAPRPGGTAPIGSTADHAKEGT
+>GCF_020097155.1_00910
+MPAAETTSPASAPTRPAPGGVRSVLRQWPLLLALVLMWCAVWQDFSAHVALTGLLFSLLV
+VVLFPMPPIPFGGRFHPGHALVFTGRFLADVVASSLSVTRVILTRGRTVRSSVVRVPLRS
+HDDIVLTLVSHALALVPGSIVLDMDRANGVLYLHVLDATTDADVADYRAKALRVEADIIR
+AVGTRADVAVLRDHPDSAPDPEGVEERRRHPAYRAELLPDTPGPVAPAPVDARPEPDAPG
+GDR
+>GCF_023573625.1_01806
+MPGSDSARRGVVRPDRIRGIVAQWPLILVMVAVWCALWQDFAPHVALTGLAFALLIIGLF
+PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVAGTVLLRGRRARGSIVGVPLRSHDDL
+IITLVSHALALVPGSIVLDVDRVRSVLYLHVLDATTDEDVAGFRAKALDVEAGIIRAVGT
+REDLELVRRFPSSAPPAARPPKEEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001527.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001527.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfbee05011298bc96235a038c3df4892e5060c44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001527.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01887
+MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGVTYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
+>GCF_003691675.1_01583
+MSIGSVPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGITYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTTLFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDLEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
+>GCF_005280335.1_00971
+MSIGSVPMTDLAPLAVMMPVLGAAVTFMLVRRPRAQVVVTVAALVLTLLLNCLLLAAVWE
+GGVASVHVGGWPAPLGITLVVDRLSALMLVVSALITLAVLLYASAQGMVNRDEGGPVSIF
+HPTFLILVAGVFNAFLAGDLFNLYVGFEILLTASYVLLTMGGTAQRIRAGITYVVVSVIS
+SVVFLIAIAMVYAATGTVNMADLAVKLGELPSDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATQMGLAATVFYVGHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFISVLFLIPALNLGGIPPFSGFLGKVGLLRGGVEQGTGLSYTLVG
+VSLLASLLTLLVVVRVWTRAFWRKVEDVEHPPAQLVAAYERTIDRGLRPRRLEPGLVLPT
+AALVVMTLAFTVLAGPLFDLADAAATDMLDRTPYIASVLDEAAAERAAETLSHDPTEVHD
+ARH
+>GCF_020097155.1_00909
+MLGSTPLTDLAPLAVMLPVLGAAITFALVGRARAQVVVTVSALTLTLVLDCLLLADVWTG
+GVAVVELAAWPAPVGITMVVDRLSALLLVVSSLITLAVLLYASAQGLINKDEGGPVSIFH
+PTFLVLVAGVSNAFLAGDLFNLYVGFEILLTASYVLLTLGGTEARIRAGITYVVVSVISS
+VLFLIAIAMIYAATGTVNMADLAVKLGELPHDLQLVLHVMLLAGFGIKAAVFPLSFWLPD
+SYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPAEHVNGLLMGVAALTMLVGILGALAQ
+SGLKRILSFILVSHIGYMVFGLALATQVGLAATVYYVGHHITVQTALFLVTGLIEQRAGT
+ASIDRLGSLAKVSPLLGVLFLVPALNLGGIPPFSGFLGKVGLIRGGVEDGGVLAWVLVGV
+SLLVSLLTLLVLVRAYTRAFWRKVEDVEHPTPQLVAAYERVTRRGLRPKPLSRGLVLPTA
+GLVAMTLAFTVFAGPLYDLADRAAVDMLERSPYISAVLGPEAADRAAVTLSHDPSEVHDA
+GR
+>GCF_023573625.1_01807
+MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGVTYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001528.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001528.fa
new file mode 100644
index 0000000000000000000000000000000000000000..992b5abe8a8682def5a92114884f4e5d5eb7b5ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001528.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_01888
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIVLINNGAIMLLFLSSGGTGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVIAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP
+AWDAEDDAELVEESSEFLDDAADPNAHYEHATESRPHVRHASPTPPAHPGPASAVRAHRA
+DGGPRP
+>GCF_003691675.1_01584
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIMLINNGAIMLLFLASGGVGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVVAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP
+AWDAEDDAELVEESSEFLDDAADPNAHYEHATEARPQVQHATPAPQAPTGSGAASRGRRP
+EGGERA
+>GCF_005280335.1_00970
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIMLINNGAIMLLFLASGGVGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVTAFLTAMIYRSWLISREDEVEVDAEDVKIASQG
+AWDAEDDSELVEEHSEFMDASTDPNAHYEHTTEARPQVQHVIPAPPTAAGSREAARGRRP
+EGGERA
+>GCF_020097155.1_00908
+MTPTVDLALLAVMGVLFATGIYLLLERSLTRILVGVMLINNAAVVLLFLTSGGAGLAPLY
+DADTAPEDYADMLPQALILTAIVIGFATTAFLTAMIYRSWQLRREDDVATDVEDVKIAAQ
+SGWDAEDDSVLTEEDSEFMDDASDPNAEYEFATAAAPRARAVRPGRATVQGGGGRP
+>GCF_023573625.1_01808
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIVLINNGAIMLLFLSSGGTGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVVAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP
+AWDAEDDAELVEESSEFLDDAADPNAHYEHATEARPQVQHATPAPQAPTGSGAASRGRRP
+EGGERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001530.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001530.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f13880bcf093bc7cdf4b220297306635e8427543
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001530.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01890
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRLWLALTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPAADGGPRRESVLGSYREL
+GATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVYGLAASDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR
+>GCF_003691675.1_01586
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRRGLGLTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGAVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDEGLNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPSPGGGPRRESLAASYRAL
+GSTLARMWREDRNTLWFLLSSAVFRDGVGAVFVYGAILGTTVYGLAASDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR
+>GCF_005280335.1_00968
+MPGMDPAASAVPDAALPRLATAAPRRQVVAWALWDWGSAAFNAVMVTFVFGTYLASDAFG
+PDERGTAWLSTALAVAGVVIALTAPVMGRRADGAGRRRLWLGVMTAAVIACTTACFLVTP
+QESSLLLGVTMIALGTVFFEFAEVQVNAILVQISTPATIGRISGIGWGAGYLGGILLLLI
+VFVGFVSGDAHWFGITGDEALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPTPGGGPRR
+ESLAASYRALGSTLARMWRQDRNTLWFLVSSAVFRDGVGAVFVYGAILGTTVYGLAASDV
+ILFAIVANVVAAAGAFAGGRLDDAIGPRRVILGSLAAMVLVAAGLALASGTLAFWIGGLA
+LCLFVGPVQSASRAFLGRLTTERTAGEVFGLYATTGRAVGFITPMLVTLALAAVPDNRVV
+IPVIVLVLIVGGVLFARVTDPVTRSAEPAP
+>GCF_020097155.1_00906
+MPRMSSPAPHAAPQPCPAPHGGAGPAPARVPRGRVVAWAAWDWGSAAFNAVMVTFVFGTY
+LASDAFGPDDRGTQWLSAANALAGVVIALTAPALGRLADGTGRRRLWIALTTGAVIACTA
+ACFLVTPEESMLGLGVTLIALGTVFFEIASVHINAILLQISTPATIGRVSGFGWGAGYLG
+GIVLLLIVFVGFVSGDDHWFGVGEERALNIRVVALVAAAWFLVFALPVLAASPEPPAARG
+ADGSPRRESLVESYRGLGRTLARMWRQDRLTLRFLAASAVFRDGVGAVFVYGAILGTTLY
+GLAAQDVVLFAIVANVVAALGAFAGGRLDDALGPRRVILGSLAAMVVVAAALVLAEGTAA
+FWAGGLALCLFVGPVQSASRAFLGRLTVPETAGEAYGLYATTGRAIGFITPALVSAALAV
+WGDSRVIIPVIALVLLAGGALLLGVREPEGPTVAGARPGTGPRAAR
+>GCF_023573625.1_01810
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRRGLALTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPAADGGPRRESVLGSYREL
+GATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVYGLATSDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001531.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001531.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d041e90e5193ad1056c2eb747bb434310cb9dd12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001531.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01891
+MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQKQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSSAQSPYGTGANQNRYQGQRGPTAS
+RAHRDFHLTRIER
+>GCF_003691675.1_01587
+MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSAAQSPYGTGANQNRYQGQRGPTAS
+RAHRDFHLTRIE
+>GCF_005280335.1_00967
+MLLSDQDIRAELASGRVGLDPLDEAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFTGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSPAASPYGTGANQNRYQGQRGPTAS
+RAHLDFHLTRIDR
+>GCF_020097155.1_00905
+MASVLLSDRDIRAELSSGRIGLDPLELSMVQPASVDVRLDRFFRLFDNHRYAHIDPAQPQ
+EELTRLVEVEPDQPFVLHPGEFVLGATYEQITLPDDVAARLEGKSSLGRLGLLTHSTAGF
+VDPGFTGHVTLELSNVATLPITLWPGMKIGQLCFFRMSSPAESPYGSGGNLNRYQGQRGP
+TASRSHQDFHLTRIPR
+>GCF_023573625.1_01811
+MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSSAQSPYGTGANQNRYQGQRGPTAS
+RAHRDFHLTRIER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001533.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001533.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3662c89531ad3dadb3022e8d532e9f3bf30c81fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001533.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01899
+MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVEGAAAWLATADAVIVAAPVYTG
+SFAADARAFLDTRRAELTDLPLVILASGGAPELARPVREKLESYGPREVAYFRGALFEER
+LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLPGAGVR
+>GCF_003691675.1_01595
+MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVEGAAAWLATADAVIVAAPVYTG
+SLAADARAFLDTRRAELADLPLVILASGGAPELAPPVREKLESYGPREVAYFRGALVEER
+LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLSGAGVR
+>GCF_005280335.1_00959
+MTTLIVTSSAHGSTREIAERVAEVLRTSQSVETVVEDVAGAAAWLATADAVIVAAPVYEG
+SLAAEARHFLDSRRAELADKPLLFLASGGGYELDPKVREKLESYGPREIAFFRGALVEER
+LGWLEKLKLKVSRNENYGDYRDWDAIEAWAKSLSGHGVR
+>GCF_020097155.1_00899
+MTALIVTASRHGSTREIAERVAEVLRTTAQTDTVVEDVAGAAAWLDTADAVVVAAPVYGD
+KLEKSAKAFLDSRRAELSQKSLVILYSGASPVPNRALADQLGTYGARDVKYLRGALVEER
+LGALEKLQIKLVKGRYGDFRDWNAVEHWAKGLSAHGVN
+>GCF_023573625.1_01819
+MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVKGAAAWLATADAVIVAAPVYTG
+SLAADARAFLDTRRAELADLPLVILASGGAPELARPVREKLESYGPREVAYFRGALVEER
+LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLSGAGVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001534.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001534.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c6c3addbbfab62bdd313f2aee864eaa4db406f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001534.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_01900
+MMVGMTAPQTPNPVPSADAPAAVPRAATRVRASELVGRGWLNTGGEQVTLEDLRGKVVLL
+DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV
+LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH
+RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGSFLVSDTGHHRLLEVAEDLTTVLRAFG
+GGDPATADAGQAELAFPTPGEKGHADGGPDEALFNEPQGLALLPEDVAERVGYDVVVADS
+VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDIAVDLADLPGEPTAISL
+SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTGALAVHAGTALEGLLDGDAGRAWFAQPS
+GLSVGADGALWVADSETSAVRWVRTGEDGRREVGTAVGAGLFDFGHVDGEADRARLQHPL
+GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG
+NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL
+DDRWGDPTQLKISSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ
+PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH
+>GCF_003691675.1_01596
+MMVDMTAPQTPNPAPTADAPAAVPRAATRVRASELVGRGWLNTGGEQVSLEDLRGKVVLL
+DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV
+LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH
+RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGTFLVSDTGHHRLLEVAEDLTTVLRAFG
+GGDPATADAGQAELAFPTPGEKGHADGGPDQALFNEPQGLALLPEDVAQRVGYDVVVADS
+VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDVAVDLADLPGEPTAISL
+SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTDALAVHAGTALEGLLDGEAGRAWFAQPS
+GLSVGADGTLWVADSETSAVRWVRTGEDGRREVGTAVGAGLFDFGHVDGEADRARLQHAL
+GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG
+NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL
+DDRWGDPTQLKVSSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ
+PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH
+>GCF_005280335.1_00958
+MMVGMTDPQTPPAVSPDAAPSDAAPAAVPRAASRVRASELVGRGWLNTGGEQVTLEDLRG
+KVVILDFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYT
+IEHPVLDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYSLVRELVAEHEA
+KGTLHRGSGPYVPPAPVARDLKFPGKAISLAGRGTAPGTFLVADTGHHRLLEVAEDLTTV
+LRAVGGGDPAGAGEEQAGLAFPTPGEKGHADGGPEQALFNEPNGLALLPEDVAERVGYDV
+VVADTVNHRLRGLRLADGGVSTVAGNGVQKLIDSERAKEASAGDAEDVAVDLSDLPGEPT
+AISLSSPWDVAWDPAAGRVVIAMAGTHQLFDFDPVAGALAVHAGTGLEGLLDGDAGSAWF
+AQTSGLSLGPDGTLWAADSETSAVRWLRTGEDGRREVGTAVGTGLFDFGFVDGEAAQARL
+QHPLGVTALPDGSVLIADTYNGAVRRYAPAGEDAAGRPVAAAVSTVARGLQEPSDVLVEH
+DADGAPAAIVVVETNAHRLVRLAVPEEYLTVDEGARQTQRPRTPMVAGDVDLAIGFAAPS
+GQKLDDRWGDPTQLKVSSSPEELLLEGAGTSTGLSRTLRLNPAVAEGVLHITARAAACDG
+EKGQPIPDHAACHLYQQDWGIPVTVHAPEGAPEGAETRLDLDLRGIH
+>GCF_020097155.1_00898
+MRRPLPADARRAWAMMEGMTEQQTSAPSVPRSGSRVRASSLVGRRWLNTGGTEVSLEDLR
+GKVVILDFWTFCCINCLHVADELRPLEEEFSDVLVTVGVHSPKFEHEADPDALDAAVERY
+DIAHPVLDDPTLVTWQAYSARAWPTLVVVDPEGYIVAHLSGEGHVAGLYSLVRELVAEHE
+AKGTLHRGSGPYVAPAPVARDLKFPGGAVSLEGRGSRPGSFLVADTGHHRIVELAADLTT
+VLRAIGGGDPAEAPAEAADLAFPTPATRGHRDGGPETALFSEPNGLLLLPEDVAARAGVD
+VVVADTVNHRLRGIDLATGEVTTLAGNGVQKLIDSERVREAAAGDESAAADLSDLPGDPT
+GISLSSPWDVAWDAAAGRVIVAMAGTHQLFSYDPVARVLAVHAGTGLEGLLDGPADTAWF
+AQTSGLSFAQDGTLWLADSETSAVRWLRTAEDGTRQVGTAVGTGLFDFGYVDGAPEQARL
+QHPLGVTALPDGSVLVADTYNGAIRRYAPAAEDAAGRPVEAAVSTVTRELKEPSDVLVEP
+GEDGAPAEIVVVETGAHQLVRISVPAEYLTVDEGARQTARPSTDVAAGDLDLSVGFAAPA
+GQKLDDRWGDPTQLKVSSSPEELLLDGAGTSVGLTRTLRLNPAVAEGVLHITARAAACDG
+EKDGPIPDSAACHLYQQDWGIPVRVHAADQAPDGAETRLDLDLRGIH
+>GCF_023573625.1_01820
+MMVDMTAPQTPNPAPTADAPAAVPRAATRVRASELVGRGWLNTGGEQVSLEDLRGKVVLL
+DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV
+LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH
+RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGTFLVSDTGHHRLLEVAEDLTTVLRAFG
+GGDPATADAGQAELAFPTPGEKGHADGGPDQALFNEPQGLALLPEDVAQRVGYDVVVADS
+VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDVAVDLADLPGEPTAISL
+SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTSALAVHAGTALEGLLDGEAGRAWFAQPS
+GLSVGADGTLWVADSETSAVRWVRTGEDGGREVGTAVGAGLFDFGHVDGEADRARLQHAL
+GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG
+NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL
+DDRWGDPTQLKISSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ
+PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001535.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001535.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b3e53f0b7f6f8e0d76549702c376cae98ae56ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001535.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01901
+MSADRVRPLRRPAAPRRGRLRLVAAVAAGLLALTGCGAGDNDPAAASVPADGVHDDAGTA
+VHTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD
+RTTVQPAQCKAPLTALDFSPIALDGAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH
+IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL
+TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD
+>GCF_003691675.1_01597
+MSADRLPPLGRPAAPRRGRLRLAAAVAAGLLALTGCGAGDGDPAAASASADGVHGDAGTA
+APTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD
+RTTVQPAQCKAPLTALDFSPIALDEAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH
+IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL
+TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD
+>GCF_005280335.1_00957
+MLALTGCGAGDEPAPEQPSAPADALHGDVGGAAPAPEEGAEGLGLGDRQDERMAAAAAER
+AVGFGFVRQRAAAPEEIDAAREDSRARRSDADRTTVQPAACKAPLTALDFSPISLDEGEA
+TRVDVGADTFTGTGTVEVARLTGSGRQEVERHLQTVNGLLADCREMTMTVQDGDASVDYR
+LAVSEAPLSEGTPAQSALVWERSLASADGPQLTAQVLTAVTADAVVMVSFVGQPEAGRKE
+FTLIAEEMLAAALAAG
+>GCF_020097155.1_00897
+MSADRTRPRPAVRRLAVASSGAALAAVLLAGCASGGDAAASSGAQAAGPSSSAATGGLDL
+GDRVDQRRAEAAAARAASFGFTRQDAVGADQIAAARGDAADRAADDGRTTVEPARCQAPL
+AALDFSPILLDQEEVSRVDVGTDSFAGTGTVEVATLDGPGRQRVEEHLQTVNTLLADCRD
+MTVTTRDADGARTYRLQMSAAGLSDGSPAQSGLVWTQTPAGRDEPATAAQILTAVGPEDV
+VMVSFTGQPQAAERQFTVMAEEMLAAAGTVTR
+>GCF_023573625.1_01821
+MSADRVRPLRRPAAPRRGRLRLVAAVAAGLLALTGCGAGDNDPAAASVPADGVHDDAGTA
+VHTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD
+RTTVQPAQCKAPLTALDFSPIALDGAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH
+IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL
+TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001536.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001536.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb166c717e025a621b4a8f17ec3c563c7932dcf9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001536.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_01902
+MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNVAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPATDAPSGAEPAARDSSTGPEEARDVR
+>GCF_003691675.1_01598
+MSAATAPARGSHPTENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVGAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHNGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLSLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLQTHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMIFHAFIGVAMTTSTGLMQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPVTDAPSGAEPVARDSSTGPEEARDVR
+>GCF_005280335.1_00956
+MLVAAAGAGALAVAAWLTGITAVRELSDPGWITRWGVPAGELVSNLAMTMAIAAIIFAAG
+ILPPHAAGTERWHRSAAQRRADAQEGPLPEHPAFTRTLRVAAVSAGVWTVAALAVGILSY
+SDLAGIPVTAGEGFTAGLVAYVAGISVGQAWFWVTVIAAVVTTLVIAVRSHNGLFWTGIL
+AMIGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVWVGGLLVLVAISDTLVGPDGAQGR
+ARAPREQGPTPLLHTALSRYSVLAGLGLVTVALSGVVNASIRMDDPAQLTSPYGMLVVIK
+FLATLGLGLVGLMHRRWVIPRLDAGPDRPSPAPARRLLWQLIAVEAVVMAAVMGLSAVLS
+RTAPPVPEELAPDATPARILTGYELPPELTGARWITEWRLDWLWVAIIAFLALWYLRSVW
+RLHRRGDRWPVLRTLSWMVGLAVLLWATSGSPAVYGRVLFSSHMMGHMTLTMISPLFLVL
+GAPITLALRALPSRTDGSRGPREWILWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFF
+RFSLETHVGHEFMNVHFLLTGFLFALVMVGSDPLPSRPAYPLRLVLLLATMVFHAFIGVA
+MTGSAGLIQASWFGNMGRDWGPSALEDQHIGGAVMWGIGEFPTVVMAVMVAVLWYRNDRR
+NAERLDRRADRDGDAELHRWNEMYARMHGTPAAPAEPAPAAASPADPTPAASAPRPRRPG
+DPRWPLSTAHPPEDPAGPEDRAAPARWPRPPSSGCWR
+>GCF_020097155.1_00896
+MPTSTAVPPATAQHPLGVPRPVLLGAAVVGVLALVLAAWFAGVTAPRELSDPGALTRWGV
+PVGKAVNNAAMAVTIGALIFAAGILPPHAAGTERWHRSPRQRAQDAEEGPRPEHPAFGRV
+MAVAAAAAGVWTVAALAVGVLSYSDLAGIPVSAGGSFTDGLLAYTLDISVGRAWFWVTVI
+AAVVTTLAIGVRSHTGLFWTGVLAMLGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVW
+VGGLLVLALISDTLVGPNGAQGRGASLRRQGPAPLLHTVVSRYSVLAGLGLVTVALSGVV
+NASIRMDDPAQLLSPYGTMVLTKAGAVLLLGGIGLLHRRWIIPRLDDDGAAESPPAARRL
+LWQLIAVEAVVMAAVVGVSAVLARTAPPVPEELAPDATPARILTGYELPPELTGDRWFTM
+WRWDWLWVAIIAFLAVWYVRAAWQLRRRGDRWPVLRTLSWLIGLAVLAWATSGAPAVYGM
+VLFSAHMVGHMVLTMIVPLFLVLGAPITLALRALPARTDGTRGPREWILWIVHSPWGAFI
+TNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFIFATVMVGADPLPSR
+PPYPLRLVLLLATMVFHAFIGVAMTTSTGLLQASWFGSIGRDWGPDALTDQHIGGGIMWG
+IGEFPTVLMAVTVAVLWARSDTKTAARLDRRADQDGDAELARWNQMYAAMNHPGADQDPA
+RGDRP
+>GCF_023573625.1_01822
+MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWMLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPATDAPSGAEPAARDSSTGPEEARDVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001538.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001538.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a92ce345f3cdec9b46fc806045308de788532976
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001538.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01904
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATDAAPASDASPA
+ASTADGQAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVS
+GEDGQMVMQESPDGFTVPAGGSLELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLE
+VTSVVRPFTGANESYHGGQSHESEDHADH
+>GCF_003691675.1_01600
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATGASSAASTADG
+QAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVSGEDGQM
+VMQQSPDGFTVPAGGSFELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLEVTSVVR
+PFTGANESYHGGESHESEDHADH
+>GCF_005280335.1_00954
+MTTPRSARCLSAAAVMAAAALGLTACAGGADDAASSSSSAPTAATSSAPAEGQGAPLTVS
+DPWTKATEDGMTGSFGLLENSSDEDLHVVGVSAEVGAKAGLHVMVADEDGQMVMQQSPDG
+FTVPAGGSFELAPGGAHVMLMGLTEPIEPGEEVAYELELEDGSTVEVVSVARPYTGANES
+YDGGEAEESDEHADH
+>GCF_020097155.1_00894
+MTMKHPSQTVSRRLSLAALAAAGSLALAACGGASAPASSSSSAAASSATATTPEAAGSAA
+SSSATAADSSAAPLTMTDAWTKATDGAMTGSFGTLENTSDAPVHVVAVTSDRTDRVELHE
+MAADGKGQMTMQQSPDGFTVPAGGTFELVPGGDHVMFMGLTQPVKAGAEVSYTLKTEDGR
+TLEVTSVARPFTGADESYHGGEASSSMSGMGMNSSMPAGSGHADH
+>GCF_023573625.1_01824
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATDASPAASTADG
+QAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVSGEDGQM
+VMQQSPDGFTVPAGGSFELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLEVTSVVR
+PFTGANESYHGGDSHESEGHADH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001540.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001540.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a179623d925a646e8468b48036896e13abb566c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001540.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01906
+MRSAVAAAPWAPSGLEDPRPRVVRGPARLARGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLAAGGPAVAPAAGVDPAH
+LGHARPGTGALLAPGEALSSAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPALRPATSLALLSSPGRRGPPFALAA
+>GCF_003691675.1_01602
+MRSAVAAAPWAPSGLEDPRPRVVRGPARLARGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLAAGGHAVAPAAGVDPAH
+LGHARPGTGALLASGEALSGAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPVLRPATSLVLLSSPGRRGPPFALAA
+>GCF_005280335.1_00952
+MRSAVDAAPHAFGRPHPAPGRVVRGPARLARGVAGALAMTVLAALFHAAAVPGAGLPDVR
+VAAFAAVLAAPVCTALAGRALSLWRTAAAVAVAQGLFQVLYGIAAGGHAVAPAAGVDPAH
+LHHAAAAAGPLVSVSAGPAAGHVHAAEPLMLAAHAAAAVLTVLVLRRGEALVLAVAERVL
+QAVLPRAASAGPLPLPSPARVPALPAPRPTESLVLLGTPGRRGPPFALAA
+>GCF_020097155.1_00892
+MGTPTPVPSRAVAGPARVLRGAAGALAMTLLAALFHSAAASTPLPAPALLLFSAVLAAPV
+CTLLAGRALSLWRTAAAVAVAQGLFHALYSVAAGGRSVATAAGVAPAHLAHSHVGAARPL
+LTVDAASETSAHAAHAGTPGMLLAHLAAAALTVAVLRHGERMLVAAAERVLQAAPVWRLL
+VALAAGLLPTPRPVRVPAWRAPSAPAAVVVLASPGRRGPPAFALAA
+>GCF_023573625.1_01826
+MRSAVAAAPWAPSGLEDAPPRVVRGPARLVRGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLATGGHAVAPAAGVDPAH
+LGHAHPGAGALLAPGEALSGAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPALRPATSLALLSSPGRRGPPFALAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001542.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc43ed1ed7be3e371d48124b0ce25d2ccacd4c46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001542.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01908
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
+>GCF_003691675.1_01604
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
+>GCF_005280335.1_00950
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
+>GCF_020097155.1_00890
+MAKKSKIAKNEQRKVMVARNAEKRLELKKTLIDPNASDEAREAARVGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFREMAHRGELPGVTKSSW
+>GCF_023573625.1_01828
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001545.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001545.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29243ef95cf9e00b11ec6f4877eff9edac538e75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001545.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01911
+MSHTSEQSSPLADQVPPGGPDEPHAAEGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA
+TTALTPVLLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV
+QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLSFLVGAL
+LPFLTVVLAPVDFRIPLTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTL
+AVGSLLGASVA
+>GCF_003691675.1_01607
+MSHTSEQSSPLADQLPPGGPDEPHAAGGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA
+TTALTPILLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV
+QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLAFLVGAL
+LPFLTVVLAPVGLRVPFTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTF
+AVGSLLGASVA
+>GCF_005280335.1_00943
+MNESTAPSEPTVRDDVAASSGHDRPEPHAGGGLHERLNWLRAGVLGANDGIVSVAATVVG
+VAGATTAVAPVAIAGVAAVVGGAVSMALGEYVSVSSSSDSQKALIAKERRELAEDPEGEL
+EELVGLYEAEGLSRATAENVARELTEKDALKAHLRAELGMDETGVVSPWSAAGASFVAFL
+LGALLPFLTIILAPVDIRVALTFVTTLVALAGTGYAGAWLGGAPPVRAMLRVVIGGALAL
+ALTFAVGAWLGTTVA
+>GCF_020097155.1_00884
+MSHSTAPAAPSSYPDEPHAQTGVHARLNWLRAGVLGANDGIVSVAATVVGVAGATTAVTP
+VLLAGTAAVVGGAVSMALGEYVSVSSSSDSQKAMIAKERRELAEDPEGELEELVGLYEAE
+GLSRDTAEQVARELTANDPVTAHLRMELGMAEEDVVSPLAAAGASFIAFLVGALLPFLAI
+LLSPVGVRVPVTFGVTLVALAVTGYLGAWLGNAPAVRAMVRVVVGGALALALTFGVGTWL
+GVGVA
+>GCF_023573625.1_01831
+MSHTSEQSSPLTDQVPPGGPDEPHAAGGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA
+TTALTPILLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV
+QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLAFLVGAL
+LPFLTVVLAPVGLRVPFTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTF
+AVGSLLGASVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001547.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001547.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7630cda53fe9cea122b179429dbaee6f54747b80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001547.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01919
+MTTTTATPGPTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DAAGTPMLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLRED
+>GCF_003691675.1_01615
+MTTTTATPGPTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAATEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DVAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLREG
+>GCF_005280335.1_00941
+MTTTPATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDAAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHTATGAPVRAADPDWCRGGAAVLTPDERI
+DVAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLAQVSAALAELGEDEAATVTPEQ
+LAPRIYPGLEGTVARVAVQTVAAHLRHLREG
+>GCF_020097155.1_00876
+MTTTPATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVLFADDADAAVVLDPGPAEDAEGHL
+ERVRQAAEGRRIELVLVSHRHADHTGGIDAFHAGTGAPVRAADPSHCRGGGLPLTPDEEI
+VRAGVRILAWHTPGHTSDSYSFAVPESGPHGAVLTGDTILGAGTTMLDHPDGTLTDYLAS
+LARLQAAGPLTVLPAHGPVPAPLDVIARDYIDHREGRLFQLRRALDGMDPARAAMVTPSE
+LVGVIYPEVTGQVARVAEQVLAAHLAYLRRG
+>GCF_023573625.1_01839
+MTTTTATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DAAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001549.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001549.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c5e8847f2d0f170553b31f15076a02d56adcbaa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001549.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01922
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV
+GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
+>GCF_003691675.1_01618
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVVAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEDLVGRIRNAGAVFV
+GPHAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
+>GCF_005280335.1_00938
+MEADRPRGPGPAAAVVVPRRCTPTPAPPTSLEDPVLSVTDLRQIDTAAADLSRIIPRADV
+DVASTVPVVAPILEQVRTGGEAALLELAERFDGVRPPALRVPAEALAAALEGLDADVRAA
+LEESIRRARLVHAAQLPQDSTVELGEGASVQNHWIPVDRVGLYVPGGRAVYPSSVVMNVV
+PAQAAGVGSLAVTSPPQADHGGLPHPTVLAACALLGVDEVYAAGGAQAVAMLAHGVRDER
+GGWLCAPVDMVTGPGNVYVAAAKRALQGIIGVDAEAGPSEIAVIADGTARADWVAADLIS
+QSEHDPLAASVLITDSEDLVRDVLAAIEAQVPGSFHEEQIRVALTGPQSGVLLVRDLDQA
+VEVSDRYATEHLEIQTRDPEAVAARIRNAGAVFVGPHAPVPLGDYSAGSNHVLPTSGTAR
+HSSGLSTVTFLRLQQRIRYTETGLKELAEGISVLAEDERLPAHGVAVRARFA
+>GCF_020097155.1_00873
+MEADRTALDPQEEPVLSVTDLRELDTAAADLSAIVPRAEVDVAYTVPVVAPIIEQVRTGS
+EQTLLDLAERFDGVRPPALRVPAEALTAALEGLDPAVRAALEESIARARKVHAAQVPSGS
+TVELGEGAVVENRWVPVERVGLYVPGGRAVYPSSVVMNVVPAQAAGVESLVVTSPPQRDH
+GGLPHPTVLAACALLGVDEVYAAGGAQAVAMLALGVRADDGDGWLCAPVRMVTGPGNVYV
+AAAKRALQGVIGTDAEAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSADL
+LRDVLASVEAQVPGSFHEEQIRVALTGPQSGVLLVRDMEQALEVSDLYATEHLEIHTRDA
+DALAARVRNAGAVFVGPYSPVPLGDYSAGSNHVLPTSGTARFSSGLNTVTFLRSQQLIRY
+GEAGLKALADGISALAEDERLPAHGVAVRARFA
+>GCF_023573625.1_01842
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV
+GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001550.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001550.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4cb03622c1f56f48ad10ab20df2d755659135ddb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001550.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01923
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR
+>GCF_003691675.1_01619
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR
+>GCF_005280335.1_00937
+MSGSVRVSGAVRVDAWLWAVRVYKTRSAATAAVRGGHVRVNDEPVKAAHTLAVGDRVRVR
+KDQRERILEVTGLIGTRVGAPVAVTNYIDHSPPPIPRELLAVPHRERGAGRPTKRDRRKL
+DELRGRASDERS
+>GCF_020097155.1_00872
+MGAVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRA
+STGRG
+>GCF_023573625.1_01843
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001551.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001551.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2544c75bde9628fee369263be31bbbfc17a5088b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001551.fa
@@ -0,0 +1,17 @@
+>GCF_002008305.4_01924
+MTLVEYTRRHPDADHLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVLCPSDATGETE
+ILTSRGGGGTKTWMAGSEALCGGWSAATPPVDEAGPMTFTVTVDNDKPFRMVLTAPSA
+>GCF_003691675.1_01620
+MTLVEYTRQHPDADYLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVMCPSDATGETE
+ILTSRGGGGTKTWMAGSEALCGGWSAATPPVDEAGPMTFTVTVDNDKPFRMVLTAPSA
+>GCF_005280335.1_00936
+MPHRRRRPCVPVALSVAAALGLSLSACASTTTAGVGSQSPAPSSAAGAASSAAGTSSAAP
+TTSAALTTSGTAAEIAGDEAAAQAQDDAATRTALNRAVAEDGIPYAELDPSLTPVPDGAS
+ILWEGLAVGAQSLRVDARAGEEYTVVLLCAEQDGSRRSLVMATVPGEDFSDVMAESPGCG
+HWSAGLPAREADGPLTLTGVVPDGGPFRMVVYRSEG
+>GCF_020097155.1_00868
+MTLEEYTRQNPDSDYLHPETESVLQEKVGTGTQQITVDAQEGAVLRVILLCPSDATGKTD
+IHTSRGAEGEKTWMAGSEALCGGWSAATPPVEKAGPMTFSATVDNDKPFRMVLTAPAA
+>GCF_023573625.1_01844
+MTLVEYTRRHPDADHLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVLCPSDATGETE
+ILTSRSGGGTKTWMAGSEALCGGWSAATPPPVDEAGPMTFTATVDNDKPFRMVLTAPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001553.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001553.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a061862ffc860b9fd3ef367276dd68f4704d0ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001553.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01927
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGNGFKELQENDRVEFETQDGPKGLQ
+AANVTKL
+>GCF_003691675.1_01623
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGGGFKELQENDRVEFETQDGPKGLQ
+AANVTKL
+>GCF_005280335.1_00934
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGSGFKELQENDRVEFETQDGPKGLQ
+AANVTKI
+>GCF_020097155.1_00865
+MAVGTVKWFNSEKGYGFIAPEDGSADVFVHFSAIQGNGFKELQENDRVEFETQQGPKGLQ
+AADVTKL
+>GCF_023573625.1_01846
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGGGFKELQENDRVEFETQDGPKGLQ
+AANVTKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001557.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001557.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5770223a6e69d008b898df9d708815a15ffa8db0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001557.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01932
+MAAVDPAPTDARERRDLVVPVPGPEDPPERAWLVLPHRHPVPTLLEETRDAVVGLAETLA
+AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFVRRPEGLAAVAWRSAAG
+LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRINGAWT
+PGQVAAEFAALLGITRVLWVPPAPRPDTGPWGGPGHLASWVRLQGDGEAAVHWRGDRFNP
+EHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAEYDPAERGPRSLLDTLPLGAAVLRP
+AFEDAAGEEAAAAACAALHPGRPQLSFPAPPLLRLAGALNDLVLLQPRP
+>GCF_003691675.1_01628
+MAAVDPAPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETLA
+AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRPEGLAAVAWRSAAG
+LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRINGAWT
+PGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPGHLASWVRLRGDGEAAVHWRGDRFHP
+EHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAAYDPAERGPRSLLDTLPLGAAVLRP
+AFEDAAGEEAAAAACAALHPGLPQLSFPAPPLLRLAGALNDLVLLQPRP
+>GCF_005280335.1_00927
+MPAAETVPADAAGRPDARPRVPGPREQPERAWLALPRRHPVPALLDEARDAVAGLAETLA
+EVLPVTVLTDPADHAVRSLIPPEVDLLAAPVDSPLLGRTGPGFVRRPEGLAAIAWRPAAG
+AGGPGPRDAGVAAAVAAAAGLPLLTPMLRAPRDAWVADGEGTAVVAADPVLDGRTNPAWT
+PEQVEAEFAALLGITRVAWLPPVPRIPTGPWGGAGHLGAWVRLLGGGEAAVHWRADRFHP
+EHLHGAAALRILQDAPDAAGRPLRVRTVPGGALPPEHDPAEIGPRSLVDTVPLGSAVLRP
+AFEDAATEEAAAAACAALHPGLRPVPFPGPPLLRLAGSLSDLVLVQPHP
+>GCF_020097155.1_00861
+MSTPAVPEPPRAPAPWEVPERLWLALPAVHPVPGLLAEARDAVAGLAETLGAHAPVAVLT
+DPDDADAARLLPGVVERVPVRGASPLPGREGPTFVHAAGTRGSVEAVHWRLPSDAAGTAG
+RAAATADAVARSAGLPLRTPLFSAPAGTWAADGDGTAVVSAALLDPAVNEGWTRAQAEDA
+LAGLLGAERVLWLPPVAGHAAGPWDGGGAAQPHPHPWLRFVAPGEVAVHWQPGRLHPDHA
+ASAAALHALTGARDARGRALSVRTVRALPPGPDADLEARGPLSALDLLPLAPGVVLRPAH
+ADPEADAATAEAAAALFPGAEQVPFPGPPLLRLLGTLSDLVLPQPPGARTRRPSPAPAHP
+EGPRAAP
+>GCF_023573625.1_01851
+MAAADPVPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETLA
+AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRPEGLAAVAWRSAAG
+LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVTDGEGTAVVAADPVLDGRINGAWT
+PGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPGHLASWVRLRGDGEAAVHWRGDRFHP
+EHPYAAAALRFLQGADDAAGRPLRVRTVTGAVQPAEYDPAERGPRSLLDTLPLGAAVLRP
+AFEDAAGEEAAAAACAALHPGLAQLSFPAPPLLRLAGALNDLVLLQPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001559.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001559.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32bb633ce004842fd708bb6b97e1e6de019e4193
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001559.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01934
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSAAGAGGEPTTVTIMTHDSFNLPQEL
+VQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEYT
+PQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVAT
+SPVASSPGLALLAATTEKYGDDGWQDWWRGLKENGGKVADSWSDAYNSDFSGGEGKGRFP
+VVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFMLTEEVQSALPES
+MYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR
+>GCF_003691675.1_01630
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSASGAGGGEPTTVTIMTHDSFNLPQE
+LVQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEY
+TPQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVA
+TSPVASSPGLALLAATTEKYGDDGWQDWWRGLMENGGKVADSWSDAYNSDFSGGEGKGRF
+PVVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFMLTEEVQSALPE
+SMYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR
+>GCF_005280335.1_00925
+MTTAPHRVRTRPRRHGALAALSVAALALTGCSVADRGGSGDQGSSSAEARTVTIMTHDSF
+SLPDELIARFEQESGHTLVTTAPGDAGSVVNQLLLAKDAPTVDGVYGIEDHSAHRLVSEG
+VIAEHVPADLPDSARDLVVDGRMTPVDQGQVCLNVDTPWFQEQGLAAPTTLEQVAAPEYA
+ELTVVTSPVSSSPGLALLAATVAEFGEDGWQDWWRTALQGGMQVDASWSDAYNTSFSGGE
+GTGTRPIVLSYSSSPAFAPDTDVVAASCTPQVEYAGVVEGAENPEGARAFVDFLLTEDVQ
+AAIPDAMYMYPVDSSVPLPEAWAEHAPLVEDPIVPDAGLLDSRREDLLKEWTALHEEAAS
+>GCF_020097155.1_00859
+MSVHRTATTRRGVLAAACLSALALTGCSVSAPSTGSSSSAASSSAAPSSASGSSSTSASG
+TAAAGSKGTVTIMTHDSFALPKELIAQFEAESGYRLVTTAPGDAGAVVSQVLLSKDAPVA
+DGVYGVENHSAHRLVDQGAVQDVAPADLPASAEDLVVDGKMIPVDQGQVCFNTDPAWFTE
+HGVAEPTSIDQLRDPEYAKLTAVTSPVTSSPGLALLAATTEKYGDDGWQGWWEDLLKGGA
+KVDSTWSDAYSTDFSGGEGKGEFPVVLSYSSSPAFAPQTAVIEDSCTPQVEYAGVLTGAE
+NPEGAKAFVEFLLSKDVQAAIPENMYMYPVDDTVELPAEWAANGPLVEDPITPDPAEIDT
+EREGLLKEWTALSESAGSR
+>GCF_023573625.1_01853
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSAAGAGGEPTTVTIMTHDSFNLPQEL
+VQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEYT
+PQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVAT
+SPVASSPGLALLAATTEKYGDDGWQDWWQGLMENGGKIADSWSDAYNSDFSGGEGKGQFP
+VVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFLLTEEVQSALPES
+MYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001560.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001560.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5062f40a64791384b883b088d4e980c4b706c0b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001560.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01935
+MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD
+ADAFTGAVDLTAFGETLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA
+VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG
+ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR
+PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLVAVVVSGVTAARTQRALRLRETPPA
+RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP
+ARALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALAAQRALDGALLLPLGVSAVTV
+GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP
+WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN
+YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL
+>GCF_003691675.1_01631
+MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD
+ADAFTGAVDLTAFGQTLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA
+VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG
+ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR
+PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLAAVVVSGVTAARTQRALRLRETPPA
+RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP
+AQALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALAAQRALDGALLLPLGVSAVTV
+GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP
+WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN
+YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL
+>GCF_005280335.1_00924
+MDGPARGGGLLTVGLTSVPAPVGGPGAPPGAPGPAASGGRRRRRTAGGDGIGAWWLLAAV
+VPVAFLLVFFAWPVGAMLWRGVSAEGVLDLGAFAEVLGRERTWRIVGQTLGMAAAGTVLA
+VALGLPAAFVLHRRAFPGRAALRAVITVPFVLPTVVVGVAFRALLAPGGPFGWTGLDQST
+AAVVLAMVFFNVSVVVRQVGALWASLDPRQAEAARTLGSSGWRAFRTVTLPQLAPALASS
+AALVFLFCASAFGIVQTLGRPGVGTLESEIWVQTVVYFDLGTAAVFSTLQFLVVLAAVLV
+SGATARRTRRALRLRDAPVRRLTRADAAPVAVTLATALLVLAPLATLLVRSFHSSEGWGL
+RNYRLLASSPGAGFSGGVTPAQALEHSLRIALDATLLTLLIGVPLALLLTRPVRSAAGRR
+AQRGLDGALLLPLGVSAVTVGFGFVVSLRAEAPALAASGALVPIAQAVVALPLVVRSLVP
+VLGAVDPRLREAARTLGAGPLRVLATVDGPFLLRGLGVAAGFAFAVSLGEFGATSFLSSP
+DYQTLPLLIVKLLGRPGADNYGMALAAATVLAVLSAGTMMACERLGPRAAASRGGI
+>GCF_020097155.1_00858
+MPTPAPARGRRRATLRPPRGRRAAGDGLAPLWLLSAAVPVAFLLVLFAWPVAAMLWRGVA
+SVDAAGDPTGGLDLSAFAQTLGAPRTWRILGNTLGLAAAGTAASVALGVPTAFALHRRAF
+PGRGLARAVVTVPFVLPTVVVGAAFRALLAADGPLGWTGLDQTSTAVVMAMVFFNVSVVV
+RQVGGLWAALDPRQAEAARTLGASPWRAFRTVTLPQLAPAVAGAAALVFLFCASAFGIVQ
+TLGRPGPGTLETEIWAQTTVYLDLRTAAVLSTVQLAVVLAAILASGAAAARARRALRLGE
+APARPLTRADAVPAAVTLAVLALVVAPILALLAGSLHSAEGWGLRNYRLLATSPGTGFAG
+GVTPAQALEQSLRTAVDATVVTLVVAVPLALVLTRPVRSRAGRAAQRALDGALLLPLGVS
+AVTVGFGFIVSLRATAPDLAASGALVPLAQSVIAVPLAVRALVPVLGAVDPRLREAARTL
+GAGPWRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLAAADRPTLPVLIARLIGRP
+GADNHGMALAAAVVLAVLSAGALLACERLRPRGAAPSGGL
+>GCF_023573625.1_01854
+MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD
+ADAFTGAVDLTAFRETLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA
+VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG
+ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR
+PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLAAVVVSGVTAARTQRALRLRETPPA
+RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP
+AQALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALVAQRALDGALLLPLGVSAVTV
+GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP
+WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN
+YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001561.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001561.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7891e43d62658570bd8b19ee95abf94cb62cbc26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001561.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01936
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEDGPAVASQA
+>GCF_003691675.1_01632
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEAGPAVASPA
+>GCF_005280335.1_00923
+MARTTRTSRGATPGSATRGHDDDGRAGLRLRALSVAYPDGATPVRGLDLELAPGEIVALV
+GASGSGKSTVLRGIAGLEDVVGGVVEIDGEDVAAVPTHRRGVGMVFQDGQLFPHRSVARN
+VAYGLEAAGWPRERRRARVAELLELVDLAELAERPVQSLSGGQAQRVALARSLAPRPRVL
+LLDEPLSALDADLRARLAVQIREVLRAAGVTAVVVTHDLAEAAVMADRTVRLGAGGRLAG
+PGEGEPDEGAGPGPEGDAR
+>GCF_020097155.1_00857
+MPARMHHHDAAPALRLRGLAVAYPDGSVPVTRADLDLAPGEIVALLGPSGSGKSTVLRGI
+AGLEDVPAGAVELAGRDVTAVPTHRRGVGMVFQDGQLFPHRTVARNVAYGVEAAGWDRSR
+RDARVAELLELVDLAALADRPVQTLSGGQAQRVALARSLAPSPAVLLLDEPLSALDADLR
+TRLAADIRTVLRAEGVSAVVVTHDAAEAAVMADRTVRMGADGVLHGAAADGARTAG
+>GCF_023573625.1_01855
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEDGPAVASQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001562.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001562.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5069d6a3235ebcdecb4b1704aaa39e6f6d11ad5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001562.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01937
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL
+>GCF_003691675.1_01633
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAAVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRITDLAGRAEAAEAALLRHRDGADLVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVPTGPDVQRHRTDPL
+>GCF_005280335.1_00922
+MSSPPRAGSSRGRLSATDVVDAAVGILQDFGMGDLSMRRVASVLGVQASALYWHVPDKQT
+LLARVADRIVAEAEEAVRHRGIADLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLH
+ALLTEAAPTPEEGERALALLLGGVSLRQQRAQAEALGVRVGPDVQRHRTDPL
+>GCF_020097155.1_00856
+MSTSSARGRLSAEDVVDAAVGILQDFGMGDLSMRRVASMLGVQASALYWHVPDKQTLLAR
+VADRIVADVERACAARRVEDLAGRAEEAEAVLLRHRDGADVVLSALALGLGGLGLHRLLV
+DAAHTPEEGERALAALLGTAALRQQRNQAAALGLRLGPDVQARRTGAL
+>GCF_023573625.1_01856
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001563.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69d56884202173362656ec7d03a4d7783e170732
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001563.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01938
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIQLRVEDDAAG
+>GCF_003691675.1_01634
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWEFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSAFWSTVTVDLPPERPVIVRLGSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIRLRVEDDAAAG
+>GCF_005280335.1_00921
+MRVVAAPLAMLPGVDHGPALRMDLHPVPGGIVYVARDLVLRELGDDVRGHVHAGMVGTAQ
+LHAFWSTVTVDLPPDRPVIVRLRSDRDAELLSLLEVLAPVEMRVVSYRLDESPVGTQRSS
+YLLPDVDPEIVARAESPRVPLEAIEATQEEEDALRRSSGVFLSRRRTDRFLRRTLPTVTH
+SLSFSDEADVADVYVDGSVLRSSRIGGAAAVGGPSMWAVQAVNGATTPLEVELEALVLGH
+VVSAWAGVPGERVTIHSDSRAALALLNAARRERLTLGGARGERVRRTLRRLLAAVDLAQA
+ADVRVETTWVKGHVGVQGNELADDLARAAARHAGVGTSEEDLRRRLDRLIDLHEEAEAEA
+GQTPARAVAAEGHRPMPPGRRPGPRL
+>GCF_020097155.1_00855
+MDNSSTHPREGQVRSLHFDTDASSPDALLDPMWAFTGPRASRAGAPAPDGADVLARRARP
+AHPGAALVRAATSLFTLPGPPGMPHRSRSAALEAARAPAGYLSPVPHRLALPRPARPRPA
+PPRMRVRQDGVRVVARPLAMLPGVDHGRALRLDLHPVRDGIVFVSRHLELRELGDDVKGL
+VLTGVVPAARLGYFWDTVAGDLPEGRPVIVRLRSNDDAELLTLLRAIAPPWLRVVSYRLD
+ESPVGSQRSSYLLPDVDGEAVAASGAERVPLETLREAHQASAEVERASRVFLARRRVDRF
+VRRSVPDLMHSLSYTDPAEVRHVYVDGSVLRGTRTGGAAAVTRSGPWAAHALPGATIPLE
+AELEALTLGHLMAAWSGTPDERVLIHSDSRAALALLREAHRERLTLGDARGERIRRALRR
+LLAAVDLAGSAGVEVSTLWVKGHAGTHGNELADDLARSAARNTAAGVSADEMRRRMRHVV
+QLWDATTHPQA
+>GCF_023573625.1_01857
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIQLRVEDDAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001565.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001565.fa
new file mode 100644
index 0000000000000000000000000000000000000000..724735d5be7b016bcacaf4dffdc17dfa35568f92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001565.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01942
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVARQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAIMSGTADLVVAGGVQSMS
+AIPLSLSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADSRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG
+RYGLQTMCEGGGQANVTVIERL
+>GCF_003691675.1_01638
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
+>GCF_005280335.1_00914
+MPEAYIIDAVRTPVGRRGKGLAQVHPLDLAAAPLREIVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSHSNRAAAEFGFADPFTGSESWAARYGNEEISQFRGAEMMARHWNLDRDVLEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG
+RYGLQTMCEGGGQANVTVIERL
+>GCF_020097155.1_00852
+MGEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPIRELVGRQDVDSAEYDEVILGCIDQLG
+PQAMDVARSAWLAAGLSEDVPGSTIERQCGSGQQAIHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAASASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAFALRRMGLGIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
+>GCF_023573625.1_01861
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001567.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001567.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c61049ef12b079f1e90133c7cf1618ea888ba9c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001567.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01944
+MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPFD
+LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPDVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQTRCVAVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL
+LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
+>GCF_003691675.1_01640
+MTRRQKPTYDVVTPLDVDYLDAFGEATEEDRAHWDRARAYGREVLERIDGHWDRAEYPLD
+LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPDVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQTRCVAVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL
+LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
+>GCF_005280335.1_00912
+MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPLD
+LVARAGELDLLTDGLEVPGHPVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+AGPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTGDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPNVATFKDAVRVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQARCVAVARLQASGRLRDEQASLLKYACTRGARRVAQTARDMLGGNGIL
+LEHRVIRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
+>GCF_020097155.1_00850
+MRRQKPTYDVVTPLDVDYLDAFGEATEEDRAHWDRARAYGREVLERIDGHWDRAEYPLDL
+VARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHCA
+SPEQQERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNGA
+AGGITFVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDAR
+LPGVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQERL
+AQMLDEVTAMQTRCVVVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGILL
+EHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
+>GCF_023573625.1_01863
+MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPLD
+LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPGVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQTRCVAVARLQAAGLLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL
+LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001568.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001568.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32b12498a62fff9950ee2877b4d143510aa6ab83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001568.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01947
+MSTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH
+VLTLTGAGRIFCGGGDVQAMAAAPAGPERRAMIQELGEAAGEVAVALTGSRLLVLAGVNG
+TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR
+RLNGTEAVGWGLATEAAAGDAFAARLAELEDELVAGPAHTYGPTKALTRGADVEALRAHV
+RQEAASIAAASEHPEAVRRVEAFAGR
+>GCF_003691675.1_01641
+MTTAPTPSPHDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH
+VLTLTGAGRIFCGGGNVQAMAAAPAGPERRAMIQELGEAAGEVAVALTGSRLLVLAGVNG
+TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR
+RLNGTEAVAWGLATEAVAGGAFAARLAELEDDLVAGPAHTYGPTKALARGADVEALRAHV
+RQEAASIAAASEHPEAVRRVEAFAGR
+>GCF_005280335.1_00911
+MSGDGGAADVATVRVEARPGVVRLTLDRPAQGNALSLAMARELTAAVRASEADPDVHVLT
+LTGAGRFFCGGGDLAAMGAASPAERPAVLRELADAASEVALALVRSRLLVVAGVNGTAAG
+AGLGLVLNADVVLVGDDALLLAAYAGIGLVPDTGVSWWLPRAVGPVRAAELTLRGRRLTG
+AEAVEWGVASEAVSGDEFEARLAALEDELAAGAVHAYGPTKALLRGPEIVGYAEHLDRET
+AAISAASGHPEAVRRVDAFLRR
+>GCF_020097155.1_00847
+MTTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH
+VLTLTGAGRIFCGGGDVQAMAAAPAGPERRAMIQELGEAAGEAAVALTGSRLLVLTGVNG
+TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR
+RLNGAEAVAWGLATEAVAGDAFAARLTELEDELVAGPTHTYGPTKALARGADAEALRAHV
+RQEAASIAAASEHPEAVRRVEAFAGR
+>GCF_023573625.1_01866
+MSTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH
+VLTLTGAGRIFCGGGDVQAMAASPAGPERRAMIQELGEAAGEVAVALTGSRLLVLTGVNG
+TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR
+RLNGAEAVAWGLATEAVAGDAFTARLAELEDELVAGPAHTYGPTKALARGADVEALRAHV
+RQEAASIAAASEHPEAVRRVEAFAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001569.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001569.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c26eeebfd9b66f26131061f4aae2f5638eeb10b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001569.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01948
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG
+LGDVLKMFK
+>GCF_003691675.1_01642
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG
+LGDVLKMFK
+>GCF_005280335.1_00907
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG
+LGDVLKMFR
+>GCF_020097155.1_00846
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG
+LGDVLKMFK
+>GCF_023573625.1_01871
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAARNAVYKRTTFG
+LGDVLRMFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001572.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001572.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21fce1d21d1b36a61481110dee550a860d325835
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001572.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01966
+MHEDEGRRRHYGHFYGLEDLPEDDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEAQPDEVAHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD
+VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAERLPGDVAVQPV
+PASRVLLGGVRAPLEAPVVEALDLDAAPTEDWTVAGQTVPAEQLRQTHLDWYAQNPQAVE
+VGMRKYADQLRLLGLTG
+>GCF_003691675.1_01660
+MNEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEAQPDEVEHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPKDAAVVRIPVVYD
+VSRFPWQVTLRNWKVAPGAAERPGEDPPVLPYHDLRVLAEAATGRRRQVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAGHLPGDVAVQPV
+PASRVLLGGVRAPLEAVVVEALDLDAEPTEDWTVAGQTIPAEQLRQTHLDWYAQNPQAVE
+VGMRKYADQLRLLGLAA
+>GCF_005280335.1_00893
+MHEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEVQPDEVEHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD
+VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTVLTRVAERVAEHLPGDVAAQPV
+PAARVLLGGVRAPLEAVVVEALDLDAEPTEDWTVGGETIPAEQLRQTHLDWYAQNPQAVE
+VGMRKYADQLRLLGLAA
+>GCF_020097155.1_00833
+MSEETPMDDQTRTAGAEPGDEGVQVRGAAERAPSSDLPADEGRRRHYAHFYGLEPLPEGE
+LLTVMGGCQAEATRLLLCGEPGRAEGGTPASVRVPPMFELGPDDLPHLLALLKRTTVLVV
+KPVRDDYQGLPLGLGQLESLLPAGARSIRVPALYDSSRFPWLVTLRHPTRPWEDPPVVPY
+HDLRTVAEAAAEAGLIPWPAALGGPGEAGAYDAGPRLPLSAEALRGLAAESVARLRAREE
+HFGTVRVSDAVADERGVGFHTVNHPDNPLLEALARTVLAELGVDKEVHAPDRLLLGHVLA
+PIEEQVVDALGLQTAPRAAWRVGGAEVSDAEVRRAHLGWFRANPEALAPGLERHGALMRE
+LGLLA
+>GCF_023573625.1_01892
+MNEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEVQPDEVAHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD
+VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAERLPGDVAVQPV
+PASRVLLGGVRAPLEAVVVEALDLDAEPTEDWTVAGQTVPAEQLRQTHLDWYAQNPQAVE
+VGLRKYADQLRLLGLTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001573.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001573.fa
new file mode 100644
index 0000000000000000000000000000000000000000..047c718cb68238e02bc64dedf9a4a24a854b3891
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001573.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01968
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGVTGGLQLVVADDGSPVPPRVDPGLPFDVVT
+VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR
+RHLAEAWLERAWADGWRPGHEVPADALLAEPAWLRDGYRATDDLRRADSTGYRYVISAVL
+TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALVLVSRIPATTSRGHGLSLAGPLRAEARVRVPEGADGAAAAVVAVDAVLR
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAAPEDLPPTPARGDLDAVRSVPDW
+SVDVQVPLRPAAAGARPDTDAVAAWLLRLERAGVERVEVLGEPGERAERDVLAVLTCARA
+RWRPRRGGTARVWRVPASRLGWAPVAAVPDLEAWWGGWG
+>GCF_003691675.1_01662
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGLTGGLQLVVADDGSPVPPRVGPGLPFDVVT
+VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR
+RHLAEAWLERAWVDGWRPGDEVPADARLAEPAWLREGYRATDDLRRADSTGYRYVISAVL
+TVAREVYADAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALVLASRIPATTARGHGLSLAGPLRVEARVRVPEGADGAAAAVVAVDAVLC
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAASQDLPPTPARGDLDAVRSVPDW
+SVDVHVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPGERAERAVLAVLTCARA
+RWRRRRGGTARVWRVPASRLGWAPVATVPDLEAWWGGWG
+>GCF_005280335.1_00891
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGVTGGLQLVVADDGSPVPPMVGPDLPFDVVT
+VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAAVAAVAEAPRDAAVVGRR
+RHLAEAWLERAWADGWRPGHEVPADARLADPAWLREGYRTTDELRRADSTGYRYVISAVL
+TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALALASRIPATTARGHGLSLAGPLRVEARVRVPERADGAAAAVVAVDAVLR
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAASQDLPPTPARGDLDAVRSVPDW
+SVDVRVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPGERAERAVLAVLTCARA
+RWRRRRGGTSRVWRVPASRLGWAPVAAVPDLEAWWGGWG
+>GCF_020097155.1_00832
+MTAPVAGREAAAETAGPEASVPEVSVVVPHYRAPADLERVVAALAAQDHPASRLQLVVAD
+DGSPEPPVLPAGLPFEAVVVAQEDHGFRASAARALGASAAEGRILAFLDGDMLPEPGYLT
+AACAAPAASVDAVVVGRRRHLDPALLESGWRPGEPVPEAARLPEPAWLAEAYQRSGDLAA
+ADSTSYRYVISAVLTVAREVYADAGGFDPAFVGYGGEDWELAHRLWRVGGAFRHQPAAVA
+WQAGEDFGGRGDAAERTAVKQREALRLAARITATTARGHGLSLPGPLRVGARVRAEASGD
+AAAVVGVDALLAAAPGARVGVTGLGSGAARAALADPRVWIMDGGGEAARADLPPAPARGD
+LGAVRGIPDWSCDVRTPLRPAAPGARPDAARAADWLLRLERAGVERVEVLGEPQAAEEPG
+EAGRGERPVLAVLTCSRALWRSRRGGDSRVWRVPAARLGWAPVARDVDLEAWWGGWG
+>GCF_023573625.1_01894
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGLTGGLQLVVADDGSPVPPRVDPGLPFDVVT
+VRQPDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR
+RHLAEAWLERAWAHGWQPGHEVPADARLAEPAWLREGYRATDDLRRADSTGYRYVISAVF
+TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALVLASRIPATTARGHGLSLAGPLRVEARVRVPEGADGAAAAVVAVDAVLC
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAADEDLPPTPARGDLDAVRSVPDW
+SVDVHVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPAEPGERAVLAVLTCARA
+RWRHRRGGTARVWRVPASRLGWAPVATVPDLEAWWGGWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001574.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001574.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a92fd072461e425b2b73d745502fed00e61b91f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001574.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01969
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALQRVGAEVELLTAEDVAAFRGLV
+PLLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPAGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVAGVVVSSQHERALLADLVDVAADVVPLPVQDRRAAAARAEPVVPESMA
+GLDQDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR
+YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEGCARMLF
+DVLRRVHRWT
+>GCF_003691675.1_01663
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV
+PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA
+GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR
+YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLGPGVDLSPGAEDCARMLF
+DVLRRVHRWT
+>GCF_005280335.1_00890
+MESQPQGRVLYVIVGPPEHGVVRHARQTAAALRRVGAEVELLTAEDVAAFHGLVPLMAEA
+RSLGAAVHLDVTDALFGPTAAAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRRRGEAYA
+RLARHAAGVVVSSQHERALLAELVDADADVVPLPVEDRRAEAARAESVVPENMAGLDQDV
+VLFGFVYPGKGHALALEALTELHRQWGPNSGAPRRLTALGPVSAGHDDLVAELTRDAEAR
+GLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGRYTEEME
+RLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPEHTWLDPAVDLSPGAEDCARMLFDVLRRV
+HRWT
+>GCF_020097155.1_00831
+MTSHAQGRVLYLSVGSRGHGVVHHGLLTAEELAQVGLDVESLHTEDATGFVGLAPVLARA
+REARRAVHVDVTDSLFGPSPAAAADTLSRILPDGATVTLHDVPQPAEGEARFLERAEAYV
+RIAQAAAGVVVSSEHERALLHAIVDVDAHVVPLPVEDRRAAREAVRLPEALEGLDRDVVI
+FGHLYPGKGHAEAIDALAELDRQWGPSPHRPRRVTALGAVAARHEFLVDELTARAEVSGL
+QFRVTGFVPDEVLDPALRAAAVPLAAHHNVSASGSLASWMSVGRRPIVPAGRYTQEMARL
+RPGTLRIVQVGTSGPEYALAEAVAEAVEEPSRTWQARGTSLAPGPRACARMLAAALADVH
+GWAWPR
+>GCF_023573625.1_01895
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV
+PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA
+GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSIGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRTIASAGR
+YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEDCARMLF
+DVLRRVHRWT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001575.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001575.fa
new file mode 100644
index 0000000000000000000000000000000000000000..978a64481777aeebb4f9674e73290f7f7cee54df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001575.fa
@@ -0,0 +1,64 @@
+>GCF_002008305.4_01970
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR
+PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR
+ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGAEPGLLPPDASDD
+GDGAAAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDAL
+AALRAGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAV
+ADIGHIADQSGAWLTPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVA
+AAHVAVYREALARARGALPGVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPD
+GRVPATDLPVTVGHVAAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEV
+AAHPGSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHL
+VWTLILALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMT
+PPLHHLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTA
+ARRDDAAY
+>GCF_003691675.1_01664
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPDAPAHQWWPPRALHAEWLAEHR
+PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR
+ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGLLPPDASDDGDGA
+PVPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDALAALR
+AGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIG
+HIADQSGAWLSPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHV
+AVYREALARARGALPSVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVP
+ATDLPVTVGHVAADAGLPLAQARNRAAELAIGEILVFLDVDCIPAAETVGVLATEVAAHP
+GSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTL
+ILALRRADLARIGCFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLH
+HLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTAARRD
+DAAY
+>GCF_005280335.1_00889
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR
+PDVLHVHFGFEHFNPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR
+ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVSQGDDDAPGLLPPDASDDGAAA
+PARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQATVQDEDALAALRAG
+CAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIGHI
+ADQSGAWLAPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHVAV
+YREALARARGALPSVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVPAT
+GLPVTVGHVAAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEVAAHPGS
+VVMGRPRYLRPGWTRAVEEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTLIL
+ALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLHHL
+EDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRTPTADELAVARRDDA
+AY
+>GCF_020097155.1_00830
+MSLTVQHVPAGHPYARSVRPLDGAAAPDVEFWPDPPVPGAAEGVWWPPRALDPAWIAEHR
+PDVLHVHFGFEHFTPEQLRAALDAQHAHGGAVVVTVHDLQNPHLQDQDPHRARLRVLLDA
+ADAVITLTPGAAAAVEAASGRAPLVLPHPHVVPLDALPDDGAADGERPGVDRPARLLMHA
+KDLRAQVDPVGLLPVLAAARDALAARGLAVEVTVDVQDGVRDEAALAELEAGAEAHGFAL
+WRHARLDDAELHAALRDADVSVLPYRVGTHSGWVEMCRDLGVPVAVAEVGHIADQARAWT
+TPELLAAFDPDDPASLADALAALLTAAPDARAAAPAARAAQRRRVAAAHVAVYRQALAVR
+RGTAATVSVLVITGHRDAHLARVLAGLERSHRRPDQVVVVFMGQPDGAVPATDLPVTVGH
+VAADHGLPLATARNRAAELATGEVLVFLDVDCIPAADTVGVLAAEVAAHPGSLVMGAPRY
+LAPDWTAALAAEGVDADAAPTDGDLRRHAVPHRARTHLRPGPSEEWALVWTLVMAIGAAD
+LARIDGFDEGFAGYGAEDTDLAFRARDAGLTLRISPAEAFHQHHGVHRPPLHHVADIVVN
+ARRFRTLHGTWPMGGWLAAFAERGLIRWDPDGDLLELVREPTPDDVAAARVDDAAY
+>GCF_023573625.1_01896
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR
+PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR
+ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGALPPDASDDGDGA
+AAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDALAALR
+AGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIG
+HIADQSGAWLSPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHV
+AVYREALARARGALPGVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVP
+ATDLPITVGHVSAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEVAAHP
+GSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTL
+ILALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMVPPLH
+HLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTAARRG
+DAAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001576.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001576.fa
new file mode 100644
index 0000000000000000000000000000000000000000..069f07df95812acfd4334e01ecd1fe1be064dd0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001576.fa
@@ -0,0 +1,39 @@
+>GCF_002008305.4_01971
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAELLPADVPVIPLPSDL
+VPGHEQPARSPLHWSPVGPEIRARFDALHAAAQRVGPDVCVVDVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRT
+TTTSTARAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPTAADRLAGLLLVAPDEYRRRWEAAIEG
+ALG
+>GCF_003691675.1_01665
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAELLPADVPVIPLPSDL
+VPGHQQPARSPLHWSPVGTEIRARFDALHAAAQRVDPDVCVVDVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRA
+TTTSSAGAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPAAADRLAGLLLVAPGEYRRRWEAAIEG
+ALG
+>GCF_005280335.1_00888
+MSDGAAAVSRPGASARPSRRRRVLYYAHQHGSGHVRHAANLAATGAFDVTVVSAHPDAAR
+MLLAGTPVLPLPSDVVPGHVQPERSPLHWTPVGPQIRDRFAALHDAARDVRPDVCVVDVS
+VEAALFLRLAGWPVLHRRMHGERTDPAHALVYAEADGLFAHYAEELEDPAWREAHAGRTA
+FLGVPDVTGRLGARATTTTATTTAAGGSAPRVAVIAGTGGGGVRAADLARAAAAVPEATW
+EVYGPVAGADELQAPGGAAGSRSSDADATTGTAPTAGVALPANVTLHGWVEAPASRAAEA
+DVVVVSAGHNAAVDAARSGRPVVLAPEPRPFDEQHVFAREARRAAGVPWCAWEDPDADWA
+GAVRGALADPSAADRLAALLLVEPGEYRRRWEAAVEAALEATQG
+>GCF_020097155.1_00829
+MSGRRLRVLHYAHQHGSGHVRHAATLIRADVADVTVATAHPDAARLLPTGTRIVPLPTDI
+VPGHGQPEGSPLHHTPVGPAIQARFDALHDAARAVRPDVCVVDVSAEAALFLRLAGYPVV
+HRRMHGDRTDPAHRLVYAEADALFAHYGEVLEDPAWQAEFGARTAHLGVPDADGRLGRTA
+APARAGEAPRVVAVTGTGGGGVAARDIARAARSTPGARWHVIGPVRDAGGADLPENLELQ
+GWVEDVPAALAAADVVVVSAGHNAAVDAAHSGRPVVLAPEERPFAEQRRFAEAVERAAGV
+PWRAWEDPEADWAGAVARALGDPAAADRLAAALLRPPAEHAAGWGALLERAAASAQ
+>GCF_023573625.1_01897
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAALLPADVPVIPLPSDL
+VPGHQQPARSPLHWSPVGTEIRARFDALHAAAQRVDPDVCVADVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRA
+TTTSSAGAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPAAADRLAGLLLVAPDEYRRRWEAAIEG
+ALG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001577.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001577.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a2a2847697e7192f9c02e86d5050ce48348cefa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001577.fa
@@ -0,0 +1,38 @@
+>GCF_002008305.4_01972
+MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRVPGDVVAVLPAE
+GAGPGRAGARVREEAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATLA
+EVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHQWVSDAVPVRGRA
+VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHHA
+LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA
+QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDPH
+GVPRPSADAADLESL
+>GCF_003691675.1_01666
+MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPGDVVAVLPAE
+GAGPGRAGARVREAAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATLA
+EVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGRA
+VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHHA
+LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA
+QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDPQ
+GVPRPSADAADLESL
+>GCF_005280335.1_00887
+MRISVLTHMLHPIRSPYAGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPADVVPVLPAE
+GAGPGKEGDRLREEATRRACEMVLADDSDAVLNNSLSPAPLELLRERPMITVLHTPATLA
+EVLAVVDHPDWRAPQHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGRA
+VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHQT
+LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA
+QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYLDLLEQAAEDARDGELV
+>GCF_020097155.1_00828
+MRIDVLTHPLHPIRSPYEGGLEMHTAMTVEHLVAAGHQVRVHARAGTRIPGADVVSLLAA
+APDAPGAEGQAVREGALAGACQRILADAPDAVLNNSLSPQPLIRLRSLPMLTVLHTPATL
+EPVLEVTDAPGWTPPAHHRWASVSVSNALAWRHRLPSVDVVPNGIDLDRWVSDRAPVPGR
+AVWSGRITPEKGLHMAIDAARAVGMELHAAGPVSDPAYYAERVAPRLGEDVVHHGHLDHT
+ALPDLLATGEVFLSTPLWAEPFGLATVEAMALGVPVAALLTGAMGEIVAPQAGALAVHHS
+VEALADAIRYARRKDRARVADWARRFSADTMVAGYLDLLEQAVADHADDAELRKVPA
+>GCF_023573625.1_01898
+MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPGDVVAVLPAE
+GAGPGRAGARVREAAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATLA
+EVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGRA
+VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHHA
+LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA
+QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDPQ
+GVPRPSADAADLESL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001580.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001580.fa
new file mode 100644
index 0000000000000000000000000000000000000000..215bb34a619cf039f8f6722449e4d635a13e69d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001580.fa
@@ -0,0 +1,54 @@
+>GCF_002008305.4_01979
+MSTAPTRVRLGMPTVRPVHGEGEILLNTPFPESAREQLGNGQMRANIRRATHTIRAKRAG
+VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL
+VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR
+NRREIRDIFRREMPDTDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS
+VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV
+TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG
+PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR
+KALRTEKDAAAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA
+GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH
+VEEDGR
+>GCF_003691675.1_01673
+MSTAPTRVRLGMPTVRPVHGEGEVLLKTPFPESAREQLGNDQMRANIRRATHTIRAKRAG
+VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL
+VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR
+NRREIRDIFLREMPETDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS
+VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV
+TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG
+PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR
+KALRTEKDAAGGPLARAKTAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA
+GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH
+VEEDGR
+>GCF_005280335.1_00879
+MTRTALGMPAVRPAHGHGNIVLDEPFPSAARTQLGNAQMRANIHHATHTIRGKRARVVGE
+LPDWAELRQAGSALKQQVMADLPALLEQFEQRVTERGGVVHWARDAEEANRIITGLVKAK
+GVDEVIKVKSMATQEIDLEHALQAEGIAAVETDLAELIVQLGHDKPSHILVPAIHRNREE
+IREIFVREMPETDESLTSDPSALADVARVHLREKFLTTSVAISGANFGVAETGTLTVVES
+EGNGRMCLTLPETLITVMGIEKIVPTFQDLEVFLQLLPRSSTGERMNPYTSMWTGVTPGD
+GPQEFHLVLLDNGRSAVLSDPEGRPALHCIRCSACMNVCPVYEQTGGHAYGSVYPGPIGA
+ILSPQLTGVQEGANGSLPYASSLCGACYDVCPVAIDIPSILVHLRDQDVRATHARKKEET
+RVPLPSQMDLMMKGARTVMSSGTAMSLAERGLPLGRLAAGRDATLGWLPGIAGGWTDQRD
+VPSPPRQSFRNWWRGNAEHTEERVARDGGRRDVAAEDETTTTDGQEQR
+>GCF_020097155.1_00814
+MSTAPTRVRLGMPTLRPVHGEGEILLKTPFPESAREQLGNGQMRANIRRATHTIRAKRAG
+VVGELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL
+VTAKGVDEVIKVKSMATQEIGLDAALAQAGVAAVETDLAELIVQLGHDRPSHILVPAIHR
+NRREIRDIFLREMPETDESLTSEPADLAEASRRHLREKFLSTKVAISGANFGVAETGTLA
+VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV
+TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG
+PIGAILSPQLTGVDAGENGTLPYASSLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR
+KALRTEGDGDAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA
+GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH
+VEEDGR
+>GCF_023573625.1_01905
+MSTAPTRVRLGMPTVRPVHGEGEILLNTPFPESAREQLGNGQMRANIRRATHTIRAKRAG
+VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL
+VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR
+NRREIRDIFLREMPETDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS
+VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV
+TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG
+PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR
+KALRTDEDAAAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA
+GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRVAMDGVAGLDRPEDEH
+VEEDGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001581.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001581.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03dcb9cdf8efd9b019bd7ebcf56ee0242501f0ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001581.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01980
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAGAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEARR
+>GCF_003691675.1_01674
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPTSAGVRRGPSARVEEARR
+>GCF_005280335.1_00878
+MRVALFATCIVDAMYPKVALATVRILERLGHEVVFPRGQGCCAQMHVNSGYLDDALPVVK
+NHVRTFQGADYDVAVAPSGSCVASLGHQQPMVARAAGDEALARDAEEVAANTYELAALLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGDRQERLLRSVADIDYRALPDAEECC
+GFGGTFSLKNPDVSGAMAEEKIGNIERTQARLCTGGDASCLLHLGGVMSRRGTTAPDGSP
+VTTLHFAEILAATRENPLDVSGPVDLSIPAQGPARRRRQKEATR
+>GCF_020097155.1_00813
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYVEDALPVVR
+NHVRTFMKADYDLAVAPSGSCVASLGHQQPDVARSCGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGTRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASICTGGDASCLLHLGGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEAHR
+>GCF_023573625.1_01906
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAGAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001584.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001584.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f47556548e4e8d7ad5834a0e94b35321639be49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001584.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01984
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGAGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLPSVATAVAD
+ELGLDPRKDVRVTSEVLAEA
+>GCF_003691675.1_01678
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGVGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGALTLPSVATAVAD
+ELGLDPQKDVRVTSEVLAEA
+>GCF_005280335.1_00873
+MLIGVPTEVKNNEFRVALTQGGVLELVRRGHEVLVQAGAGVGSGISDQVYLDAGAQLVQD
+PDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPECTRAILDSGTTAIAYETV
+TRGRALPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIAETVADADLVVGSVLI
+PGAAAPKLVTAEMVEQMRPGSVLVDIAIDQGGCFENSRPTTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTAALTNATLPYIQRIADLGWREALAADEGFASGLNAHEGALTLPSVAEAMAG
+PLGLDPRKDARTTADVLASA
+>GCF_020097155.1_00809
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGVGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRALPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRMRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTAALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLSSVATAVAD
+ELGLDPQKDVRVTSEVLAEA
+>GCF_023573625.1_01910
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGAGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLPSVATAVAD
+ELGLDPRKDVRVTSEVLAEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001586.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001586.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aab1ff14caaa3fc7c069f5bc4468a724a780b0bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001586.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01988
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARRH
+VVDALSGGMTAWVRISATSTDHWQRDLEALAGLDGVRGVVLAETKEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVIESSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>GCF_003691675.1_01682
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARQH
+VVDALSGGMTAWVRISATSTDHWQRDLEALTGLDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVIESSVVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>GCF_005280335.1_00869
+MPVRNRRAAALPAKLSRSWLLVNAARPEDFAPALASEADSVIFDLEAAVPEDKKDAARQH
+VVDALSGGMTAWVRIAATSTDHWQRDLEALAGVDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVVDSSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>GCF_020097155.1_00806
+MPVRNRRAAALPAKLSRSWLLVNAARPEDFAPGLASEADSVIFDLEAAVPEEHKDAARQN
+VIEALSGGMTAWVRISATTSEHWARDLEALEGLSGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGRLPGAVDGPPGAGDDEAAVAASSEVTHSMGMTGRLCLNRGQVEWVNRALSPSEDELTW
+AHDLLDKHAAGAAVGDGSYLPRLRRAEKIADLADSYGLWNA
+>GCF_023573625.1_01914
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARQH
+VVDALSGGMTAWVRISATSTDHWQRDLEALAGLDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGRLPGAIDGPPGNTDGEDAVIESSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001588.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001588.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d51b473b7910ed4d92690582c1cc4a7288dca0fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001588.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01990
+MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR
+FGTESLQYGPGQGTEEMRAAAATVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD
+VVVVEDPTFVGALTTFATWQLEAVATGTDDQGLVPAALDETLTRLAAEGRRVAFLYTIPS
+FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT
+MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT
+GLYRERAGALVDAVREHWDPGVEFITPQGGFFLWATLPAGVDTLEVMHRGIEAGAVFVPG
+AAFTPVEGTHSTLRLAYSFVDAEKLVEGVRRLAPAVNESIARAR
+>GCF_003691675.1_01684
+MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLISLAGGNPWLADLPLDELGRIASDLMTR
+FGTESLQYGPGQGTEAMRAAATAVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD
+VVVVEDPTFVGALTTFTTWQLEAVATGTDDHGLVPAALDETLTRLAAEGRRVAFLYTIPS
+FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT
+MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT
+GLYRERAAALVDAVREHWDPAVEFITPQGGFFLWATLPVGVDTLEVMHRGIEAGAVFVPG
+AAFTPVEGTHSTLRLAYSFVAAEKLVEGVRRLAPAVNESIARAR
+>GCF_005280335.1_00867
+MRHLRDHLSHRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR
+FGTESLQYGPGQGTEEMRAAAAAVMAADGIPDADPELVVITPGSQAAIDTACRAFGNPGD
+VVVVEDPTFVGALTTFNTWELDAVATGTDEHGLVPAALDETLTRLAAEGRRVAFLYTIPS
+FANPSGALLPADRRAEVAAICERHGVLIVEDNPYGQIAFDGDPVAPIAAEHRDGVVYLGT
+MSKIFSPGVRIGWALVPAELKREFYLSAESAFIHASTYSQMLSTAFVTQLDWQGHVRHVT
+GLYRERAGVLVDAVREHWDPGVEFITPRGGFFLWATLPGGVDTIELMHRGIEAGAVFVPG
+GAFTPVEGVHSTLRLAYPFVEAERLVEGVRRLAPVVNDAVARAR
+>GCF_020097155.1_01757
+MSTLDPAGARAHLARRATTVQQSAVRDVFDIAMDPDLVSLAGGNPWLAGLPLEELGATAA
+RLVAEQGTASLQYGPGQGLECMRVAACAVMAADGIPDADPELVVITPGSQAAIDTACRAF
+ADPGDVVVVEDPTFVGALTSFQTWELEAVATPTDEHGLVPADLDATLARLEAEGRRVAFL
+YTIPSFANPSGLLLPADRRDDVAAVCERHGVLIVEDNPYGQIAFDGAPVAPIAAAHRERT
+VYLGTMSKIFSPGVRVGWALVPEALHREFYLCAESAFIHASTTSQMLSTAFVTEYDWQDH
+VRGVTGLYRSRAQALQAAIAEHWDPGFTFTPPAGGFFLWGSLPAGVDAVELMHRGIAAGA
+VFVPGAAFTPVPGTHSTLRLAYSFVDEETLAEGVRRLAPVVNTAVEGAR
+>GCF_023573625.1_01916
+MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR
+FGTESLQYGPGQGTEEMRAAATAVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD
+VVVVEDPTFVGALTTFTTWQLEAVATGTDDHGLVPAALDETLTRLAAEGRRVAFLYTIPS
+FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT
+MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT
+GLYRERAGALVDAVREHWDPGVEFITPQGGFFLWATLPAGVDTLEVMHRGIEAGAVFVPG
+AAFTPVEGTHSTLRLAYSFVDAEKLVEGVRRLAPAVNESIARAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001591.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ccaf31730c49c61d57c73c6dea6a90f50bb3b7c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001591.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01993
+MTEKTSIEARKPAGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHAIADIMETRGNQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>GCF_003691675.1_01687
+MTEKTSIEARKPEGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPQGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>GCF_005280335.1_00864
+MTEINDRKPEGLPDLIRHYIDGQSVDSVDGDTFDVLDPVTNQPYIKAASGKTADVDKAVA
+AAKAAFESGVWSQALPRERSRVLHKIADIMETRGDQLAAMECFDTGLPIKQAKGQAARAA
+ENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAIATG
+NSVVLKPAEFTPLSASLWPGIFEEAGLPKGVFNMVHGFGEEGFAGDPLVKHPDVPLISFT
+GESRTGQIIFGNAAPHLKGLSMELGGKSPAVVFADADLDAAIDATIFGVFSLNGERCTAG
+SRILVAREVYDEFVERYAAQASRVKVGMPNDETTEVGAIVHPEHFEKVMSYVEIGKSEAH
+LVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDSDEEALELANNTK
+YGLAAYIWTNDLKRAHNFAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRSIDF
+YTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>GCF_020097155.1_00802
+MTEKTSIAARTPEGMPDVIRHYIDGEFVDSIDGDTFDVLDPVTNEPYIKAASGKSADVDA
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQAKGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPTGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKA
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNFAQDVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQESKETGDA
+>GCF_023573625.1_01919
+MTEKTSIEARKPQGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALELAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001592.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001592.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66291241fffe13dd8b52aeb81e59af9388f3505e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001592.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01994
+MTNLESRQKTSSGFFVTKEVPIDPENPLPTPTSEAPDILRSASMELVVTDLAQSREFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL
+GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD
+GFSYTREGQGEESLPEWKQGEYKLGNQL
+>GCF_003691675.1_01688
+MTNLESRQKTSSGFFVTKEAPIDPENPLPTPTSEAPDILRCASMELVVTDLAASREFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL
+GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD
+GFSYTREGQGEESMPEWKQGEYKLGNQL
+>GCF_005280335.1_00863
+MSNYAGRTRTSVGTYVGQEGPVKTDNPIPTPKAEAPDVLRCASMELVVTDLEKSRQFYVD
+VLDLVVTEEDEDTVYLRSMEEFIHHNLILRKGEIAAVAAFSYRVRTPEDLDKAVAFYTEL
+GCRVERNKDGFVKGVGDSVRVEDPLGFPYEFFYEVDHVERLAWRYDLYSPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVAF
+ATHEKHNILAICDKLGSLRMSDAIERGPGRHGVSNAFYLYLRDPDGHRVEIYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASLVLDLDGNVKEVVARTDDSEMAVTIGAD
+GFSYTRAEEGEDSMPEYKKGEYKLGNQL
+>GCF_020097155.1_00801
+MSNLESRKKTSSGFFVTEEAPITPANPLPTPKAEAPDILRCASMELVVTDLAASRHFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLILRKGETAAVAAFSYRVRTPEDLDKAVAFYTEL
+GCRVERNKDGFVKGVGDSVRVEDPLGFPYEFFFETEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAAKFMQDLGFRVTEDIQDEQGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVARTDDSEMAVTIGAD
+GFSYTREDEGEESMPEYKQGEYKLGNQL
+>GCF_023573625.1_01920
+MTNLESRQKTSSGFFVTKEVPIDPENPLPTPTSEAPDILRCASMELVVTDLAASREFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL
+GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPIVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD
+GFSYTREGQGEESMPEWKQGEYKLGNQL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001594.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001594.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e4ee95bf19ddad0a0fabf34fad57e8c3bd9c1b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001594.fa
@@ -0,0 +1,56 @@
+>GCF_002008305.4_01998
+MTTSAPTLSSHFADTFPELALPWQAQVTDGPQLVLLNAGLAAELGLDAEWLASDDGVRFL
+TGEQPGPHARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA
+RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVATGHPVRRETVLPGAVLARTAAS
+HLRVGTAQYAAALPEQAHPTEVLRRIVDEAIARHHPHATDAEHPALALYEAVIAAQAELV
+SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYAYGNQGPIA
+AWNLARLGEALVPVLDDDPDRAVALAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV
+AALTDRLFPWLAAARADWTSFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA
+DWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEGGDLAPVHRLLEAVTDPFTPRPGFER
+YAEPGPADGAPFVTYCGT
+>GCF_003691675.1_01692
+MTTSVPALSSHFADTFPELALPWQAQATDGPRLVLLNAGLAAELGLDAEWLASDDGVRFL
+TGEQSGPDARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA
+RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVATGHPVRRETVLPGAVLARTAAS
+HLRVGTAQYAAALPEQAHPTEVLRRIVDESIARHHPHATDAEHPALALYEAVIAAQAELV
+SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYAYGNQGPIA
+AWNLARLGEALVPVLDDDPDRAVPLAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV
+AALTDRLFPWLAAARADWTSFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA
+EWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEDGDLTAVHRLLEAVTDPFTPRPGFER
+YAEPGPADGAPFVTYCGT
+>GCF_005280335.1_00859
+MPVRHNTQPLVRDLFTTEAKAARGGRPAAGMFLSSGDCTAAEICAGAGLDYLLIDGEHAP
+LSLENVQAQLRTIAGYGVPVMTRVPFLDWISIKQYLDLGAQTLLVPMIDTPEQAAEAVRA
+LRYPPHGDRGVGSALARSGRWNRIEGYLQHDEEHVSLFVQIETVRGVENAAAIAAVPGVD
+GVFVGPSDLSASMGLIGQQSHADVVAAVRRVIEACNAAGTTVGVNAFATDQAQAYADAGA
+DFVNVGADVALMARGAEALADRWCPTPGTGADEGAGEGAGAGAGARANARPARRTDGGRP
+TRPPAPHAWECGVMDDVAPAHPALAPQPGRPALRHRFADLFPELAVPWQAQETDGPELVL
+LNTGLVTELGLDADWLASDDGVRLLTGEQLGPDARPVAQAYAGHQFGHYSPRLGDGRALL
+LGELVPPRRTRDANDAPQALPTWRELHLKGSGRTPFARGDADGQAVLGPMLREYAVSEAM
+HALGVPTTRALAVVATGRPVRRAGWQPGALLARTAASHLRVGSFQYAAALPERADPVAVL
+RRLVDEAILRHHPHAAEAENPALALYEAVIAAQAELVARWMLVGFVHGVMNTDNMTLSGE
+TIDYGPCAFLDAFDPAASFSSIDTQGRYAFGNQGPVAAWNLARLGEALVPVLDDDAGRAV
+ELAQEALGGFQATHLAAWRGGLRAKLGLSEEVTDADVAALTDRLFPVLAAARTDWTGFWV
+RLAEHVPGGRGRGRAGRGRRRTECPAECRSGRADGRRAGGGADAGPGRGRPGCRGRVAAR
+LAGAGPRRGPDAGGEPRLHPAEPPARRGPHRRRGRGPGAGAPPAGGRHRPVHPAPGPRAV
+RRAGPVGRGPVRDVLRDVRRGRRGLPYSRSPLPAPRPNSHRPTAFVWESGNLPPLSCGET
+GVPVSHTKGDEGRTLLLTRGCGGARPLTPGRATSAARSGRRGPAGPPRSRGR
+>GCF_020097155.1_00795
+MPVPALQHRFADRLPELAVPWQARPAPAPTLAALNAPLAAELGLDPAWLATDAGLAFLTG
+TEPGPGARPVAQAYAGHQFGSYSPLLGDGRALLLGELTAPDGTLHDVHLKGSGLTPFSRE
+GSDGLAALGPMLRELVVSEALHALGIPTTRALAVVATGGPVRRQRVLPGAVLVRVADSHL
+RVGTFQHAAALVHAGRAPEDLLTRLVAESLERHHPGHADDAAPALALLRAVVAAQAELVA
+RWMLMGFVHGVMNTDNMTVSGQSIDFGPCAFLDGFDPDAVFSSIDRGGRYAYGAQPRIAL
+WNLNRFAETLLPLLAPDPEAAVAAAEEALGGFAPAFDAAWQGGLAAKLGLARSADSDALA
+AELLRLLAQDRADWTASWANLSDLPLPADWLARWRALDPDPELARAANPLRVPRNRPLQA
+ALDAAEDGDLADVERILAAVREPFTPRADASDLDVPPAPGAGGEAPFVTFCGT
+>GCF_023573625.1_01924
+MTTSVPALSSHFADTFPELALPWQAQATDGPQLVLLNAGLAAELGLDAEWLATDDGVRFL
+TGEQPGPGARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA
+RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVGTGHPVRRETVLPGAVLARTAAS
+HLRVGTAQYAAALPEQAHPTEVLRRIVDEAIARHHPHATDAEHPALALYEAVIAAQAELI
+SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYACGNQGPIA
+AWNLARLGEALVPVLDDDPDRAVALAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV
+AALTDRLFPWLAAARADWTLFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA
+DWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEDGDLTAVHRLLEAVTDPFTPRPGFER
+YAEPWPEDGAPFVTYCGT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001595.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001595.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38ab12785c3cada878b7733242d7aa74907472b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001595.fa
@@ -0,0 +1,44 @@
+>GCF_002008305.4_01999
+MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGEIALVDPQGVPYDRPPLSKEFL
+TGDADARRLLLAPPTWFAEHGVELVEDAAVRVVPGGVHPDGGPAPHRVETASGRVLEADA
+VVLATGGRPRALDVAGADHPDLITLRTRSDAEALRDRLTFGAEVAVVGGGFTGAEVAAAA
+RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHVEHGVAVEVGRAAWIEHRDADGGAALP
+AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD
+AARARESAWATSRHWEPALRSGAAAAAALLGEQTDAPGAPWFWSDRYDAHVEAVGDMTVP
+AGGRIVDREVRGVVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA
+VPVKSLARG
+>GCF_003691675.1_01693
+MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGGIALVDPQGVPYDRPPLSKEFL
+TGDADAHRLLLAPPAWFAEHGVELVEDEAVRVVPGGVHPDGGPAPHRVETASGRVLDADA
+VVLATGGRPRALDVAGADHPDLITLRTRADAEALRDRLTFGAEVAVVGGGFTGAEVAAAA
+RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHAEHGVAVEVGRAAWIEHRDADGGAALP
+AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD
+AARARESAWAPSRHWEPALRSGAAAAAAILGEEADAPGAPWFWSDRYDAHVEAVGDMTVP
+AGGRIVDREVRGTVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA
+VPVKSLARG
+>GCF_005280335.1_00858
+MSGDVDARAGAPASVVVVGGGVAGFGAVRELRRRGHTGSLALVEPQGVPYDRPPLSKDYL
+TGETDAHRLLFAPPSWFAEHDVELVEEAAVRLTPGGAHPDGDPVPHRVELASGRVLEAEA
+VVLATGGRPRPLDVEGATHPDLITLRTRADADALRERLHFGAEVAVVGGGFTGAEAASSA
+RQALAGVTLVTATDAPALRAVGPALAARLHRMHAEHGVAVEVGRVARIEHRDDDGGAALP
+AAHRLHLGDGRTVDADVVVLAGGTVPDTALAEEAGLEVADGILVDEAGRTSVPGILAVGD
+TARATGSAWGPSPHWEPALRSGAAAAAALLGEEPEPPGAPWLWSDRHGCHVEAVGDMAVP
+PGGASVDREARGAAVASFVLDAEGRMRGAASIDDPMTVKAARRIIDRGIVVDPQALADPT
+VPLKSLARG
+>GCF_020097155.1_00794
+MTVPASVLVVGGGVAGFGTVRELRRRGFEGKLTLVDPQGLPYDRPPLSKDFLTGETDAHR
+LLFAPPAWFAEHAVELVTARVDRMDLTGEHPAAVLDDGTVRAADAVVLAPGGRPRPLDVP
+GGDRPGVLVLRTRADAEAIAARLHFGARVVVVGAGLTGSEVASAAREAMAEVTLVSASPA
+PAAAAVGPALAARLHALHAARGVDVVQGRVLRIEHADDAPGLDAPHRVHVALADGGEAAL
+DADLVVAAVGILPDAALAAEAGLELAVDGGILVDAAQRTSDPRVLAVGDAARRRDAAYAA
+PAMHWEPALQDAADAAAALLGEDLPERGAPWFWSDRHGVHVEGVGAMRPPEGGRIVDREV
+RGTVVASFALAADGAMVGAASVDDPMAVKAARRIVDRGIVVDPERLADPSVPVKALLRG
+>GCF_023573625.1_01925
+MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGGIALVDPQGVPYDRPPLSKEFL
+TGDADAHRLLLAPPAWFAEHGVELVEDEAVRVVPGGVHPDGGPAPHRVETASGRVLDADA
+VVLATGGRPRALDVAGADHPDLITLRTRADAEALRDRLTFGAEVAVVGGGFTGAEVAAAA
+RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHAEHGVAVEVGRAAWIEHRDADGGAALP
+AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD
+AARARESAWAPSRHWEPALRSGAAAAAAILGEEADAPGAPWFWSDRYDAHVEAVGDMTVP
+AGGRIVDREVRGTVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA
+VPVKSLARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001596.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001596.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0af30f0bde4b37b2acdaef6c63dd67b04ee3e9b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001596.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_02000
+MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW
+LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA
+>GCF_003691675.1_01694
+MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW
+LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA
+>GCF_005280335.1_00857
+MAEPIHIGAAADIPEGEAVVVPAATAGTSDDVAVFHAEDGAFYAIDDTCTHEDASLAEGW
+LEGTQVECPLHSAQFCLKSGEALCLPATRPVGTHPVQERDGQLYLTPGA
+>GCF_020097155.1_00793
+MSREINVGPASAVPEGESLLVPNDTTGTKDHIGVFHAEDGAFYAIDNTCTHQDYALSEGF
+VEDCRVECPLHGASFDLRTGEALSLPATKPVGTHRVEERDGDLWLTVEDGE
+>GCF_023573625.1_01926
+MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW
+LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001599.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001599.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da5a055b5b6e43e0bc444cd1ae03b0942b9e4d48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001599.fa
@@ -0,0 +1,51 @@
+>GCF_002008305.4_02006
+MTGGRGAGPGAVAFSTHGGPGSIYAEAEEMRVVAGRHEHAAEEAAGASWQVDAAAFGLGR
+SATWLASAALLQDRLAEAVGRVRSLSEQCAELHRDLLSAAARYEEAERAAAGIMAAEDAS
+LEELPGLLWRDGHDGLTTREAERLVRDLVQAVPEAIVSAALAATGFPLLAALARIDVKML
+TRAQKRVLKRPVSTAAKKGTDAASDLTEALRVSPDEAWTVAADALALAGAAPRGAVTPHG
+APQDRPAAPARLDGSAAGLASLIPRGEGDGDLTVTEVVQENGSRAWVVGLPGTRGGLIPD
+PESTDPWDAGGLLDALGSESEITAPAVRAALEAAGVPHGVPLVLAGYSQGGVHAVNLAGR
+EDFTSVYPVAGVMTIAAPSGNAVETGRTAVLEFSADGDLAVAADGAPTPVSARRAEVVFH
+PAGHGWDAPGGGFRTGSPLAVKADLDAAHDFEGQVDLIRQFEAAEPAARAEVAGLSAALA
+GLTAGTVASSRAVRLRRTPPEGGHRPPGSR
+>GCF_003691675.1_01716
+MTGGRGASPGAVAFSTHGGPGSIYAEAEEMRVVAGRHEHAAEEAAGASWQVDAAAFGLGR
+SAAWLASAALLQDRLAEAVGRVRSLSEQCAELHRDLLSAAARYEEAERAAAGIMAAEDAS
+LEELPALLWRDGHDGLTTREAERLVQDVVQAVPEAIVAAMLAAAGFPLLAALARIDVKML
+TRAQKRVLKRPVSSAAKKGTDAASDLTEALRVSPDEAWTVAADALTLAGAAPRGAVTPHG
+APQDRPTAPALLDGSATGLASLIPREEGDGDLTVTEVVRENGSRAWVVGLPGTRGGLIPD
+PESTDPWDAGGLLDALGSESEVTAPAVRAALEAAGVPHGAPLVLAGYSQGGVHAVNLAGR
+EDFTSVYPVAGVMTVAAPSGNAVETGRTEVLEFSSDGDLAVAADGAPAPVSARRAEVVFH
+PAGHGWDAPGGGFRPTSPLAAEDDLGAAHAFDAQVDLIRQFETAEPASRAEVAGLSAALA
+GLTAGTVASSRAVRLRRTPPERDHLPPGSR
+>GCF_005280335.1_00836
+MTGGRGAGPDGVAFSTHGGPGSLYAETEQMRAVAAGHDRAAGEALRVAGTAESAGAGLVR
+APRVSPTAAVLQARLWEGLERVRALSDRCARMDRDLRAAAVRYEEAERAAAGIVAAEDVG
+LGALPLEAWRRGRDGLTTREAERLGEAAVQAVPEAVASAVLTAAGFPALAALARIDLKKL
+SWWQRKALKRPVSRGASRLVEEASEGTDLLRVSPDEAWTAVGAVARALSIAADREVAVAG
+PPEDRPDAPARLDGSASDLLGLIPRGGVEGELTVTRVERERGGPAWVVGLPGTQGGFAPD
+HASRNPWDASGLADALTADSAATAPAVRAALEAAGVPHGAPLVLAGYSQGGVHAVNLAGD
+AGFTAAYPVAGVVTVAAPSGNAARTGGAAVLEFSSDADLATAVDGAPVPASRHRAEVVFH
+PGGQGWGPPPAPGEEPGAAPAGGFRTAGPDAVGEDLAATHDFDGHLAMVRQFEAADPAAR
+AEVAGLSATLAGLSAGAVASSRSVRLRRAPAPREAAGSTSPVAPGGPGRR
+>GCF_020097155.1_00773
+MSAPAFRVTGGPGSVYADLGSLEAVAQRQRDNGDLARRAGQWCTVLGLDLVSPARTAPSA
+EVLRARLEDGRAGLERLAERLEDMRRSLEHTAQAYRQVESGNAAMIGLIDPALAGVPEVT
+PESLRDGATASETAGVISEELRAAQEKAYVDAAQRLLLALVGGVPGIPESLAALDFQAKQ
+LPWWHPAKHAWNKGKGEAVDRVTGALPAIVEEGVDSGVLPTATAQDASRELARALVSAGA
+LPRGEGEVRVEPGARDRPAPPLLDGRASTLLSLVPEQDGADGAGAVTVTRVDRPDGPGGT
+ASTWIVGLPGTTTRGGAGDNPFDTLGIVESLADEPGVTRAVQEALEREGVPHGSTVVLAG
+YSQGGMRALDLAADEQFASAYRVEGVLTAGAPANDAAAPAEAAVLQFASEADLIWGLGGG
+HDRPAASRATVMFDAPAQVPLPQPGEVRPFDGLDEFDGALAGHARSEYARLIEGFERAPA
+QDRAEVADLQARLALLTGGAVVSSRVLTLRRTSTEPAVDQRAREVREAAEAAGQRPGPRF
+GPRLP
+>GCF_023573625.1_01944
+MTGGRGAGPGAVAFSTHGGPGSIYAEAEEMRVVAGRHEHAADEAAGASWQVDAAAFGLGR
+SAAWLASAALLQDRLAEAVGRVRSLSEQCAELHRDLLSAAARYEEAERAAAGITAAEDAS
+LEELPALLWRDGHDGLTTREAERLVQDLVQAVPEAIVAALLTAAGFPLLAALARIDVKML
+TRAQKRVLKRPVSSAAKKGADAASDLTEALRVSPDEAWTVAADALTLAGAAPQGAVTLHG
+APQDRPTAPALLDGSATGLASLIPRAEGDGDLTVTEVVRGNGSRAWVVGLPGTRGGLIPD
+PESTDPWDAGGLLDALGSGSEVTAPAVRAALEAAGVPHGAPLVLAGYSQGGVHAVNLAGR
+EDFTSVYPVAGVMTIGAPSGNAVETGRTAVLEFSSDGDLAVAADGAPTPVSSRRAEVVFH
+PAGHGWDAPGGGFRTASPLAVEDDLGAAHDFDAQVDLIRQFEAAEPASRAEVAGLSAALA
+GLTAGTVASSRAVRLRRTPPERDHLPPGSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001600.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001600.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0aba0a1b16b5ddb5fe604bc84a674c7ae0a60cdf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001600.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02007
+MPPLIGPQQIATALRAVGLDDDAARLVAWADPARREREAAEQALADLAVAQTQLRAALGG
+LVSAATDVRSAIQTGWRGEAAGAYGEAVRRAAALAAELEREAGEWLALRATAERDAEDAR
+RNAEARQRAAEETALAVLRSLAVAA
+>GCF_003691675.1_01717
+MSPLIGPQQIATALRAVGLDDDAARLAAWADPARREREAAEQALADLAAAQTQLRTALGG
+LVSAATDVRSAMHTAWRGEAAGAYGEAVRRAATLAAELEREAGEWLALRATAERDAEDAR
+RNAEARQRAAEETALAVLRSLAVAA
+>GCF_005280335.1_00835
+MLQLIGPQHLAAALQAAGLDDDAARLLAWADPARRDRDAAQAALDELAVAQESLRGALAG
+LVAAARDVRAGAAVAWRGPAAGEYADAVAEAVGAAEGLEREAGEWLALRATAEREAEDAR
+QDAEARLRAAEETARAALRALAVAA
+>GCF_020097155.1_00772
+MLLPPTAQALLRTLVAAGLDDDAARLAVGLTDAHADLQAARAAQDALADAAEDLRDLLAL
+LEELTRGVAAALDVDWRSEAGAEYGERTDGLHRTATDRQDEAREWAGLLGRARSEAEQAE
+RDAELRVRRAEEGASALLRAMAAA
+>GCF_023573625.1_01945
+MSPLIGPQQIATALRAVGLDDDAARLVAWADPARREREAAEQALADLAVAQTQLRTALGG
+LVSAATDVRSAMHTAWRGEAAGAYGEAVRRAATLAAELEREAGEWLALRATAERDAEDAR
+RDAEARQRAAEETALAVLRSLAVAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001605.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001605.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f5c87eea8dec20956433cf84fff0632e488d9aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001605.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_02012
+MTETTDAPTTGKRRATFNTLEVSELRRLTEDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGTFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVPEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA
+>GCF_003691675.1_01722
+MTETTDVPTTGKRRATFNTLEVSELRRLTDDSVEITFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA
+>GCF_005280335.1_00830
+MTETTVTPATGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGQEVRRSYSICAIPKRGEIRVAVKKDIGGKFSTWANEVLEVGEKIDVMNPQGAFTSRS
+HVTSLNDAEKVAAEKVAQNKNTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDAEKLTTLLDRVIDVDGTD
+EWFLCGPFELVQLARETLSARGVDEDDVRFELFTTGRPENPQGHSGRVVEADPSGDNVTI
+EFNLDGLSGKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTDGEYEMDENYA
+LEKDEVEAGYVLTCQTRATSDSITVDYDA
+>GCF_020097155.1_00767
+MTETTDAPITGKRRATFNTLEVSGLRKLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAELRRSYSICAVPQRGEIRVAVKKDLGGTFSTWANEVLEVGEKIDVMNPQGAFTSRT
+NVTSMNDPEAVAAEAVKQDQTHLVALAAGSGITPIMAIAKSVLAASDSARFDLIYANRSA
+MDVMFAEEIGDLKDKYPARFTVNHVLSREQRVAPLLSGRIDDEKLNTLLDRVIDVENTDE
+WFLCGPFELVQLARDTLSERGVAEDDVRFELFTTGKPEAPQGQSGRGVEADPSGDNVTIE
+FNLDGLSAKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTEGEFTMEENYAL
+EKDEVEQGYVLTCQTRPTTDSIKVDFDA
+>GCF_023573625.1_01950
+MTETTAAPTTGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAENKDTHLVAFAAGSGITPIMAIAKAVLAASESSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001606.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001606.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cbc3ebc9af8f6b878425140db36cc12e28647c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001606.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02013
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAKDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDRRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
+>GCF_003691675.1_01723
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAEDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDHRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
+>GCF_005280335.1_00829
+MTVADGVAEVRLNAPKKMNSLDEAALADLHEAYRRAAAGVESGEVRAVLLHGEGRGFCAG
+RDISAVDPAEDDATAYLRDKVTPVLRAMSEIGVPTFAAVQGACLGVGLGLAIATDVVYVA
+EDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELISGEEAVRAGLFSRSVPA
+DELLEFTRAKAAKAAQGATLAFRASKELVRQIRDERVGLWESLDAENIAQGDLCNTADYA
+EGFKAFQEKRRPEFTGRG
+>GCF_020097155.1_00766
+MIELAIADRVAVITLNAPQKMNSLDEQALADLADAYAQASAGAESGEVRAILLRGEGRGF
+CAGRDISNVVPADDDATAYLRDKVTPVLKAISEAPVPTFAAVQGACLGVGLGLAIASDVV
+YVAENAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELISGAEAVQAGLFSRA
+VPAEELDGFTREKVAKVADGATLAFRASKELVRQIRDRRVGLWESLDAENVAQGELCDTA
+DYAEGFTAFQEKRKPEFTGRP
+>GCF_023573625.1_01951
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAEDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDHRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001607.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001607.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8adad7a399bf69ca35894261bc7dbf6ec924c664
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001607.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_02016
+MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTVKAVIEDAGIDPSVVDDVILGNAN
+GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE
+SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD
+GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETVVDTDEGPRPGSTPEV
+LASLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI
+MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG
+HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVERV
+>GCF_003691675.1_01725
+MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTIKAVIEDAGIDPSVVDEVILGNAN
+GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE
+SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD
+GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETVVDTDEGPRPGSTPEV
+LASLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI
+MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG
+HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVEKV
+>GCF_005280335.1_00805
+MTTPSPQPQALLVGGKRTAVGRYGGALSAVRPDDLAALTIKQVIEDAGIDPAAVDEVILG
+NANGAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAG
+GVESMSRAPWVMEKPTTAFAKPGAAFDTSIGWRFVNPRFADGEFGEKFTFSMPETAEEVG
+EVDGITREDADAFAARSHGRAIAAIEAGRFKDEIVPVTVKGRKGAETVVDTDEGPRPGST
+PEVLAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLA
+PEIMGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPEIVNADGGAI
+ALGHPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVEKV
+>GCF_020097155.1_00764
+MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTVKAVIEDAGIDPSVVDDVILGNAN
+GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE
+SMSRAPWVMEKPTTAFAKPGAAFDTSIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD
+GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETIVDTDEGPRPGSTPEV
+LAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI
+MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG
+HPLGSSGSRLVVTLLGRMEREGADKGLATMCVGVGQGSAMLVEKV
+>GCF_023573625.1_01953
+MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTIKAVIEDAGIDPSVVDEVILGNAN
+GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE
+SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD
+GITREDADAFAARSHARALAAIEAGRFADEIVPVVVTGRKGAETIVDTDEGPRPGSTPEV
+LAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI
+MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG
+HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVERV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001608.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001608.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b923c1677e9a0839e58de809b7660f76e2ed0b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001608.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02017
+MTDFSHFSALHVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPRGAHPHVDEIAQA
+ILFESDAKFERMQAFLDRKKK
+>GCF_003691675.1_01726
+MDDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKCEPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPEALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA
+ILFESEAKFERMQAFLDRKKK
+>GCF_005280335.1_00804
+MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPEALEVAAHALADRIAKQDPLAVRISKRVFHLPREAHPHVDEIAQA
+ILFESEAKFDRMQAFLDRKKK
+>GCF_020097155.1_00763
+MADFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKREPGRFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETGLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRISKRVFHLPREAHPHVDEIAQA
+ILFESQAKFERMQAFLDRKKK
+>GCF_023573625.1_01954
+MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA
+ILFESEAKFERMQAFLDRKKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001611.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001611.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98ea83ad3b3af697f12f5a692703a1e59b2bb55a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001611.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02021
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARHFQPKVVHVDADNRIVELGVD
+PADGLLDGLSRPPLSREWNEAQAEL
+>GCF_003691675.1_01730
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARNFQPKVVHVDADNRIVELGID
+PADGLLDGLSRPPLSREWNEAQAEL
+>GCF_005280335.1_00798
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAAQILPGELVSIVDVTNGARLETYTI
+AGERGSGVIGINGAAAHLVHPGDIVILIAYAQMDEEEARHIQPRVVHVDGENKIVELGAD
+PADGLLDGVSRPPLSREWNEAQAEL
+>GCF_020097155.1_00759
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDAEARHFQPKVVHVDADNRIVELGVD
+PADGLLDGLSRPPLSREWNEAQAEL
+>GCF_023573625.1_01958
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARNFQPKVVHVDADNRIVELGVD
+PADGLLDGLSRPPLSREWDEAQAEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001613.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001613.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17700e25a241eaeab5b6e8f1c4fb58485e897890
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001613.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_02023
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART
+VGQQALGALTIHERALKLKELALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVAQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKEQQGEVRGA
+VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG
+YTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTATTTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE
+DVEAGTAVHPFYKSLAELTVGDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP
+RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>GCF_003691675.1_01732
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART
+VGQQALGELTIHERALKLKELALFLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKDQQGEVRGA
+VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG
+YTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTAATTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE
+DVEAGTAVHPFYKSLAELTVGDQFASGLRTITLEDITAFAEETGDRFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP
+RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>GCF_005280335.1_00796
+MTVTLPSLPEILPSYVNGAWWTPQSPSKVTDVTDANTGERLTGVSTDGLDTAAAIEHART
+VGRKSLGELTIHERALKLKELALYLNSRIQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSNVITDGPVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+SFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSLQLISGSARDLLDHLDYRDHVSF
+TGSAATAQTLRKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVDAVVEALSARLGKVVLGDPRVEGTTMGALASKEQQGEVRGAV
+QRLVDAGGQVRLGGPDASTGDADAESGAFFAPTVLSFEDARTPEVHAVEAFGPVTSVVGY
+TDVEDAVALAALGSGSLVATVATDDGETARAFAAGIGAHHGRVHFLNRQTATTTTGHGAP
+VPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRED
+VEAGTAVHPFYKSLAELTVGDQFASGLRTVTLQDITDFAEETGDKFYAHTDEEAAMANPF
+FPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITPR
+VSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>GCF_020097155.1_00757
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGELMARVSTDGIDTAGAIEHART
+VGQRNLGELTIHERALKLKELALYLNSRIQELYDLSFATGSTQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVTEACVRMMVESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAGTAQTLRQHENVLNGGVRFTAETDSLNAAILGPDAGVDTPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPEAMVEDVTAALTERLSSTVVLGDPRAEGTTMGALASKEQQSEVRKA
+VQTLVDAGGQVRLGGPEGSTGDADAEAGAFFAPTVLTFADADTPQVHSVEAFGPVTSVIG
+YTDVADAVRLAALGSGSLVATLATNDGATASEFIAGIGAHHGRVHVLNRQTAKTTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAVQGSPDMLTAITGVWHQGAAAQTATRE
+DVEAGKAKHPFYKALDELQIGDQFASGLRTVTIEDITAFAESTGDKFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLDDLRFITPVTYDDAIRVTLTAKRITP
+RVTDEYGEVAWDCRLHNQKDELVAQYDVLTLVAKTWPMPEAEPKA
+>GCF_023573625.1_01960
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART
+VGQQALGALTIHERALKLKELALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKEQQSEVRGA
+VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG
+YTDVADAVALAALGSGSLVATVATNDGETARAFTAGIGAHHGRVHVLNRQTATTTTGHGA
+PVPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE
+DVEAGTAVHPFYKSLAELTVGDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP
+RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001615.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001615.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40e086076df6afbed3773fcad121241aa71db225
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001615.fa
@@ -0,0 +1,33 @@
+>GCF_002008305.4_02025
+MTTSRLPLLGALAVGALALAGCAGGGAEPSSPAPSSASSTTTAASSASPAASSSTAPTSP
+AASASTASMGGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSEVGLSAASPLERQT
+ELRQRAAGLEQTVDAGASPASTRSAEQQACLDATRSDLERDAEAGAADLGLTAQPETAAT
+TGGGPTSTPVPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLAGLG
+VESVTRTEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDRAAS
+IVADVLAALDGEG
+>GCF_003691675.1_01734
+MTTSRLPLLGALAVGALALAGCAGGGGAEPSSPAPSSASSTTTAASSAPTSPAASSSTES
+TGAAESTAGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSEVGLSAASPLERQTEL
+RQRAAGLEQAVDAGASPASTRSAEQQACLDATRSDLERDAEAGAADLGLTAQPETAATTG
+GGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLAGLDVE
+SVTRTEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDRAASIV
+ADVLAALDGEG
+>GCF_005280335.1_00794
+MTPSRLPLLGVLAVGALALAGCAGGGAEPSSPAPSPASSSASPTTTAASSASTSPAASAS
+ASSTPTATALSLDLPEELSGESATRLRAVVQDAAGPAAELGQTFSSPLERRAALEEDAAI
+VDALEEDAGDDAGRRACVDATRAAREADQASGAAQAAWYAQPQTASTTGGSTDGTAASGR
+PGLQVEPLGVQVAVYPDEATARSVAEAARDAAEACEGQEMSSMGVSSVEPLTGAPGETAF
+TVVPVSGSIIYAVSTVVQVGDRVYAVSQGEDGAGVPEGAEERAVALVEDLEAALEG
+>GCF_020097155.1_00756
+MTHMTAVPSRRLRAGFALGAAALVLTGCAGGGGSASSSTAAGSPTAGGAGSSVTSPAASS
+SAASSSALSLSMPDRFGNEARTGLTEAVTAAAPEGFEVTTRSVSPLERKTDLEDQATILT
+DGPLEPAAEGSSASPTYTEAQQRCADAAAERFRTEAAAGGAQLRSDAMPTVAGGGYTSVR
+ADVVAYPDVSAAVAALADGSAPIELCTDVQVPGAEQPTDIAPVTGIGDEAVGGELAGGRW
+LAVRRGTDVVSVMVAGPGETAPAGAADQARALAEQVLEAVPAG
+>GCF_023573625.1_01962
+MTTPRLPLLGALAVGALALAGCAGGGGAEPSSPAPSSASSTTTAASSASTSPAASSSTAP
+TSPAASASTESTAGASASSSLSLEMPPALDGQRTLAVQTAVQRAAGPGSEVGLSAASPLE
+RQTELRQRAAGLEQAVDAGASPAPTRSAEQQACLDATRSALERDAEAGAADLGLTAQPET
+AATTGVGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLA
+GLGVESVTRTEHEGGAAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDR
+AASIVTDVLAALDGEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001618.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c0412596ccf1f38f6462c7d6d21ee025ca6f09d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001618.fa
@@ -0,0 +1,19 @@
+>GCF_002008305.4_02028
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR
+>GCF_003691675.1_01737
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR
+>GCF_005280335.1_00791
+MTLTEDHHNGFGMAHGGAVFAFADSCFALTCNDPGGDGSTITVASGVDVNFLAGTRAGQT
+LVAEGRLVAAAGRSAVYDITVTTDDGTPVAAFRGRSRTIPAPGR
+>GCF_020097155.1_00752
+MTETPHHPALVGDRVARWLGVTLEAAEKDHARIRMTLGEEHHNAFGMAHGGVVFAFADCC
+FALTCNDPASDGSTLTVASGVDVNFLSGTRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TLVAAFRGRSRTVAVKGA
+>GCF_023573625.1_01965
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001619.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001619.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9cae7a6b62f8ce74f29aa9cf49eacf39f5d9789b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001619.fa
@@ -0,0 +1,27 @@
+>GCF_002008305.4_02033
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
+>GCF_003691675.1_01740
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
+>GCF_005280335.1_00787
+MTELDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKWWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGSGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVRLALLRRDWDSARASV
+>GCF_020097155.1_01226
+MDTHRSTPVVALRPVEAGDEEFLWTWIHGTPDAEWKRWDAPYFHAAEQAAPMGRAAFARS
+FAPWPDDADRRIITADGAAIGLVTRHEEAPAGGGWWELGILLFDPSRWGGGIGTRALAAW
+TEATLTETDAHVLTLTTWSGNARMAGAAERAGFRMCARVPESRAWDGRRWDSLRFALLRG
+DHEGEQASAPEPPARRPELADLTVVTGRIPDAAALRALYDAVGWTAYTRNPDALAAGVAG
+SACVATAWAGQELVGLARVVSDGHTIAYLQDVLVHPERRRQGVAGKLLDAVFAPFAHVRQ
+QVLITDEEPGQRAFYEACGFRQFGGGGPVPGRTFVRFAG
+>GCF_023573625.1_01968
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001625.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001625.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d18152613ba1d11a5a5d7fab5f7234be3b8a88bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001625.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02052
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALHRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSAPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQTGE
+>GCF_003691675.1_01758
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALHRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSTPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQAGE
+>GCF_005280335.1_00770
+MTTVFYDDQGRPEPPETAGEAETLLGFLEFLRATFAWRTGGLDEAALRRRLDGHPSEMTL
+GGMLKHLAFVEFWWFEAVALGAPTSEPWVSVDWAADEDWDWHSAAEDSAADLRALWEGQV
+ERSRQAVQELLAADGDPLGRVLESYDGRRRVTLRWILTHMIEEYARHNGHADLLREQIDG
+QTGE
+>GCF_020097155.1_00740
+MTTVFYDEQGRPEPPHAADEAATLLAFLDFQRATFAWRTSGLDDAALRRRLDGHPSEMTL
+GGMLKHLAFVEFFWFEVTAHGKPTSEPWVSVDWDADADWDWHSAAEDAAEELRDLWRESV
+ERSRAVVVRLLADGPAALDTTHPAWGGRADVSLRWILTHMIEEYARHNGHADLLREQIDG
+QTGE
+>GCF_023573625.1_01986
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALRRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSAPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQTGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001626.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001626.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5397a6176e29864618e44e4c74234c0b82efdfbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001626.fa
@@ -0,0 +1,79 @@
+>GCF_002008305.4_02053
+MASPSPASAHPSAPESGTGLGFTGVEGITGLTASEVAEREAAGLVNVQSRDTSRSLGQIL
+RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ
+DDVLVIRDGARVPLPMAQIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP
+KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT
+IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF
+AVSALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLAAPASADASPDAH
+DDGAPAEVGDGARAVLAWFGADPDVNPTAAALREPFTAVPAVDPAAQVAFSSARRWSAVA
+FGPEAGAAAGTWLLGAPEALVDERLLGPDAAEAVRAQVHADADAGRRVLLLARTDEPLIG
+DALPAGGVPVAVVTFRENVRPDAAETLGYFHAQGVRAVVISGDSPRTVAAVAREVGLEVA
+GQAYDGRTLPDDPDALADVMEEHSVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA
+LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY
+ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP
+SGAVILLSMVALQTYVRLTAGDVDLARQQAAFMITLTLVGLWVLSVMSRPLSARVVVLIL
+AMYAVLAAVVLVPVSRWYHQMEVPPTDVLVAALVIAAVGCGLIELIHQVHRRHVARMLAA
+AGA
+>GCF_003691675.1_01759
+MASPSPASAHPSAPESGTGLGFTGAAGITGLTAAEVAEREAAGLVNVQSRDTSRSLGQIL
+RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ
+DDVVVIRDGARVPLPMARIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP
+KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT
+IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF
+AVSALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLTAPASADASPDAH
+DDGAPAEVGDGARAVLAWFGADPDVNPTAAALREPFTAVPAVDPAAQVAFSSARRWSAVA
+FGPEAGAAAGTWLLGAPEALVDERLLGPDAAEAVRAQVHADADAGRRVLLLARTDAPLIG
+DALPAGGVPVAVVTFRENVRPDAAETLDYFHAQGVRTVVISGDSPRTVAAVAREVGLEVA
+GQAYDGRTLPDEPGELAAVMAEHDVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA
+LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY
+ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP
+SGAVILLSMVALHAYVRLTAGDVDLARQQAAFMITLTLLGLWVLSVMSRPLSARVVVLIL
+AMYAVLAAVVLVPASRWYHRMEVPPTDVLVAALVVAALGCGLIEVIHQVHRRHVARVLAA
+AGA
+>GCF_005280335.1_00769
+MTPPAPAPPPAAAPGALSGVSGLTSAEVAEREAAGLTNRQSKDTSRSLAEILRVHVLTLF
+NLAIALCAVVVISLGRWLDLLFSLAAIANVVIGVVQEYSAKRKLDRIALLHQDDAVVVRD
+GARVSLPMARIVRDDVVVLRRGDQVPVDGEVLASDGLDLDEALLTGENDPVPKAPGDAVL
+SGSSVVAGTGLMRATAVGPASHAARLSAEARRFSAIRSELRGALEKVARWLTIGLVPIIA
+VIVHGQMTAVGGWAHALAQPREAALEPALIASVAAVTSMIPQGLALMTTIAFAVSALKLA
+QHEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFHELLAPASASPSTSTSTDDDGAPA
+DVDAAARAVLAWFGADPDANPTAAALHEPFADAPPHEPADHVAFSSARRWSAVAFGPEVG
+AATGTWLLGAPEALLGDADARPGEAGTGRDDVAAVRAQADALSDEGLRVLLLARTDAPLA
+GNALPAGRVPAAVVTFRENVRPDAAETLGYFHAQGVRTVVISGDSPRTVAAVAREVGMDV
+PGHARDGRTLPEDPEALADVMAEHDVFGRVSPDQKKAMVAALQSRGHVVAMTGDGVNDAL
+ALKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPAVLGEGRQVIANMERLAHIYLTKTT
+YALLFGVVFSLLAWQFPLLPRQASTVDFIMIGLPTFFLALLPNPRRYVPGFLGRALRFAI
+PSGVVILLSMVALQVYVRLAADHVDLAQQQTAFMITLTLVGLWVLSVMSRPLTRRVVLLV
+LAMYAVLAAVVLVPASRWYHQMEVPPADVLVAALVIAAVGCALIELIHQVHRRHVARVLA
+AAGA
+>GCF_020097155.1_00126
+MTHTPPSPAPAADAGPAALAGLTSAQVAERVAAGRVNVQPKDTSRSFGTILRSHVLTLFN
+LVIALCATVIVVLGRWFDLLFSLAAVANVVIGVVQENSARRALDRIALLHQDGVLVVRDG
+ARREVRIEEVVLDDVVVLRRGDQVPVDGAVLTSEGLDVDESLLTGESDPVPKAPGDAVLS
+GSAVVAGTALVRATAVGADSHAAKLAVQARRFTRAHSELRAALEKVARWLTIALVPIVAV
+ILHGQVTAAGGWSRVLGSEDQPALEAALVATVAAVTAMIPQGLALMTTISFALAALKLAR
+RAVLIQEQPAVEILARVDTVCLDKTGTLTEGGIVFHGAHAPVGAPALPHDDDAAVALDPG
+ARAVLAWFGADPDANPTAAALREPFPAAPASSPTGVVPFSSVRRWSAVTFGPDADAAHPG
+MAGTWLLGAPEALADAAHLGPERTAALTEACTAPADRGLRTVLLCRASDAPAGETLPAGR
+EPVAVLTFAEDVRPDAAQTLGYFREQGVAVKVISGDSPRTVAAVARAVGMEVPGDAVDGR
+TLPADPAELADVLESHEVFGRVAPEQKQAMVAALQSRGHVVAMTGDGVNDALALKTADLG
+IAMGNAAPATKAVSRMVLLDGRFDRLPDVLREGRQVIANMERLAHIYLTKTSYALLFGLV
+FSLLAWPFPLLPRQASTADFLMIGAPTFFLALLPNPRRYVPGFLRRALLFAVPAGVTIVA
+AMLAVSWYARHLSSKPVDTAQLQTASLITLTLLGLWVLTCISRPLRPLMCGVVAGMYALL
+AAAVLVPASRWYHQMELPAPDLLAASLAIALGGCVVVEAVHRIHHARVTVPGRRAAEG
+>GCF_023573625.1_01987
+MASPSPASAHPSAPESGTGLGFTGVAGITGLTAAEVAEREAAGLVNVQSRDTSRSLGQIL
+RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ
+DDVVVIRDGARVPLPMAQIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP
+KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT
+IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF
+AVAALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLTAPASADASPDAH
+DDGAPAEVGDGPRAVLAWFGADPDVNPTAAALREPFTAVPAVDPVAQVAFSSARRWSAVA
+FGPEAGAAAGTWLLGAPEALVDEWHLGPDAAEAVRAQVHADADAGRRVLLLARTDEPLIG
+EALPAGGVPVAVVTFRENVRPDAAETLDYFHAQGVRTVVISGDSPRTVAAVAREVGLEVA
+GQAYDGRTLPEDPGALADVMAEHDVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA
+LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY
+ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP
+SGAVILLSMVTLQTYVRLTAGDVDLPRQQAAFMITLTLLGLWVLSVMSRPLSARVVVLIL
+AMYAVLAAVVLVPASRWYHQMEVPPTDVLVAALVIAALGCGLIEIIHQVHRRHVARVLAA
+AGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001628.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001628.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b459d9f25d59583cddeeda461364cee961bcd43d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001628.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02056
+MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSRWTAGAAVVGAVTAYLVGFGLRR
+GAAMIASDLHALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMAG
+VAEAMLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR
+MAPWAWALPLLVLSFKHADDVGDALAARGID
+>GCF_003691675.1_01762
+MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSLWTAGAAVVGAVTAYLVGFGLRR
+GAAMIASDLRALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMTG
+VAEAVLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR
+MAPWAWALPLLVLSFKHADDVGDALAARGID
+>GCF_005280335.1_00764
+MISLYVPGDSPLHRAPAGLKLALFAAWALAVTLAPPTPWTAGAAVGMALAAYLTGFGPRR
+GAAMLGRDLRALWVFYAFLFAAQWLFADLTAAALMVGRVLGLVLAAQVLTRTTRIAELVG
+VAEAVLAPVERIPWLGPRLARVGLRPERVGLAMGLVLASIGHLRSVAEQVRQAQASRGVR
+MAPWAWVLPLLVLSVKHADDVGDALAARGIE
+>GCF_020097155.1_00728
+MLSLHVPGDSPLHRCPAGAKVAALAVWALVVTLAPVSALTAGASVVVGVGAYLLGFGLRR
+GVRLLAADLRGLWVFYAVLFAAQWLFTDLPTAALTTARVLGLVLAAQVLTRTTRIAEMAG
+VAEAVLGPVTRIPWLGPRLARAGVRPDRVGLAMGLVLASVGHLRGLAEQIRAAQAARGVR
+MAPWAWVLPLLVLSLKHADDVGDALAARGID
+>GCF_023573625.1_01990
+MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSLWTAGAAVVGAVTAYLVGFGLRR
+GAAMIASDLRALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMTG
+VAEAVLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR
+MAPWAWALPLLVLSFKHADDVGDALAARGID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001629.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001629.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2358d9e5048fdf2fa5bd9315df42a6c7e526d0a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001629.fa
@@ -0,0 +1,29 @@
+>GCF_002008305.4_02057
+MSPDRSVTLTGVRVEADGPEGAVVLLDGVDLTLAAPRVAVIGENGSGKSTLARAIAGLAD
+VVAGEVTVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLT
+KDDVAARVAAALQEHRLTALADRACLSLSSGQAQRLAMCSVMTAGPSLVIADEPTSLLDG
+RHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWIHSGRVERTGPAEEVVEAY
+ERFLDHAVAAELR
+>GCF_003691675.1_01763
+MSPDRSVTLTGVRVEADGPEGVVVLLDGVDLTLTAPRVAVIGENGSGKSTLARAIAGLAD
+VVAGEVTVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLT
+KDDVAARVAAALQEHRLTALADRACLSLSSGQAQRLAMCSVMTTGPSLVIADEPTSLLDG
+RHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWVHGGRVERTGPAEDVVEAY
+EHFLDHAVAAELR
+>GCF_005280335.1_00763
+MEQTTGVRLRGARVEADGPEGVVALLQDVDLDLTAPRVAVVGENGSGKSTLARAVAGLVD
+VVAGEVTVHGVDAVRDVKALRRVVGMVFANPAAQAVMPTVREDVELTVKSLRDDDGRRLS
+KDDVAARVAAALAEHRLTELAERPCLALSSGQAQRLAMCSVMAGRPRLVIADEPTSLLDG
+RHRRIIADRLLAADGFQLLLVTHDLELARACDDAVWVHEGRVRAVGPAGEVVDAYAAFLD
+EAVAAESAEAAAGDPAAVNPAGASAEARP
+>GCF_020097155.1_00727
+MTGRTPPTRAPHDDDAAVRLAGVQVAAPGGPVLLDGVDLHLTAPRVAVVGENGSGKSTLA
+RAVAGLAEVTAGEVAVHGVDAVRDVKALRRTVGMVFANPAAQMVMPTVREDVELTVKALT
+DDAGRRLSRAEVAARVDAALAEHRLTDLAERPCLSLSSGQAQRLAMCSVLVGAPRLVIAD
+EPTSLLDGRHRRIVADRLLGGAERGEFQLLLVTHDLDLARACDAAVWVHSGRVERHGPAA
+ETVAAYEAFLDDAVARELA
+>GCF_023573625.1_01991
+MLLDGVDLTLTAPRVAVIGENGSGKSTLARAIAGLADVVAGEVSVHGVDAVRDVKALRRT
+VGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLAKDDVAARVAAALEEHRLTALADR
+ACLSLSSGQAQRLAMCSVMTAGPSLVIADEPTSLLDGRHRRIVADRLLAADPSAPDGFQL
+LLVTHDLELARACDEAVWIHGGHVERTGPAEDVVEAYERFLDHAVAAELR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001630.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001630.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20c1f9090a99fdaff4cbd1bbe35006bbb4b15e17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001630.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02058
+MSTSVPSSHDGHVRPAATTTADRPTDAGRPRRGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFAGPTAG
+FILGWIPSALIVGLIFWALTSRARPGLDAGRVALGAAVAGLIGGVVMVYFFGVLGFVGIA
+GMEFGAAVLSMAPFVPGDLIKLVVSVILIVGLWKAYPRAFR
+>GCF_003691675.1_01764
+MSTSVPSSHDGHVRPAATTTADRPTDAGRPRRGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFAGPTAG
+FILGWIPSALIVGLIFWALTSRARPGLGAGRVALGAAVAGLIGGVVMVYFFGVLGFVGIA
+GMEFGAAVLSMAPFVPGDLLKLVVSVILVVGLWKAYPRAFR
+>GCF_005280335.1_00760
+MPTSDTLASGRPAHSTDDRRPRRSSAGSGLARVAVFAALMAVLGLVPPVPVAGIPAPIVL
+QNLAVTLAGVILGPWRGAAAILLFNVLVALGLPLLTGGRGGLGVFVGPSSGFILGYVVAA
+AAVGLVFWALTGRARPGLRPGRVLAAALVAGLVGMVVLYAAGAVGFIVAAHMEPGAAVLA
+MGAFVPGDTVKVVLAALLVTGLWKAYPRAFR
+>GCF_020097155.1_00723
+MTSPSAPQTAVVDAPATHRPRRSPGADLARIAVMAALIAVLGAMPGIPVPGIPTPITLQT
+LGVMLAGLVLGAWRGAASVALFHLLVALGLPLLAGGRGGAAVFVGPSAGFLWGWIPGAFV
+VGLLFHLYLRGRRDGRNTGGLVAAALTACVVGGIAVIYLFGIPGMNLFGGVPLDKAAIGS
+LAFIPGDLLKAVVAALLAAGLWKAYPRAFA
+>GCF_023573625.1_01994
+MSTSVPSSHDGHVRPAATTTADRPADAGRPRHGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFNALVALGLPLLTGGRGGLGVFVGPSVG
+FILGWIPSAMIVGLIFWALTSRSRPGLSAGRIALAAAVAGLIGGVIMVYVFGAFGFVGVQ
+GMEFGAAMLSMAVFVPGDLTKLVIAVLLCAGLWKAYPRAFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001632.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001632.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1629444f0e6d4ca68313c9917f4c5f95ad86fcf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001632.fa
@@ -0,0 +1,29 @@
+>GCF_002008305.4_02080
+MNLDQLQALRAIADEGSFEAAAYELDVSASAVSQRIRALEREVGQVLLRRGTPCEPTEAG
+IGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADWEDTVLD
+LHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAGPLGSMRYVPLASPALLARHAADDVV
+DLGAMPMMRYNAKDDLQRLALSGAGLDIAPPTHLAPSFDGFHRSVRAGLGWGMLVDAQAV
+EDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG
+>GCF_003691675.1_01784
+MPKLCFMNLDQLQALRAIADEGSFEAAAYELGVSASAVSQRIRALEREVGQVLLRRGTPC
+EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW
+DDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALRARH
+AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML
+VDAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG
+>GCF_005280335.1_00704
+MNLDQLQVLLRRGTPCEPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPAD
+VLGTWFGPVLAEAADWDDLVLDLHVEDQDHSAQLLRRGEVLAAVTTEPQPVQGCAAEPLG
+SMRYVPLVAPALLARHAAGDVVDLGAMPMMRYNVKDDLQRLALSDAGLDVAPPTLPVTRL
+VRLTRAVREAAQRTLEPG
+>GCF_020097155.1_00614
+MNLDQLQALRAIADEGSFEAAAYELGVSASAVSQRIRALEREVGQVLLRRGTPCEPTEAG
+VGLVRVARHMRVLEQEAWAGLGRMAAGRSVTSLAVPADVLGTWFGPVLAEAADWDDTVLD
+LRVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALLARHAAGDVV
+DLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGMLVDAQAV
+EDVRAGRLVRVPGLDDVLVPLYWQATTLPVTRLARLTQAVREAAQRTLERG
+>GCF_023573625.1_02018
+MPKLCFMNLDQLQALRAIADEGSFEAAAYDLGVSASAVSQRIRALEREVGQVLLRRGTPC
+EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW
+DDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALLARH
+AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML
+VGAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001633.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001633.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9855b1e7da84646482e89cce8aa3cfe593348ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001633.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02081
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
+>GCF_003691675.1_01785
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
+>GCF_005280335.1_00703
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALHPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPTAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
+>GCF_020097155.1_00613
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASILWFTALGYGARLLARVLADPKAWRV
+VDLVIAVVMAVLAVRLIAGSGVWG
+>GCF_023573625.1_02019
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001634.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001634.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebcb233f575e7459d194f29afcdcce4e476b9428
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001634.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02082
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
+>GCF_003691675.1_01787
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
+>GCF_005280335.1_00701
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQRRKRGERRAALSDLVGEASSAGLYGQNAESYREALRQARADLRGERG
+>GCF_020097155.1_00611
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRAALSDLVAEASSAELYDQKAESYREALRQARADLRGERG
+>GCF_023573625.1_02021
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQRRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001635.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001635.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84f1403b7f765ed8e2f6a07f80818a89bdbacd5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001635.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02083
+MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>GCF_003691675.1_01788
+MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>GCF_005280335.1_00700
+MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQQSSPELWGRLIAAVFALDGVEEGHS
+TVSPATSRAVHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>GCF_020097155.1_00610
+MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRAVHLTGRPKERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLPPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>GCF_023573625.1_02022
+MDPDASPRVRLTADDPRPGSRPVTSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001636.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001636.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e40c0c60451120117921a2337c1d9456b561f3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001636.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02084
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>GCF_003691675.1_01789
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>GCF_005280335.1_00699
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGQLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPASVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGQEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDVVETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>GCF_020097155.1_00609
+MTTLIPTTLVGSLPKPGWLAEEETLWSPWKLEGERLREGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGVKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>GCF_023573625.1_02023
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGERLHEGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAAGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001637.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001637.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3d8700cc9b0ab3a2dd01c07d0d7784b2321e745
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001637.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02085
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGTDRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAVTSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDNEETR
+>GCF_003691675.1_01790
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGTDRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAVTSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDNEETR
+>GCF_005280335.1_00698
+MSHATLAPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDKHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEASRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLVATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQAHFVGPHRDLLERWAAAHAARDTEETR
+>GCF_020097155.1_00608
+MSHATLVPSTVPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERETG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDTEETR
+>GCF_023573625.1_02024
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQAHFVGPHRDLLERWAAAHAARDTEETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001638.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001638.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2308b022da927184ebb912c049f5f15fc23fd3bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001638.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_02086
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA
+PAHHRTTRARTPERTR
+>GCF_003691675.1_01791
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA
+PAHHRTTRARTPERTR
+>GCF_005280335.1_00697
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGERAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHDLAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAVGRGTPSSSAVPRPA
+PAHHRTTRVRTPERTR
+>GCF_020097155.1_00607
+MTAVHHPTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDTTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHDLATRQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGTPSSSAVPRPA
+PAHHRTTRVRTPERTR
+>GCF_023573625.1_02025
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSIRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPSSSAVPRPA
+PAHHRTTHARTPERTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001639.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001639.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1337ec022d4f0a4d26932c95b0de8c133814a52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001639.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_02087
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAAASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPATTPAVPETAAVTQEVR
+>GCF_003691675.1_01792
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAAASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPATTPAVPETAAVTQEVR
+>GCF_005280335.1_00696
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLTRSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSARLAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLITDLDRA
+LAVVSAAGPAVLATTPAVPETTAVTQEVR
+>GCF_020097155.1_00606
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALAGLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPETVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREAAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVSAAGPAVPAATPAVPETAAVTQEVR
+>GCF_023573625.1_02026
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAQHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTREQREAAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPAATPAVPETAAVTQEVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001642.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001642.fa
new file mode 100644
index 0000000000000000000000000000000000000000..732be5f3f796d274d575cf8203db6f364ba63afd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001642.fa
@@ -0,0 +1,43 @@
+>GCF_002008305.4_02095
+MSPSAPQRRAARAATFAATLAAAAIALTACGADAAPFSPASAPASASDGAESPAGEATAA
+SSVSEEDRVDPTQTTEVSAVTPRILLSHEDGLTLLDAESGEVVKEQDVTGFTRLSNAGNG
+KDVLVTTGNGWEVFSTGIQAKAHGDHVHHYESAPGMTGVTFPGEHPGHVVTHNGRTTLFA
+DGTGAIRTFDSTHLDKATPDLMPVMTEAETEDPHHGVALELSDGALFTTQGTEDSRDALQ
+VIDPKTGEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ
+RSGNLFGLHDSPIVLGDHKVEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGR
+AEDGSAVVLTYDGEANVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA
+EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGQPESVKPDEAADAASGHDEHTDHDH
+>GCF_003691675.1_01803
+MSHSAPQRRSARTAALSATLAAAAIALTACGADAAPSGPTSAPAPAADGAESPSGEARAA
+SSVSEGDRVDPTRTTEVSAVTPRILLSHEGGLTLLDAESGEVVREQDVPGFTRLSNAGNG
+KDVLVTTGNGWEVFSTGIQAKAHGDHVHHYESAPGMTGVTFPGEHPGHVVTHNGRTTLFG
+DGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHHGVALELSDGTLFTTQGTEDSRNTLQ
+VIDPKTSEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ
+RSGNLFGLHDSPIVLGDHKVEEEPEEAVERPTAIALIDTRTDELTTVDLGSSYWFRSLGR
+AEDGSAVVLTYDGEVTVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA
+EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGEPESVKPEEGADAESGHDEHADHDHGH
+ESDEHTDHDH
+>GCF_005280335.1_00683
+MSHSAPQCRSTRTAASDGAESTSGETTAASSVSEEERVDPTRTTEVSAVTPRILLSHEDG
+LTLLDAESGEVVKEQDVPGFTRLSDAGNGKDVLVTTGNGWEVFSTGIQAKAHGDHVHNDE
+SAPGMTGVTFPGEDPGHVVTHNGRTTLFADGTGAIRTFDATHLDKATPDLMPVMTEAETE
+DPHHGVALELYDGTLFTTQGTEDSRDTLQVIDSTTGEVTAETDDCPGSHGEAAAQPTEAG
+DVVVTGCENGPVVYRDGEFHKVEVETEYQRSGNLFGLHDSPIVLGDHKVEEEPTEAVERP
+TAIALIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVIDEETGEVTAEYAV
+IEPWKEKDEWQEPGPILKVAGNTAYVTDAEAQKLVVVDLETGETVLEKDLDFAPVEMAVV
+TGQPESVKPEEAADAESGHDEHTDHDH
+>GCF_020097155.1_00598
+MTPRILLSHEDGLTLLDAESGEVVKEQDVAGFTRLSNAGNGKDVLVTTGNGWEVFSTGIQ
+AKAHGDHFHNYESAPGMTGVTFPGEHPGHVVTHNGRTTLFADGTGAIRTFDSAHLDKATP
+DLMPVMTEAETEDPHHGVALELSDGTLFTTQGTEDSRNTLQVIDPTAGEVKAETDDCPGS
+HGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQRSGNLFGLHDSPIVLGDYK
+VEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVID
+EETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAHVTDAEAQKLVAVDLETGETVLEK
+DLEFAPVEMAVVTGQRESVKPEEAADAESGHDEHTDHDH
+>GCF_023573625.1_02034
+MTGVTFPGEHPGHVVTHNGKTTLFADGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHH
+GVALELSDGALFTTQGTEDSRNTLQVIDPKTGEVTAETDDCPGSHGEAAAQPTEAGDVVV
+MGCENGPVVYRDGEFHKVDVETEYQRSGKLFGLHDSPIVLGDHKVEEEPKEAVERPTEIA
+LIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVIDEETGEVTAEYPVIEPW
+KEKDEWQEPGPILKVAGNTAYVTDAEAHKLVAVDLETGETVLEKDLEFAPVEMAVVTGQP
+ESVKPEEGAHGDEDHDDDGHEGHDHGAEPSEGHEGHDH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001643.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001643.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6940e150ffe964173e0d1c1a5dcbe389671454c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001643.fa
@@ -0,0 +1,54 @@
+>GCF_002008305.4_02099
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD
+>GCF_003691675.1_01806
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD
+>GCF_005280335.1_00680
+MGGRLIPELLAAGFDVRAGARNPSDLADRPWSEGVEAVELDLTEADLVEAAMQDVHTVLY
+LVHSMGGGGDFVTQEQRIADIVGTAADTAGVAQLVYLSGLHPDTIPVAELSDHMRSRALV
+AERLEQAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLKNRVEPLAIRDVLY
+YLLQACALPEPVQLRAQIGNGHPQSFASVLVDYAKAAGLSRRIVIPTPFPLQTLAGFWIG
+TVTPIPVAVALPLAASLAEEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDV
+TFDADVHAAADPADPLPSDPAWSGTTVYTDERERESDLPPQDVWPVIESVGGANGWYSTP
+MLWKVRGLADKLVGGPGLIRGRRDQDRLRRGDAVDWWRVEDVEHGRRLTLRAEMKAGGRA
+WLQMSTEPRDGGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAQRRTT
+GGERRRPRSLARALVDRLPLRRNPLDRGASA
+>GCF_020097155.1_00594
+MSTPSTSRGSGLTSAAASGDTPAGTGATTASLSPLGLALPDGHDRRVLVTGATGYVGGRL
+IPELLAAGFRVRAGARTPRDLEDRPWSDRVEVVELDLEKPDLVKAAMQDVHTALYLVHSM
+GAGGDFVEQEQKIADIVATAADEAGITQLVYLSGLHPAGKPVEELSDHMRSRALVAERLE
+AAATPALTFEAGVVIGSGSASFEMIRHLSERLPIMPGPSLLKNRVEPIAVRDVLHYLVQA
+CALEEPVQLHAQIGNGRPQSFASVLVDYAEVAGLSKRIVIPTPLPLSRLAGLWVGVVTPI
+PVKVALPLAASLAEDAVVEDHAIRDVIPAPEGGLTSYKEAVRRALAAEKNGPLDVTFEAD
+VYDSSDPAAPLPSDPEWAGHTVYTDDRERESDLAPEDVWPVIESIGGRNGWYSTPLLWKV
+RGYMDKVVGGPGLMRGRRDQDHLRRGDAVDWWRVEEVDPGHRLTLRAEMKAGGRAWLQLT
+TEPREQGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAERRRTGGARR
+RTRGLVRALADRLPLRRSPLDRRAG
+>GCF_023573625.1_02039
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQPFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001646.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001646.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9aa571cdcd31b8ca31f99f50cea7fa02b173a6fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001646.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02104
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLALAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA
+>GCF_003691675.1_01811
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLALAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA
+>GCF_005280335.1_00675
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPTWLVVLGTVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLADPAVRRRVLRWSCLVAVPFVAVLAGWSIARGQWDALAVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPALYGLVLAGAAFTPALWALLGGFFLWGM
+ASQMFGAVQDVLPDREGGLASVATVLGARPTVWLAAALYAGAGLLMLGTEWPGPLAALLA
+VPYVLNVLRFRAVTDATSGAAHRGWRLFLPLNYVTGFLVTLLLIGWALARGGV
+>GCF_020097155.1_00593
+MIRTLFWASRPVSWVNTAYPFLAAVLLTGGLPWWLVALGGFFFLVPYNLAMYGINDVFDF
+ESDLRNPRKGGVEGSVLADPAVRRRVLAWSALTPAPFAAVLAGRSVLRGEWAAVAVLAVS
+LFAVVAYSWAGLRFKERPFLDAVTSSTHFVSPAVYGLVLAGAEFTPALWSLLGGFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARPTVLAAAALYAAAGLLMLPTDWPGPLAALLA
+APYLLSTLRFRHVTDATSGEAHRGWRTFLWLNYLTGFLVTLLLIWWALVR
+>GCF_023573625.1_02044
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLVLAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001649.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001649.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed33b9129bd36b1e79cdd25da8dfe0473d761787
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001649.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_02107
+MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL
+GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE
+ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTARAAEAAAVVFDAAAVTAAGE
+LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA
+DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA
+DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS
+>GCF_003691675.1_01814
+MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL
+GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE
+ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTARAAEAAAVVFDAAAVTAAGE
+LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA
+DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA
+DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS
+>GCF_005280335.1_00672
+MSAGREGVVAELEAALSRAAGLAPESAAFAELLAGLRTHAGAGKLIRPRLVELGWRAAAD
+GPVPAAERPAVDRLGAAFELLHTGLLVHDDVIDRDVVRRGERTVHEATRRRLAARGVPEA
+EAAHAGTAVALIGGDVLLVEALRLAMTCTPDPGRAAPVAAVVLDAATASAAGELEDVLLG
+LARHTGEEPEPERILAMQRLKTAHYTVSAPLRVGGAAGGGGSRRRRGAGEAAAPTWAWPT
+RWWTTCSGCSAPRSRPASPPTATCARARPPCSPRTAAATPPSAPCSTPAPATPEELEAAR
+RALEAAGAREHALQVAEELTRRAAEHLAVLPLGEAACAEFADACHAVLTRSS
+>GCF_020097155.1_00588
+MNPLAAGIGGAAPWSASAATPGLDDAGRARAAVRAELDRVFAETPLCADAPDSFHLLWAR
+LREAVSGGKLVRPRLVDLGWRTVRRAPASSGVPRGGTGEEEAADLRAVARVGAAFELLHA
+ALIVHDDVIDRDDLRRGRPTVAEQYRRDAVRDGVPAGEAEHVGRSAGIIAGDLLLTAAFR
+LAAASGARVRAAEAAESVFRAASAAAAGELEDVLLALHRHTGHHPEAGRILTMERLKTAG
+YSFEEPLRAGALLAGADPAHAEALAEAGALLGVAYQVVDDVLGTAGDPAVTGKPHDADLR
+EGKATLLTAHGRRDPRARAALDRVARAERHGEDLGELAAAVAEARAALVDAGSVEHALGV
+AEELVDQARALLDALPMAPAERAEFAATCGQILQREA
+>GCF_023573625.1_02047
+MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL
+GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE
+ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTVRAAEAAAVVFDAAAVTAAGE
+LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA
+DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA
+DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001650.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001650.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf109b5c6630c43078a50ac702d73e46e943d16c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001650.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02109
+MQTPATPSPHDRPSPVARPWMAASDVPVAGPDDVERVVLLSPAGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEAGRFLLTRRALGKAAFPGVWTNGFCGHPGPGEPPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDPR
+>GCF_003691675.1_01816
+MQTPATPSPPDRPSPVARPWLAASDVPVAGPDDVERVVLLSPEGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEADRFLLTRRALGKAAFPGVWTNGFCGHPGPGESPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDPR
+>GCF_005280335.1_00669
+MQTPATPSPHDRPSPVVRPWMAAPDLPIAGPDGVERVVLLSPAGEAVGTEAKAAVHRRTE
+DGGTPLHLAFSCHVYDDAGRFLLTRRALGKKAFPGVWTNGFCGHPGPGESPAQAVLRRAP
+QELGAEVSDVVEVLPDFRYRAADASGMEEHEICPVFQARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFEAR
+>GCF_020097155.1_00586
+MQQGPSDPRTVEEVEERVVLLGADGAPIGTEAKASVHRNAADGGTPLHLAFSCHVYGPDG
+RFLLTRRALGKKAFGGVWTNGFCGHPAPGEAPAEAVLRRAPQELGVGVREVTPLLPGFRY
+RAADAGGVEEHEVCPVFRAECDGDPVPERDEVAEWCWVEVADLTAALASVPRVFSPWLVM
+QWEQGAFGPR
+>GCF_023573625.1_02049
+MQTPATPSPHDRPSPVVRPWMAASDVPVTGPDDVEHVVLLSPAGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEADRFLLTRRALGKAAFPGVWTNGFCGHPSPGESPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001652.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001652.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46454138e4e80cf1693011ed328cc32fb0c84192
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001652.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02113
+MTGAPILPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELIDWIQEARTSHAGVLINPAAYSHTSIAIRDALAAVDRPIAEVHISNIHRREAFRHHSH
+VSAVADVVIAGAGVQGYTLAVDWLAAAVRR
+>GCF_003691675.1_01820
+MTGAPILPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELVDWIQEARTSHGGVLINPAAYSHTSVAIRDALAAVDRPIAEVHISNVHRREAFRHHSH
+VSAVADVVIAGAGVQGYALAVDWLAAAVRR
+>GCF_005280335.1_00667
+MRETGASPRTFVRETGASVVVRSYTGPMTTAPSALPLLVLNGPNLNLLGTREPEIYGSDT
+LDDVRSRTEARAAGHGLAVDFRQSNHEGELVDWIQEARTSHAGILINPAAYSHTSVAIRD
+ALSAVGRPIVEVHISNIHRREPFRHHSHVSAVADAVIAGAGVLGYELGIDWLAAAVRR
+>GCF_020097155.1_00583
+MTDSMPAATAARLPLLVLNGPNLNMLGTREPEKYGFETLEDVRALTAARAAEHGLEVDFR
+QSNHEGELVDWIQEARTGFSGILINPAAYSHTSVAIRDALAAVPVPIVEVHITNIHAREE
+FRHHSVVSAVATTVIAGAGTQGYALGVEVLAARLAR
+>GCF_023573625.1_02051
+MTATPALPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELIDWIQEARTSHAGVLINPAAYSHTSIAIRDALAAVDRPIAEVHISNVHRREAFRHHSH
+VSAVADVVIAGAGVQGYALAVDWLATTVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001653.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001653.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b17be3f61852a21906e51f7f16d7e09f0044831
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001653.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02114
+MGTQDPRARLLEKLAKVNVCMLTTAEPDGTLVTRPMGLQQAEDGGTLWFLTRATSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVRV
+DVQTAQFWESPGAVATAVELVKAKVTGGEAHPGDSETVRF
+>GCF_003691675.1_01822
+MGTQDPRTHLLEKLAKVHVCMLTTAEADGTLVTRPMGLQQAEDGGTLWFMTRSTSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNSATEAFFGEGSSPEDPQIVLVRV
+DVNTAQFWESPGAVATAVEMVKAKVTGGTAEPGDSETVRF
+>GCF_005280335.1_00666
+MGHKDPRTHLLEKLEKSNVCMLTTSETDGTLTTRPMGLQKAEETGTLWFMTRAASDVASD
+ASQRPVNVSVQDKDFWASVAGHGQVVRDDARKKEFWNPATEAFFGEGAKPEDPQIVLVRV
+DVESAQYWESPGAVGTVVELIKAKVTGGEAHPGESTTVQF
+>GCF_020097155.1_00582
+MTEQDPRTALLEKIEKAGVVMLTTAEEDGTLASRPMAVQEVEQEPGVLWFITRATGDAAQ
+DSAGRPVNVAVQEKGFWASVAGHGEIVRDEARKTEYWNSATEAFFGEGARPEDPQIVLVR
+VQADSAEYWDGGGAASVVEIVKAKVTGGEARPGDHDTVEF
+>GCF_023573625.1_02052
+MGTQDPRARLLEKLAKVNVCMLTTAEQDGTLVTRPMGLQQAEDGGTLWFLTRATSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVRV
+DVDTAQFWESPGAVATAVELVKAKVTGGTAEPGDSETVRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001654.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001654.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ed0f6d2d4b46052525ad00ce418043568de8fed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001654.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_02115
+MSDYQPRRPGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TIKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD
+>GCF_003691675.1_01823
+MSDYQPRRPGSKSTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD
+>GCF_005280335.1_00665
+MSDYQPRRPGSNPAPARRTDRAGKPALGRPKRGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPQTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLAERQAKA
+KEIGLPAFRAKQLSVHYFERYTTDPEQMTDLPKDKREVIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVRANQVIAEGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPAPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVERLNAAGIPTTLRDTRGKEIDGACGQLAAGDEDA
+>GCF_020097155.1_00581
+MEGMSDYTPRRPGSKPTPARQKDRAGKPALGRPRRGMIDEPEARQLAEDRERMHRAGVGH
+QLSAPPRRAAEVDADRPQVMPKTEGWQQPMGPDGRPQLQFKQPRVSQPPQHLADMTLAER
+QAKAKEIGLPAFRAKQLSVHYFEHFTTDPEQMTDLPKGKREEIAEAFFPPLLTEVRRLTT
+DRGDTVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTA
+EIVEQIVRANQVIAEGGLGGTRRDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDP
+APEGLGMSARHVTLSTVGLVPAIKKLAQEGVPLTFALSLHAPDDELRDELIPVNARWKAD
+EAIDAAYEYFLATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTP
+GSIWTASEKDVTREFVDRLNAAGIPATLRDTRGKEIDGACGQLAADDEDVAARA
+>GCF_023573625.1_02053
+MSDYQPRRTGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSPAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001656.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001656.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86361721b936f9fd310365f41fd92e2a20489309
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001656.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_02118
+MSVRSLLPDLGTSATGTPEAAVPPFARAVLWAHGDDAWRGEGGWTVLLDGPDRLRRLSAL
+WQAAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHVDADALA
+AAVAADRGARLLADGEVPLPADVADLAWDDAGYAAGVRELLTRMADSGGELAKVVISRTM
+TVPADDADLWRAIGELRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMPRGA
+DEEEDAALRERLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHLATS
+VRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQDGD
+GEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED
+>GCF_003691675.1_01826
+MGAMSVRSLLPDLGAPATGAPEAAVPPFARAVLWAHGDDAWRGEGGWTVLLDGTDRLRRL
+SALWQTAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHVDAD
+ALAAAVAADRGARLLADGAVPLPAGVADRAWDDAGYAAGVRELLTRMADSGGELAKVVIS
+RTMTVPADDADLWRAIGELRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMP
+RGADEEEDAALRERLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHL
+ATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQ
+DGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED
+>GCF_005280335.1_00662
+MSVPTLLPELGTAAAEAAVPPFARAVLWAHGDAAWRGDDGWTVLVDGPDRLRRLSALWQA
+AVAGREDPAAPVRGWVSAPFSDDSVEPAVLRVPARLRRSTASGIRETPQHVDAAALADAV
+AADGGGRLLPDGEVPLPADTSESAWDDAGYAAGVRELLARMAASDGALAKVVISRTLTVP
+ADDADLWRAIRALRREYPQTWVFAVGGLLGATPEILATRHAGLVGSRVLAGSLPRGEDEA
+EDAALRARLATDPRLGEEHRWAARSVLDALAPVVDLADPDPAPTVLTLPNVHHLATSVRG
+RLRDGRGTVLDVVAALHPTAAVGGTPTPEAVRVISEVEPVDRGRYAGPVGWLDQDGDGEI
+ALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKLLPMRRALGIDLD
+>GCF_020097155.1_00579
+MPPVPSVAVAALAARALSPSGSAAGRVPAFARAVVWAREDTVRVGVGGHTVLLDGPDRLR
+RLSALWRAAVAARPEPASPALAWVSSAFDDASPVPSVLRVPARVLQAGPDGVVEVPVAMP
+REALAAAVAACPGARLTEAGEVPLPADDPALAWDDAGYAAGVEEVVARMEASAGALSKVV
+VSRTETVPAGEDRLWAAVDALRAEYPQTWTFAVGGLVGATPEMLATRRDGVVASRVLAGS
+LPRGVDEGDDARLRARLAADPRLLREHHWAARSVLDALAPVVELEDAHPAPFVLTLPNVH
+HLATDVRGRLRPGEGAVLDVVAALHPTAAVGGTPTAEALEVIRAVEPVDRGRYAGPVGWL
+DQDGDGEIALALRCGQQVPGGVRLQAGGGIVPGAAAEEEVVEVGVKLLPMRRALGVA
+>GCF_023573625.1_02056
+MGAMSVRSLLPDLGTPATGTPEAAVPPFARTVLWAHGDDAWRGEGGWTVLLDGTGRLRRL
+SALWQAAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHMDAD
+ALAAAVAADRGARLLADGAVPLPADVADRAWDDAGYAAGVRELLTRMADSDGELAKVVIS
+RTMTVPADDADLWRAIGALRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMP
+RGADEEEDAALRDRLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHL
+ATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQ
+DGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001657.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001657.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08ee38593a2b31c1e36a355e92fe52f9b6aa4c66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001657.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02119
+MAPIPPDPHADHAPAVDDMPLDTTAAPDIPAAVDPVPHGMAAHVLEREVGPLRARFPGVA
+DEATVRQLLFDSYAELAETSRHPEMLPTISVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQKWSVPSIRGMSLEQVRGVRDALDLEVRGLIADLG
+EAATPLPEEGTRVGRPLDLYPPGV
+>GCF_003691675.1_01827
+MTPIPPDPHADHAPAVDDMPLDTTAAPDIPAAVDPVPHGMAAHVLEREVGPLMARFPGVA
+DEATVRQLLFDSYAELAETSRHPEMLPTISVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQKWSVPSIRGMSLEQVRGVRDALDLEVRGLIADLG
+EAATPLPEEGTRVGRPLDPYPPGV
+>GCF_005280335.1_00661
+MAAIPPDPHADRTPAVDDLPLDAASPDGRAAAPVGLEPEGMAANVLEREIEHLMERFPCV
+GDEETVRAVVMDSYAQLAATSRHPDMLPNTTVQHASARLRAMAINQGSIESRHPRVLFVC
+HGNAGRSQMAAALLENRTGGAVKSRSAGTSPAGEVISTAFDAMSEIGIPLHHSYTKGVDE
+DVLKAAEVVVLFDGAEPLDIPEGTEVQEWSVPSIRGMSLEQVRGVRDALDLQVRGLIADL
+GEEGSDAPPPGEGAPVA
+>GCF_020097155.1_00578
+MAPHPSDPAADLPAADVPLDPTGALPVVAPAPEGMASHVLDREAEHLHARYPEVGDVAMA
+RALLEDSYARLARTTRHPEMLPVTAANYAAARLRARAIAQGSVESRHPRVLFVCHGNAGR
+SQMAAALLENRSGGTVASRSAGTSPAGSVLPMALDVMNEIGLPLHHAFPKGVDRDILQAA
+QLVVLFDGAEEDLLDVPAGVEVQHWSVPSIRGLALEQVRGVRDALDLQVRGLIAELTALE
+GEEQGGAADPAA
+>GCF_023573625.1_02057
+MTPIPPDPHADHAPAVDDMPLDTTAAPDTPAAVDPVPHGMAAHVLEREVGPLMARFPGVA
+DEATVRQLLFDSYAELAATSRHPEMLPTTAVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQNWSVPSIRGMSLEQVRGVRDALDLQVRGLIADLG
+EAAADAPLPDADTRAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001658.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001658.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2f8fcf56ed73b4580f5fbe8ecd6cd08dd24dc23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001658.fa
@@ -0,0 +1,18 @@
+>GCF_002008305.4_02120
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR
+>GCF_003691675.1_01828
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR
+>GCF_005280335.1_00660
+MSTLPTTTDAHDGADPCAGAHPPHAAHRDKDAHLTRLRRIEGQVRGIHRMVDEDVYCIDI
+LTQVAAVTKALQAMSLNLTSEHLRHCVAEAAVEAEASGRTELIDEKVAEATAAIGRLLR
+>GCF_020097155.1_00577
+MEHDRHAGPGYSPQREAYLKRLKRIEGQVRGIHRMVEEDVYCIDVLTQVAAATKALHAVS
+LGLVEDHLRHCVAEAAVQAEAEGRTELIDEKVAEATAALGRLLR
+>GCF_023573625.1_02058
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001660.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f42b33dc805f30dc619bccaa550946796800cbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001660.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02123
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRRNFRRDEDEGYLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAEADEVDLTAFIGQFSDEDIETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>GCF_003691675.1_01831
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRKNFRRDEDEGHLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDVETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>GCF_005280335.1_00656
+MGAWGRNVFQNDTALDLVDEVLDGSFDLDEFRKDFRREEDEGYLDASQGAALLALGALVR
+IARNEDHADLDVLLEHAEAEEVDLTDFIDQFSDEDIQTLRELIGVVIREPSCSELYELWE
+ESGELEQWLEYSRQCLP
+>GCF_020097155.1_00574
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRRNFRRDEDEGYLTASQGAALLALGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDIETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>GCF_023573625.1_02061
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRKNFRRDEDEGHLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDVETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001661.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001661.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cef969f630e1f88747661790ccb1ca90643f9a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001661.fa
@@ -0,0 +1,14 @@
+>GCF_002008305.4_02125
+MSAGQGATTAGPVIESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPARY
+RLLIGWRTLEDHTVAFRESDSFLAWRALVTPHLAQLPAATHWSAV
+>GCF_003691675.1_01833
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDKGATSFALSRQVEDPARY
+RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV
+>GCF_005280335.1_00655
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAAELFRGARATSFALTRQVEDPARY
+RLLIGWRTLEDHTVGFRESEAFGQWRALVTPHLAQPPAATHWESVAAAF
+>GCF_020097155.1_00572
+MEDPARYRLLIGWRTLEDHTVGFRESDAFLAWRALVTPHLAQPPAATHWSAV
+>GCF_023573625.1_02063
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPAHY
+RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001662.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001662.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60f393b94582f694bd8498b84cb7eab32bedb61a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001662.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02126
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLAAWFTGHSTSPRVHA
+>GCF_003691675.1_01834
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRVHA
+>GCF_005280335.1_00654
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHG
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRVHA
+>GCF_020097155.1_00570
+MTDTPQSSSGQSRDEILARLEEIYANDPAVREHDVTLGEVAEGRVVLHRDVTAGMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPAKLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRVHA
+>GCF_023573625.1_02064
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001664.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001664.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f574dafaa8a25da61fa637f2e34d2fc6d29deac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001664.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02128
+MTTMKAAVVTQFGTEADVTEVERPTPGQHEALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD
+>GCF_003691675.1_01836
+MTTMKAAVVTQFGTEADVTEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD
+>GCF_005280335.1_00652
+MTTMKAAVVTQFGKEADVQEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSAD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFEEMRHGKIEGRVVIDYAMQD
+>GCF_020097155.1_00568
+MTTMKAAVVSQFGKEADVKEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWGACGHCQYCRTGWETLCEEQINGGYSMN
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFEEMRHGKIEGRVVIDYAMQD
+>GCF_023573625.1_02066
+MTTMKAAVVTQFGTEADVTEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001665.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001665.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7382d400eedd1a077d7a81dd2c256dd22292d9c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001665.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_02129
+MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+AALDAAWKAAPAWGATSPAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP
+LAIDHFRYFAGAIRAQEGRLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
+>GCF_003691675.1_01837
+MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMAADDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
+>GCF_005280335.1_00651
+MTVYAFPGTEGAKVEFKPRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKIISYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
+>GCF_020097155.1_00567
+MTVYAFPGTEGAKVEFKPRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAIRETLNADLP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE
+ICTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
+>GCF_023573625.1_02067
+MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADLP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASVMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMAADDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001668.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001668.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2d085bfa4482db65e803d512c206ac5bb5158e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001668.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02132
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAVRRAFAAEA
+RGDVEPGRAPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA
+>GCF_003691675.1_01840
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAAEA
+RGDVEPGRVPASFYVGVDEAGHLVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA
+>GCF_005280335.1_00648
+MLPDPSPTVTVDGLLLRPLRTADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAADA
+RGDVEPGRVPASFYVGVDEAGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAVR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVETGLDGAPFPEPKLRFD
+VPTTAA
+>GCF_020097155.1_00564
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAAEA
+RGDVEPGRVPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAVR
+LLRGALTLLAAHGVSTALLTCDETNTASVATIRACGGVLRDRVEAGLDGAPFPVPKLRFD
+VPTTAA
+>GCF_023573625.1_02070
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAVRRAFAAEA
+RGDVEPGRAPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001670.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001670.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9cae55b02f0ca3242ec6372ce25d60996b2b2d8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001670.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02134
+MLSAPTLTRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+VRGRELRGRLAEVWALAAVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELVRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAEAAPATDPAGPEEAEAPEAVADEAAPADKPRQETEKEKKERKKAEKKAEKKA
+RKKAEKKARKKKSDKKKD
+>GCF_003691675.1_01842
+MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+VRGRELRGRLAEVWALAAGDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAESAPAADPAGPEEAEAPEAVVDSEAAADEPRRETKKEKKERRKAEKKARKKA
+EKKAGKKKSDKKKD
+>GCF_005280335.1_00638
+MLSPRTLARLSSVAAFLNTAPGPRGGQEAPERFTAATQLPALVPELQEGEVRLRLAAAAA
+VRARELRERLTRVWALAATDESAAVERVNELLAEAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMATLALAETAMDGELARLRVCEGEDCENALVDGSRNRSKRFCDEANCANRTHVRSY
+RARLAEAAEAAPATDPAGPEEAEGTEAVVDEAAPADEPLQETEKEKKERRKAQKKARKKA
+EKKAGKKKSDKKKSDKKKD
+>GCF_020097155.1_00561
+MLSPHTLARLASISAFLNTAPGVRGGQEAEERLTAGTQLPALVPELQEGESRLRVAAAAR
+TRAHELRARLTELWAAADAEDVPAAVAAVNELLAETGPLRLEVSDGSADLAPAQVPADAV
+ERLTAMAALALTEAALEGELTRLRVCAGEDCENTLVDASRNRSKRFCDAANCANRTHVRS
+YRARLAEAEDTQADVEAADAAPLPEVAPEADPQDATDLEAIEAAEGVESAVQEPVKKDST
+KDKKSKSEKKARRAAKKKAEKESEAAAEGKKGKREKSKKSEKHKKKAAKD
+>GCF_023573625.1_02072
+MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+GRGRELRGRLAEVWALAAVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAESAPAADPAGPEEAEAPEAVVDSEAAADEPRRETKKEKKERRKAEKKARKKA
+EKKAGKKKSDKKKD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001671.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001671.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59952db79bbaa5b3bda498091abf9553bdddd70b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001671.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02136
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRID
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAARER
+REQGGTGGDAPRA
+>GCF_003691675.1_01844
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRVD
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAAAER
+REQGGTGGDAPRA
+>GCF_005280335.1_00636
+MSAPSPRPSADRAGTGRPARGGLRTTVKGPLVFSAVLGVIGGVIAGITASGGTQNPLRID
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSAGSGINRSSEETFQKAAAERRAQVARER
+REQDGTGGDAPRA
+>GCF_020097155.1_00560
+MSAQSPRPSDDRTRPGAGRPARGGLRTTVKGPLVFSAVLGLVGGVVAALTASGGTANPLR
+IDIGLIAFGVFFMTSLVVVAMLQLASRENPDHLSRGSGVNRSSEETFQRRAAERRAKAAA
+ERRAAQGDAGR
+>GCF_023573625.1_02074
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRVD
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAAAER
+REQGGTGGDAPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001673.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001673.fa
new file mode 100644
index 0000000000000000000000000000000000000000..804723897540163e51348f98a2e1c67a1bfe93f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001673.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_02138
+MAGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGVG
+IGTTILHTLTGLMIFLAYATTPAVARLIGAGNLAAAMDRGRDGIWLGLLLGAVLAVLGWL
+AAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVGF
+GANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTAWAPRASGMRA
+TAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQA
+LIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATVG
+LWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWTA
+AWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVV
+>GCF_003691675.1_01846
+MAGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGVG
+IGTTILHTLTGLMIFLAYATTPAVARLIGAGNPAAAMDRGRDGIWLGLLLGAVLAVLGWL
+AAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVGF
+GANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTVWAPRASGMRA
+TAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQA
+LIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATVG
+LWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWTA
+AWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVG
+>GCF_005280335.1_00634
+MAEPQGSTAAPAPQDGRALTRRILALAVPAFGALLAEPLFLLADTAIVGRLGTPELAGVG
+IGTTVLHTATGLMIFLAYATTPAVARLIGAGDHAAAMDRGRDGVWLGLLLGAALAVLGWI
+AAPWLTGALGATGEVQEHAVAYLRWSMPGIPALLAVLAATGVLRGLQDTVTPLVVAGAGF
+AVNIGLNFALVYGAGLGVAGSAIGTSAVQWGMLLTYLAVLAPRFRRAGTSLAPRASGMRA
+TAQVGSWLLLRTASLRAAILITVMAAAGAGDMTLAAHQLVFTLFSTLAFALDALAIAAQA
+LIGAELGASRPATARRLTDVMVRWGLGFGVVTGGLLALAAPWLPALFTTDPQVQAAATVG
+LWVLAAGQPIAGYVFVLDGVLIGAGDARYLALAGLVNLAVYAPVLWVLAQVAAGGLGWTV
+DWSDPAAHVPDAGEQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRVGAH
+>GCF_020097155.1_00558
+MPSRPPHDDAAPAPEDRRALARQVLGLAVPAFGALIAEPLFLLADTAIVGHLGTAQLAGV
+GVGTTVLHTVTGLLVFLAYATTPAVARMVGAGNPAGALDRGRDGMWLGLMLGFVLGAAGW
+LAAPWLTGALGAAGEVHSHATEYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGGG
+FAVNIGLNWALVYGAGLGVAGSAIGTAAVQWAMLAVYLAVLAPRFRAAGTRPGPRADGLR
+ATAQVGSWLMLRTASLRAAILITVAAATGLGDVTLAAHQLVFTLYSTLAFALDALAIAAQ
+ALIGAELGASRPRTARRLTDLMVRWGLGFGVVTGAGLAAAAWALPPLFTPDPGVHAAATA
+GLLVLALSQPVAGYVFVLDGVLIGAGDARYLALAGVVNLAVYAPVLWGLARLAAGGADAG
+AQVALLWLGFAGVYLGMRAATLGLRARRDAWMRLG
+>GCF_023573625.1_02076
+MAGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGVG
+IGTTILHTLTGLMIFLAYATTPAVARLIGAGNPAAAMDRGRDGIWLGLLLGAVLAVLGWL
+AAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVGF
+GANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTVWAPRASGMRA
+TAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQA
+LIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATVG
+LWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWTA
+AWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001674.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001674.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4bceb3431d863dafdac7d0b0a80a2351a3216ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001674.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_02139
+MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW
+TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV
+VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE
+EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT
+GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP
+GPTAPTTALAPLLALLG
+>GCF_003691675.1_01847
+MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW
+TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV
+VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE
+EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT
+GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP
+GPTAPTTALAPLLALLG
+>GCF_005280335.1_00633
+MPAGWPGRTPGPRTAPDWEPGRFHWGDAVVVLAYAGLMLFGLGLPLAMLLGLVPGDLAAF
+DLVRDGFTVNMVSYAILTALVLIVAWRPLVTSLRVFRTGTWWKILLLPAVWFTCILVNVL
+VLSLIGEAQTSANQAALEEMSAQAPPVLMILMTVVGAPLVEEYLFRHLLVGKLSRWVNVW
+VCAVVSMLAFTLLHFLGTGGQFDLVETVPYLTLAIAITVTYILMGRSFGYAVLLHMVNNG
+IAIAMLYLVAPLLPDVLPEPTAPAAALSPLLALLG
+>GCF_020097155.1_00557
+MSVPPPGPHDAGALPPPGSTAPTSAAGEAPEGWPPAGWPGRASAGGAPQGWPPSGWPGRT
+ASARTAPSWEPGRLHWGDAAVVVLYVLMMVVGLGYLLAVLLGLAPRDPAAMDVMDGFRVN
+LVSYAVLVVAVLAVSWRPLVASLRVFATHTWLKILLLPALWLVTVLVNALLLSLIGQAQT
+SANQAALEEMTTQAPALGMVLMTVVGAPIVEEYLFRHLLVGKLSRWINVWVCAAISVAAF
+TLLHFLGTGGDFQWVETVPYLTLAVTITVTYVLIGRSFGYAVLLHMVNNGIAIAMLYLVA
+PLLPSAPAPVGPGALLSPLLALLG
+>GCF_023573625.1_02077
+MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW
+TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV
+VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE
+EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT
+GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP
+GPTAPTTALAPLLALLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001675.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001675.fa
new file mode 100644
index 0000000000000000000000000000000000000000..901d72d9f8e63468344b212e9a639d6c4dad4ebf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001675.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02140
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFVTA
+>GCF_003691675.1_01848
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFVTA
+>GCF_005280335.1_00632
+MALFSQPVFINLPTTDTERIREFWTSLGAQAIEDFSDENSVCIELTESTFAMYLSPGYYT
+DFIGDREIADCMTTNSALMALTVGDAAAVDALADRAIEAGAAEVPLPVDLREEMVDSGMH
+SREIVDPDGHQWEFVTA
+>GCF_020097155.1_00556
+MRTRWSTVLVMALFSQPVYINLPSTDTERIREFWTSMGADIDEDFSDENSVCVQLTESTF
+AMYLSPGFYTDFIGDREIADCLTTNSVLLQLTAPDRGAVDALVRAAVEAGGSEVPLPDEL
+QEDMTATGVHSRQVVDPDGHQWEFMAA
+>GCF_023573625.1_02078
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFITA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001676.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001676.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59ea1cceed8193362915abac0fd622929fcf6d90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001676.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_02141
+MPAPAATTTTTPPATPRERQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVD
+PRVGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQI
+LLGVFGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALAIVVLLP
+RLTTAVPATLVAVVVVTALVMAAGLAVPRVGDRGALPDALPVLGLPDVPLTWETLRLILP
+FSVGIAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTM
+MNVKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPA
+TLRAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDDGD
+AVTYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYARHG
+IHAEVTGLNEASAAMHARLTGRLGA
+>GCF_003691675.1_01849
+MPALPAAPPPALTPLQRQSVLRTLRSPRLLGTEVLAAVVVALALIPEAIAFSIIAGVDPR
+VGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQILL
+GVFGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALAIVVLLPRL
+TTAVPATLVAVVVVTALVMAAGLAVPRVGDRGALPDALPVLGLPDVPLTWETLRLILPFS
+VGIAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTMMN
+VKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPATL
+RAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDDGDAV
+TYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYARHGIH
+AEVTGLNEASAAMHARLTGRLGA
+>GCF_005280335.1_00716
+MTPASTASARVAAPPNSREPSPEQLQSVRLTLRSPGRLKTEVLAGLVVALALIPEAIAFA
+LIAGVDPQVGLFAAATMAMTIAFVGGRPAMVSAATAATALVVAPLVASHGLDHLIAAVIL
+AGGLQVVLGLLGVAKLMRFVPRSVMVGFVNALAILIFTSQLPDLMGVPWLVYPLTALGLA
+IILLLPRVTTAVPAPLVAIVVVTVIVLLAGADVPTVGDKGRLPDSLPALLVPDVPFTLET
+LQLLFPYALGMAVVGLLESLMTAKLVDDITDTRSSKTRESWGQGVANVVSGLFGGMGGCA
+MVGQTMINVKASGARTRISTFMAGVFVLILSVTLGDVVALVPMAALVAVMIFVSLATFDW
+HSIRPSTLAFMPKSETAVMLVTVAATVLTHNLAIGVGLGVLAAMVMFAQRVSHLATVTRT
+LEGQGRDAVARYRVQGELFFASSNDLYTQFDYAGDPARVVIDFSQAHLWDASTIAALDAV
+EEKYRRHGATVEITGLNVASRAMRARMSGRLGGGH
+>GCF_020097155.1_00554
+MPASPAAPPPALTPLQRQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVDPR
+VGLFASFTMAVTTAVVGGRPAMISAATGAVALVVAPLSHAHGLDHLIAAIILGGLIQVAL
+GLLGVARLIRFIPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALGIVLLLPRL
+TTAVPSTLVAIVVVTALVMAAGWSVPRVGDRGELPDALPGLFVPDVPLTWETLRLILPFS
+VGMAVVGLLESLLTAKLVDDVTDTRSDKTRESWGQGVANIVSGLFGGMGGCAVVGQTMMN
+VKANGARTRISTFLAGVLLLVLVVALGDLVGQIPMAALVGVMVFVAGAAFDWHSVRPATL
+RAMPRSETAVMLLTVLATVVTHNLAIGVGVGVLTAMVLFAQRVSRLARVERVVTDDNGGT
+AVYRVHGELFFASSNDLYSQFEYALDPPRVVIDLSAAHVWDASTVAALDAVVTKYAQHGI
+AAEVTGLNEASAAMHARLTGRTGA
+>GCF_023573625.1_02079
+MPALPAAPPPALTPPATPRERQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAG
+VDPRVGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVI
+QILLGVLGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALVIVVL
+LPRLTTAVPATLVAVVVVTSLVMAAGLTVPRVGDRGALPDALPALGLPDVPLTWETLWLI
+LPFSIGMAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQ
+TMMNVKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVR
+PATLRAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDD
+GDAVTYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYAR
+HGIHAEVTGLNEASAAMHARLTGRLGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001677.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001677.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b3cd921b5db1f397abb5b3f35bb5f4719c33a74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001677.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_02143
+MNLRTLLREALTAARTAPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPAARV
+LTVTDSGGTGFLTGATVATLAGLDSAEAALARDMPVDTVNAAIGAGGTRVAVTHVVGTVD
+RGVELTRGRLPGPGEVVVPEAKLAELGLAQPSGALESGDGRQWAVVGAFEALTPFEDLAD
+YAIAVPAAPASLVVQQVRVLAPDTAGTRAMQDSALAVIDPDPRSSQVQTARALAAGNATI
+TGELAGLGRSLLLLILGAGAFFVAIVVLADVLIRRRDLGRRRTLGIGRADLVLLVAVRTA
+APAVLGAVVGAGTGYAVVVGQGGALGLDFVAGVAVLAALTAVVASLLPAAFAAFRDPVRV
+MRTA
+>GCF_003691675.1_01850
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTGIGRGGARVAVTNVVGTLD
+RGIVLTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGGQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA
+>GCF_005280335.1_00629
+MNLRTLLREALTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPAARV
+LTVTDSGGTGFLTGATVTTLAGLDAAEAALARDMPVDTVNAAIGAGGTRVAVTHVVGTLD
+RGVELTRGRLPGPGEVVVPEAKLAELGLAQPSGALESGDGRQWAVVGAFEARTPFEDLDG
+YALAVPATPASLVVQQVRVLALDTAGTRAMQDSALAVIDPDPRSSQVQPARALAAGNETI
+TGELAGLGRSLLLLILGAGAFFVAIVVLADVLIRRRDLGRRRTLGIGRADLVLLVAVRTA
+APAMRGAAVGAGAGHGLVLAQGSALGSAFVVGAAVLAVLTAVVASLLPAAFAAFRDPVRV
+MRTA
+>GCF_020097155.1_00553
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTWIGRGGARVAVTNVVGTLD
+RGIELTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGRQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA
+>GCF_023573625.1_02080
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTGIGRGGARVAVTNVVGTLD
+RGIVLTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGRQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001678.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001678.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c5b842e08644fc01c18655c050aeb138e2866ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001678.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02144
+MNAELSVADLRFAYTRGAEELFDGLTHRFTPGAVTALTGPSGRGKSTLLYVLGLMLTPSA
+GVVRLGDVDASALPDRRRARLRATSVGFVFQDAELDPSRPILDSVVEPGLYAGLSRRELE
+GRARILLERFGLGHRAEHRPGQVSGGQAQRVAVCRALVNTPAVVLADEPTGNLDPDNASL
+VLDALAEAAGEGRTVVVATHDPAVVARADEVVRL
+>GCF_003691675.1_01851
+MTGPATPGTPAAPVVPAALAVEDLRFAYTRAAEELFDGLTHAFTPGAVTALTGPSGRGKS
+TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV
+EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPAVVLA
+DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL
+>GCF_005280335.1_00628
+MNAELSVADLRFAYTRGAEELFDGLTHRFTPGAVTALTGPSGRGKSTLLYVLGLMLTPSA
+GVVRLGDVEASALPDRRRARLRATSVGFVFQDAELDPSRPILDSVVEPGLYAGLERRVLE
+ERARALLERFGLGHRAEHRPGQVSGGQAQRVAVCRALVNTPAVVLADEPTGNLDPDNASL
+VLDALAETAAEGRTVVVATHDPAVVARADEVVRL
+>GCF_020097155.1_00552
+MTGPATPGTPAAPGTPAALAVEDLRFAYTRAAEELFDGLTHAFTPGGVTALTGPSGRGKS
+TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV
+EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPAVVLA
+DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL
+>GCF_023573625.1_02081
+MTGPATPGTPAAPVVPAALAVEDLRFAYTRAAEELFDGLTHAFTPGAVTALTGPSGRGKS
+TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV
+EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPVVVLA
+DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001679.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001679.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0227b644b4dacba7932a108efbc09ea35971febf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001679.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02145
+MTRPLRWATLAGVLLIVAVLAFWAGRATLTPPAQAEQRPSEDALVTVAEQELGRVITLGV
+SVTREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVITVQGELPQWRALGEGATG
+SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAADTVELGQLVVLESLPAA
+LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAIIPAGTAVTVPHGEHEWEAV
+AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL
+RTQPDGAARVTVVRDGVQEERTVIVRGSADGLAVVDGVDAGETVRVLNGAP
+>GCF_003691675.1_01852
+MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV
+SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG
+DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP
+LSVDAKTTAVGTTLAGGENVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV
+AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRAVTVLGSADGLAVVDGVDAGEQVRVLNGTR
+>GCF_005280335.1_00627
+MSKVTRWAALVLTLVLVAALAFWAGRATLTPPAQADQRPSEDAVVTVAEQELGRVITLGV
+SVAREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVIAVQGELPQWRALDEGATG
+SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAAGTVELGQLVVLESLPAA
+LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWEAV
+AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL
+RTQPGGAVVVTVVQDGVEEERTVTVRGSADGLAVVDGVDAGETVRVLNGAP
+>GCF_020097155.1_00551
+MTRPARWAALVLAVVLVAALAFWAGRVTLTPPAQAEQRPSEDAVVTVAEQELGRVITLGV
+SVTREQAPAAVNALSGVVTRAGQSGEVAAGDVLYAVAQKPVIAVQGELPQWRALGEGATG
+SDVTAFQRMLTATGTKVKATGTWDEATATAWNAWLTTRGYPAADTVELGQLVVLESLPTA
+LSVDAKATAVGGTLAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWKAV
+AGESISDEQGLIRITLTAPDGGVVCGEDCDTLPADPTTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR
+>GCF_023573625.1_02082
+MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV
+SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG
+DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP
+LSVDAKTTAVGTTLAGGEKVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV
+AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001680.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001680.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d2ae9a0e457a6ab562f3fe90852bf16295d7bdc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001680.fa
@@ -0,0 +1,29 @@
+>GCF_002008305.4_02146
+MVGLVGALLLAGCASGADAGASAHAETGSTPSKVWDAATWKPTEVIEPVLATEPEKEAAY
+REQMDRLAESGGTPEILQVQRKDWSTTPLESDQKVASCMRADGFPVEVSPTGGLRYSTPP
+AAQARAWALAMNTCIAQHPVDPSYTQDWSEPQLRLVYDYWDQYLIPCLEAQGFTVDTSTR
+PSKESFVTAFFTPGRHDWWPLQATMRGVPEERQTQVVQTCPELPPQDVFWGTSG
+>GCF_003691675.1_01853
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN
+SVGPTGGIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLIP
+CLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPPQ
+DVFWGSSG
+>GCF_005280335.1_00626
+MKTKFAAVTAAAVTAVLTLSGCATTAPSTSAAATGSPTEKVWDPETWTPTEKIERRMTEA
+DERERWYESQLARNAAFLGIRNPPAVTRRGWATSRQEQARWSAQCMTERGVPATYNEVMV
+GVTYDTPPPSQEAAVKLVSWTCDALFPIDPSLDQEFSDAQLRLLYDYWDQYAIPCLEDHG
+ITVDTSQRPSKETWLAAFNTPERISWWPVQDSIMGLTDARSAEVSEACPVQPPDSMLFGY
+SE
+>GCF_020097155.1_00550
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKEAAQREQVERMAREAGTPELLQVRRMDWSSTTLESSQKIGECMAAAGFPV
+EVTPTGGLRYPTPPESQKRAWNLAENTCAVKHPVDPAYAHDWTEPQLRLVYDYWDQYLIP
+CLEAQGLHVDTSSRPSKESFVTSFFTQDRHDWWPFSTTMVGVSEERKAHIAQTCPELPPP
+DVFWGTAP
+>GCF_023573625.1_02083
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN
+SVGPTGGIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLIP
+CLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPPQ
+DVFWGSSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001681.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001681.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27c814bcd6c1788f9a424c46019b476bd96c7432
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001681.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_02147
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLV
+AVVLNVWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALIAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPARTFVRETAPSEGTFVRE
+TAPSAASGPDVVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNLVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRSELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPEGYDTVIEHDASNVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGS
+HAELLAAKGAYHRLYMSQFKGGEDDDGAASRDDAR
+>GCF_003691675.1_01855
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLV
+AVVLNVWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALVAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPDGTFVWETAPSESAFVRE
+TAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGS
+HDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR
+>GCF_005280335.1_00622
+MSGTEKHGSTAAPQGEVGELTDAEIAAFQEAGVTDEWGEGPPRKAKAFWPSAMRLLGLFA
+PERTGLILVSLMVLVAVVLNVWAPHVLGQAMDVIFGGLISRDMPAGLTREQVIEGLRGQG
+QGQAADMLSGMAFVPGQGIDFAELARLILIVLGMYVVAQLFMWLQGRVLNDLVMRIVFRL
+REDIEAKLNRLPLSYFDTRQRGDLLSRTTNDVDNVQQAMQQAFATLVYSVLTIIGIVGMM
+FWLSWQLALIALIALPVAGVMVGVIGSKSQKLFTAQWRETGRLNGHIEESFTGHELVTVF
+GRQADMAERFDERNEAMYEASFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMT
+LGAVTAFIQYSREFNQPLGQVAGMSNMLISGVASAERIFELLDEDEQDSDAEVARRASDD
+DVAEPADASVRETGASADDDVAHLPQPVAGRVEFEHVRFSYTEAKPLITDLNLVAEPGQT
+IAIVGPTGAGKTTLVNLIMRFYEVDGGRILVDGVDTRTVSREELRSHTGMVLQDAVLFGG
+TIRENIRYGRQDATDEEVVAAAKATFVDRFVHTLPEGYDTVIEQDASNVSAGERQLITIA
+RAFLAQPSLLILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVME
+HGDIVEQGNHAELLAARGAYHRLYMSQFKGGEDDGGGAASGEDAR
+>GCF_020097155.1_00547
+MSEQLTDQEIVELQESGATDEWGGGPGRKAKAFWPSAKRLLGLFRTEKAGLALVAAMVLV
+AVVFNVWAPHVLGRAMDVLFGGVISKGMPAGVSREQVIEGLRGQGQGQAADMLSGMDFTP
+GQGIDFDALARLILTVLGMYVVAQGFMWLQGRVLNDVVMRIVFRLREQIEAKLNRLPLSH
+FDTRQRGDLLSRATNDVDNVQQAMQQAFATLVYSVLTIFGIVGMMFWLSWELALIALIAL
+PVAGVVVGVVGKKSQALFTAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAERFDERND
+AMYEASFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQVAGMSNMLISGVASAERIFELLDEPEEEPDDVVAARADDDVAHLPQPVAGRVEFE
+HVRFSYTEAKPLITDLNLVAEPGQTIAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVD
+TRRVPRQELRAATGMVLQDAVLFGGTIRENIRYGRLEATDEEVLAAAKATYVDRFVHTLP
+DGYDTVIEQDASNISAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQQAMAALR
+NDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGSHEELLAARGAYHRLYTSQFRGGEDEH
+HDDGAPASR
+>GCF_023573625.1_02085
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLAVVAVMVLV
+AVVFNVWAPRVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALVAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPDGTFVWETAPSESAFVRE
+TAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGS
+HDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001686.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001686.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1426a391548a8a49075553e4dcb564ab2b028df0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001686.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_02152
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADALDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFEACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEGGVPASAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF
+SAGDATSALSFEKRRAPEALSFEKRRSRPDAVVVNPPRRGIGAELADALEDSGAPTVLYS
+SCNPTTLAQDLARMPSYRVARVQLFDMFPQTLHAEVLTLLTRR
+>GCF_003691675.1_01865
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEGGVPASAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF
+SDGDATSALSFEKRRAPEALSSKKRRPRPDAVVVNPPRRGIGAELADALEDSGVPTVLYS
+SCNPATLAQDLARMPSYRVARVQVFDMFPQTRHAEVLTLLTRR
+>GCF_005280335.1_00610
+MQCHHYDAGRCRSCALMGVPYGVQLTDKDAAVCARLDAAVPAEAWLPPQASAESGFRNKA
+KLVATGTAAAPRLGILDPEQHPRHHDGTGHDLRDCGLYEDGMEAAFHAIAETIPAAGLEP
+YDVAARTGELKSVIVTLSPDRELMVRFVLRSAARLDALRAAVPGLRSALAGLGTPAAVVT
+ANLHPEHVALPEGPDEVHLAGDPTLRMELNGIGLRLRPQGFFQTNTDVTRRLYATAAAWL
+AEAAAADGTPVHSAWDLYCGVGGFAFHLARPVAEGGAGVAEVWGLETSEDAVAAARDTAA
+ELGLAGAVRFTAGDATRALSPGRREPSEALSSGKREAWDALSSGSREPSDAGAHPDDDAA
+PAAMPDAVVVNPPRRGIGPELAARLQDSGVPHVLYSSCNAASLAKDLAAMPAYRARRAQV
+FDMFPQTGHAETLVLLSRA
+>GCF_020097155.1_00534
+MQCPHFDAGECRSCALMGVPYGAQLADKDAAVRARLAEATDARTRWEAPAASAESGFRNK
+AKLVVTGTAAAPRLGILDPRQHPRHHDGTGVDLRDCGLYEDGMEAAFHAIAGAVTAAGLE
+PYDVAARTGELKNVIVTRSPDRELMVRFVLRSADRLEALRPEVPALREALAALGTPAAVV
+TANLHPEHVALPEGPEEVHLAGDATLRMELNGIGLRLRPQGFFQTNTDITQRLYATAAAW
+LAEAAAEGGTPVERAWDLYCGVGGFAFHLARPVAEGGAGVAEAWGLEVSAEAIEAAREAA
+AELGVAERVRFTAGDATTALAAPGGTRPDAVVVNPPRRGIGAELAGRFEESGVPFVLYSS
+CNAATLATDLTAMPSYRVARAQVFDMFPQTGHAETLVLLARR
+>GCF_023573625.1_02095
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLTMRLNGVGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEAGLPAAAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF
+SAGDATSALSFEKRRAPEALSSKKRRPRPDAVVVNPPRRGIGAELADALEDSGVPTVLYS
+SCNPATLAQDLARMPSYRVARVQVFDMFPQTRHAEVLTLLTRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001688.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001688.fa
new file mode 100644
index 0000000000000000000000000000000000000000..043d8197bf025de0419995b0dbea8b55d52e5a43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001688.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_02157
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTAFGVAPGDLGGAIGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPHMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR
+>GCF_003691675.1_01870
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTVFGVAPGDLGGAVGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPQMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR
+>GCF_005280335.1_00601
+MQVLLALTPILLTLALLLTRLPAWVAPAAGGVLAAALAPTVFGVDPGVLAAEVGRGVPTV
+VEILAIIAGGITLSRVMEHSGAHARLALWLSAGNGPTLATALLMVHGIIPFLETVTGFGV
+SLIVGVPLLLGLGFTAFRSALLAVLALTIGPWGSMAPGTLMGARLYDLDFQAVGVTAALF
+NLPASLVAGAATVLLLRGAQGMRGDGEPARTVPWLAVGLLSGAAQWALILGANLSVGTAP
+AGAVGTFVLTVAWLLVIRRGRLTPGPGRDVVPYVTLMAGTVFGTTVEDALGLTGVLSVVG
+TPALWSFVAVGAGVALLGLGPHARRTVPGEAARLWVGTAIPNALYVAFGLTLSAGGVSQA
+LAGALSGMGPAYLAAIPVIGAFSGFVTASNTGAMALMGPLQMDTGAALGVPPTWTNGLHN
+AAAGWGIIAGPARIQVAHAMAVGAQTPEMPGWAVSRRALLAVLLPAMVVGIALMSLLGLA
+VLPRV
+>GCF_020097155.1_00523
+MQVLLALAPILLTLGLLMTRLPAWAAPAAGSVAAVVLGLTVFGVDPAVLGAAVGHGVPTV
+LEILAIIAGGITLSRVMEHSGAHARLGGWLSAGNGPTLATALLMVHGVIPFLETVTGFGV
+SLVVGVPLLLGLGFTAYRAALLSVLSLTIGVWGSMAPGTLMGARLAGLDVQEVGVTAAVF
+NLPASLVAGVATVLAVRGARGLRDDSAPARLAPWLGVALASGTAQWALILGANLLVGTAP
+AGAVATFALTLAWLLVIRRGRLTPGPGRDVVPYVTLMAGTVLGTTAEDALGLTGPLSVVG
+TPALWSFVAVGVGLRLLDLDAAARRTVPRESLRLWRGTAVPNALYVAFGLVLSAGGASPA
+LAGALSGLGESYLAAMPFIGAFAGFVTASNTGAMALVGPLQMDTGAALGVPPAWSNGLHN
+AAAGWGIIAGPARIQVAHGMAAPAQTPDMPGRAVSPRGLVAALLPASLAGVAGMSLMGWL
+LLPR
+>GCF_023573625.1_02100
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTAFGVAPGDLGGAIGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPQMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001689.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001689.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c0cef686773391f04ac54df0d224ac9c9a66838
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001689.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_02158
+MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA
+QVDALRALLGAERPDRWGVNLFVPDAVNTAIPAAARTEAARSARAAAVAAYRAGLTADGA
+ADLPAVADVVPDPDAERADFEAMLVAAEEQAWPLVSFTFGLPAADVFARLAAAGVPAGAT
+VTDAAEARAALEHGAAFLVVQGHRAGGHRGTSDPAAEPTRAELPTVLAAVRDVVGTGAAS
+AAPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA
+DDGRARTALTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAVGDLERVH
+LWAGTEAHRVREAPAADVLASLTP
+>GCF_003691675.1_01871
+MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA
+QVDALRALLGAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARAAAVAAYRADLTADGA
+ADLPTAADVVPDPDAERADFDALLTAAEEQAWPLVSFTFGLPAADVFARLAAAGIPAGAT
+VTDATEARAALEHGAAFLVVQGHRAGGHRGTSDPAAEPPRAELPAVLPAVRDVVGTGATS
+AVPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA
+DDGRARTGLTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAAGDLERVH
+LWAGTEAHRVREAPAVDVLASLTP
+>GCF_005280335.1_00600
+MSAAQLPDDVVRARLIPPARVLAAPMAGGPSTPELVAAVVRAGGSGFLAGGMRTAAQVRE
+QVDALRGLLGGGDGSVDGSDAARRWGVNLFVPDAVNTAIPAADRTERARAERRAAVAAYR
+ERLAAEGERAAGGAAAEGAGGAPTLPSPDDVTPDPARERAEFAAMLTAAEEQAWPLVSFT
+FGLPEPAVFARLAAAGIPAGVTVTDADEARSARAHGAAFLVVQGHRAGGHRGTLDPAADP
+VERELPSVLAQVRAVVGTRVPVVAAGGVGAAAHVRSLLAAGADAVAAGTAFLLAAEAGTS
+VAHRAGIRRCAAGEGFVGPDGAARTVLTRAYTGRWARTLATDFAAAHPDAPAAYPELNAL
+TTGLRAAAATAGDLERVHLWAGTQAHTAREAGAADVVAGLTP
+>GCF_020097155.1_00522
+MSSTTVPSVPAPVPAPLDPPVPVLAAPMAGGPSTPELAAAVIRAGGGAFLAGGMRSAAQV
+REQVDGLRALLTAPEEAGRFGVNLFVPDAVNTAVAASARGGAARIARAQAVASYRERLAP
+LAADLGAELPSVLTVTPDPDAERAAFEDMLAAAEEQSWPAVSFTFGLPAPDVFARLDAAG
+IPAGVTVTSPAEAMAAVASGARFLVVQGPKAGGHRATLDPQGRPGITDLRTLVFAVRHAL
+GPAAVPLVAAGGITDGAQVRPLLEAGAVAVAAGTAFLLTPEAGTSAAHRTALRQASAGVA
+FAHPDDGAASTALTRAYTGRWARGLVTPFMDEHHDAPAAYPEVNGLTGPLRRAAAEEGDL
+EHVHLWAGTGAHRVEEVGAAEVLASLAPRAEP
+>GCF_023573625.1_02101
+MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA
+QVDALRALLGAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARTAAVAAYRAGLTADGA
+AGLPTAADVVPDPDAERADFDALLTAAEEQAWPLVSFTFGLPAADVFARLAAAGIPAGAT
+VTDATEARAALDHGAAFLVVQGHRAGGHRGTSDPAAEPTRAEMPTVLAAVRDVVGTGAAS
+AAPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA
+DDGRARTGLTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAAGDLERVH
+LWAGTEAHRVREAPAADVLASLAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001690.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001690.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b8ee85af6b2e381a87414991d86f07bcc88a26f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001690.fa
@@ -0,0 +1,46 @@
+>GCF_002008305.4_02159
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVYNLAANAPRSVSVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLMVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGVTDDDARRPAADVVA
+SPDGRGTRLPPGRRPQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIV
+QEALTNTLRHGGPDADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTA
+LFGGTLETGPRVGAGYRVSAHLPYSAV
+>GCF_003691675.1_01872
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSMSLLMVPLTVYNLAANAPRSISVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLMVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGVTDDDARRPAADVVA
+SPDGRGTRLPPGRRPQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIV
+QEALTNTLRHGGPDADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTA
+LFGGTLETGPRVGAGYRVSAHLPYSAV
+>GCF_005280335.1_00599
+MNPLHRIDQWMRAHPVRTDVLVSVLLFAVLGLTPWVMLGSLAGPTPGSIVASILIALALI
+APWAFRRVRPVASAAAVAAAAVAHLVAGPEFSLALVLVPMTVYNLAANAPRWASFTGLVA
+ALLGGVANGIRVGLFPDPAMRPDGVYEPVDPSLEALLVMVFGCAAVVLTAWAFGDVVRHR
+RLAVRALEDRNRRLETMALQERRLAASDERNHIAREMHDIVAHSLQVIISQADGARYAAA
+AKPELAVATLDTIGLTGRAALADMRQLLGVLRETGETVAGVPGVAPDDGAPGPAAGASDE
+GAAGAADEGAAGAADEGAAGAGTAGAGTTPGAGRTRLPADVASRDGRGARQPPGHRPQPT
+LADVPALIETMRLSGLEVSLLETGAPRRPLPPGGELAAYRIVQEALTNTLRHGGPQASAF
+LTLAWTGRGLDVQSDDDGRGADADPGTRGSGHGLRGVAERVALFGGTVETGPRAGAGYRV
+SAHLPYSAV
+>GCF_020097155.1_00521
+MNPLRRLDVLLRRHPVRTDVTAAVLLTLVLVLAPLVMLGGGVGSPAAWQTAGTVVAGLLM
+TGAWGLRRVRPVAAAGVTVAGALLHLAVGPEFTIALAMVPATVYNLAAIGPRWASLAGLA
+TGLAGGLANGLKVWLFPPRFTTPDGVQVQSPAEPVAMVVMAVLCGMAVLTAWAFGDVVRN
+RRLAVQALEDRARRLETQALQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYAA
+AAKPELAVETLETIGQTGRSALADMRQLLGVLRGPAEPTGGPDRARRDPAAPDGHRAPPG
+LADLPALFQTLRLSGLEISLLEQGSPRRDLPAGGELTAYRTVQEALTNTLRHGGEGAHAF
+LTLRWTARGLEIQADDDGRSQADAETTGSGQGLRGIAERVALFGGTMEAGPRVGAGWRVW
+AELPYADV
+>GCF_023573625.1_02103
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVCNLAANAPRSVSVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLVVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLPGVLRETGETVAGVPGVTDDDTRRPADPAPD
+RADPTGTRPDVVAAPDGRGARLPPGRRPQPRLADLPALVETMRLSGLEVSLLETDTPRRA
+LPAGGELAAYRIVQEALTNTLRHGGPDADAFVTLAWTARGLDLQIDDDGRGAAADPATRG
+SGQGLRGAAERTALFGGTLETGPRVGTGYRVSAHLPYSAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001691.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001691.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8792ed198e6060982270510908a800c3bd4a02d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001691.fa
@@ -0,0 +1,14 @@
+>GCF_002008305.4_02161
+MTGSILDHPAPTTSRASDPAAERAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA
+LTAGAGLLAGAVAWATARPVLEDDAPGD
+>GCF_003691675.1_01874
+MTGSILDHPTPTTSRASDPAAEQAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA
+LTAGAGLLAGAVAWATARPVLEDDAPGD
+>GCF_005280335.1_00596
+MTAAVVILGLSLFTQVEGLPRLLVTAASGLLAGAVTWSVTQPVLEDEVLHG
+>GCF_020097155.1_00519
+MSAAPAPSPAAPAVPPVTAVPPAAREPEGTSPSDRERERGDAECLAFFLALVTAALVMAG
+LALATDLGPLLRVLLSLGASGLAGALTLAFTRPSLED
+>GCF_023573625.1_02105
+MTGSILDHPAPTTSRASDPAAERAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA
+LTAGAGLLAGAVAWATARPVLEDDAPGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001693.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001693.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eba046935d09fc216405ec28dda4b816455bcce9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001693.fa
@@ -0,0 +1,80 @@
+>GCF_002008305.4_02164
+MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL
+PGGSEDVSDLAGTGAEPGPLARLDGVEEAYALRMAWATARAADAEFGTTVMPLPRDPALA
+GLTVTAGTLPAADDARGVTLDAQTADRHGVAVGDVVTLAGESGPAPATTPLDAVVTGLTQ
+PSPDPMLSGQAQVWASSAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA
+GVDVDVATPDEAVRSAVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD
+LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG
+LHPAGLAVSVAVGVAVTVLAALAPAVAATRVAPLEALRPKDEVTAGSRGGRVRAAIGLVL
+AVGGTALMLGGVSVREPVSAIGGGALCFVGVLLLARLFVPAAVRGAAVLARPAGVPGHLA
+GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD
+PARAAEAVAATEDVQAVALATPVGTTENGSPVLATPAADLRAVVARLPEGVTGLGDPGTA
+LVPDWVEADPVRAEVAGAAQTFAPVRAGSLSSGVYVAAEPLREAGWDGAADAAVPGQLLV
+ALDPGVPVDRLQGLSEDVTRAAGDGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI
+ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGAIAIEAVLIAAVAAVLGCALGVCYG
+WAGAQLVLADLSATAGAGTAVRPVVPWLELGLVVAVAALAGLAASLLPARRAARLSPVAG
+LAAV
+>GCF_003691675.1_01878
+MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL
+PGGSEDVSDLAGTSAEPGPLARLDGVEEAYALRMAWAAARAADAEFGAAVMPLPRDPALA
+GLTVTAGALPAADDARGVTLDAQTADRHGVAVGDVVALASESGPDSTTTPVDAVVTGLTQ
+PSPDPMLSGQAQVWASPAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA
+GVDVDVAAPDEAVRSVVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD
+LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG
+LHPAGLAVSVAVGVAVTVVAALAPAVAATRVAPLKALRPRDEVTAASRGGRVRTAIGLAL
+AVGGTALMLGGVSVREPVSAIGGGALSFVGVLLLARLFVPAAVRGAAVLARPAGVPGRLA
+GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD
+PARAAEAVAATADVQAVALATSVGATEDGSPVLATPAADLRAVVARLPEGVTGLGDPGTA
+LVPDWVDTDQVRGQVAGAERTFVPVRAGSLSSGVYVAAEPLREAGWDGAAGAAVPGQLLV
+ALDPGVPVDRLQGLSEDVTRAAGTGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI
+ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGTIAIEAVLIAAVAAVLGCALGVFYG
+WAGAQLVLADLSATAGAGTAVRPAVPWLELVLVVAVAALAGLAASLLPARRAARLSPVAG
+LAAV
+>GCF_005280335.1_00593
+MWTVALSQLRAQPRRYVSLVLAILIGTMFLAASFLVSASAQATLRTTLGNTYSAADLVVL
+PEPSDHADEDPTAAFPGLAGTPAEPGALGRVDGVEEAYATQFTWAGGSAGGTEFTATLLP
+VPGDVSLLPVTLTEGAFPAADDARGVTLDTGTAERTGVAVGDEIALTGAPGAGGETATVV
+GLTTRSPDPTLSSGAQIWAAAPVIAAVNPPQDGEAGGSGAYSPHVLLRLTDGADRDAVAD
+AAAAVLAQEGVAASVTTPDEAVRDTLAEAGGGTDVFGWVLGGFAALALLVTALVIGNTFQ
+VLVAQRTRDLALQRTLGSTAGQVRGSVLTEAVVVGLVGSVLGVALAVVGLLAGVAFVRSA
+FDLPTLTFGMDPAGLAITVVVGVLVTLVAALSPAVAATRVSPLQALRPREEVTVASRVGV
+VRTVVGAVLAVGGTALMLWGAFRPEPLTAVGGGALSFIGVLLLATLFVPAAVRGAAVLAR
+PAGVPGRLAGLNATRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDL
+VLSLPADGDAARAAEAVAARDDVAAVALALPVGATENGSPVLATPGADLRKVVAELPDGE
+DGLGDPGTAFVPGWVDEDTVTATVAGTEQTFSAVRAGDLSSGVYVEADSLRAAGWDGSPL
+ATDGVEVPGQLLVALAGDVPVDRLQALSEDITAAAGEGASIIDGGAPTRAVYAQVIDVML
+WIVVGLLAVSVLIALIGVANTLSLSVIERTRENALLRALGLPRGGLRGMIAIESVLIAAV
+AALLGCVLGVFYGWAGSQLILGELVETVGRGGTVLPTIPWLELALVVGVAAVAGLAASLL
+PARRAARLSPVAGLATV
+>GCF_020097155.1_00516
+MWTVALSQLRARRRRYASVVLAVLIGTMFLAASFLVASTAQATLRTTLGSVYAGADLVIQ
+PEDDPETSADASGPPPGQRLAALAGTPETPGALARLDDVAEAWAPTPGFAEAAAPGGGTP
+RPAAVIPAPAHPDLLGVRAVAGALPDPADARGVAVDEETARALGVGVGDELPLTGEPTRA
+PVRATVTGLTSVSPDPMLSSQAQVWASRPVAQDLAPDGQVPYTTAVLLRLAPGADREAVA
+EAAARALHDDGVPAAVQTPDQAVRDQLASLSGGTDLLGWVLGGFALLALVVTALVIANTF
+QVPVAQRTRELALLRAVGAEARQVRGAVLLEAVATGLTGAVAGVVLAVGLTAAVVAVARG
+ALGADALTLGVDWLPLAGAVALGTAVAAVAALGPARAATRVAPVQALRPVDEAPVRSRVG
+LVRAGLGLLLAVGGAALMWWGAWGSAFAAALGGGVLSFLGVLLLARLFVPGAVRAAAVLA
+RPAGVPGRLAGLNAVRHRRRTAATASALLIGTTLVALVLTGGRTAQIRLDALLDEEYPVD
+LVVSVPAGGDLAAATRALGAVDGVGSVAAASPVGATVNGSPAYAVEADALRSVVAALPDG
+QDRALGDGASVLVPAWAGATTEVVVDGRVSGLASVRGSGLTTGVFLTPETAEWVRRHGVA
+ADAGTASDAAGPAAEDQAVAGLVLVAAADDVSVNRLQEMSAALTAAAGAGASIVDGGAAE
+RAVYAQIIDALLWIVVGLLAVSVLIALIGVANTLSLSVIERTRENALLRALGLTRGGLRG
+MIAVEAVLVAGVAAVLGCGLGVLYGWAGSQLVLGQLVAQLGEDRALVWPEVPWAELALVV
+AVAAVAGLLASLAPAGRAARLSPVEGLATV
+>GCF_023573625.1_02109
+MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL
+PGGSEDVSDLAGTSAEPGPLARLDGVEEAYALRMAWAAARAADAEFGAAVMPLPRDPALA
+GLTVTAGALPAADDARGVTLDAQTADRHGVAVGDVVALASESGPDSTTTPVDAVVTGLTQ
+PSPDPMLSGQAQVWASPAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA
+GVDVDVAAPDEAVRSVVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD
+LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG
+LHPAGLAVSVAVGVAVTVVAALAPAVAATRVAPLKALRPRDEVTAASRGGRVRTAIGLAL
+AVGGTALMLGGVSVREPVSAIGGGALSFVGVLLLARLFVPAAVRGAAVLARPAGVPGRLA
+GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD
+PARAAEAVAATADVQAVALATSVGATEDGSPVLATPAADLRAVVARLPEGVTGLGDPGTA
+LVPDWVDTDQVRGQVAGAERTFVPVRAGSLSSGVYVAAEPLREAGWDGAAGAAVPGQLLV
+ALDPGVPVDRLQGLSEDVTRAAGTGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI
+ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGTIAIEAVLIAAVAAVLGCALGVFYG
+WAGAQLVLADLSATAGAGTAVRPAVPWLELVLVVAVAALAGLAASLLPARRAARLSPVAG
+LAAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001694.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001694.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc88103cce59d7efe8c50faa53a697d05b396943
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001694.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_02167
+MTSLLRILRFAPQLNRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAVAGETDVAEAV
+TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT
+GRVVNRLNRTINELTQFLQFFANNAFTMLITTAAVLVITAFYWWPLAILLAVVFPVYMWL
+TARTSTKWQVWEGEKNTEVDIASGRFAEVVSQMSVVRAYNRQDHELSGFRDRFLRTVGIT
+RQQSRFWHGMDAGRRLALNVAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM
+SFLVDSAQRAVAGSKDYFEVLAEERERAGGAALAVAGASAESAGADAPRVPAEPRADVVP
+GAPDVPADVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGARVALVGESGGGKSTIAHLL
+LGLYPVTSGRIEVFGQDVAGLDLAVLRGRIATVFQEPSLFSGTVRENIAYADPDASDERV
+RAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSA
+LDTKSERLVQAALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGQVQEIGTPAELAESGG
+IYAQLLELQRAGTQEARKMLKEYGLSG
+>GCF_003691675.1_01881
+MTSLLRILRFAPQLHRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAVAGETDVAEAV
+TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT
+GRVVNRLNRTINEITQFLQFFANNAFTMLVTTAAMLVITAFYWWPLAILLAVVFPVYMWL
+TARTSAKWQVWEGEKNTEVDVASGRFAEVVSQMSVVRAYNRQDHELTGFRDRFLRTVEIT
+RQQSRFWHGMDAGRRLALNVAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM
+SFLVDSAQRAVAGSKDYFEVLAEERERAGGAALAAASASAESAGADAPRVPAEPRADVVP
+GAPDVPADVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGARVALVGESGGGKSTIAHLL
+LGLYPVTSGRIEVFGQDVAGLDLAVLRGRIATVFQEPSLFSGTVRENIAYADPDASDERV
+RAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSA
+LDTKSERLVQAALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGQVQEIGTPAELAESGG
+IYAQLLELQRAGTQEARKMLKEYGLSG
+>GCF_005280335.1_00585
+MLAAVLTLATPFLIGAATDRIVAAIAGETTVEDAVVAVTWLAVAFLAVEVTTTLVVSVGG
+YWGDVMAARMRTILSTRYFDQLLHLPQRYFDTAITGRVTNRLNRTINELTQFLQFFANNA
+FTMLITTTAVLVITAFYWWPLAILLAIVFPVYMWLTAKTSAKWQVWEGEKNIEVDMASGR
+FAEVVSQMSVVRAYNRQDHELAGFRERFTRTVGITRKQSRFWHGMDAWRRLALNVVFGAM
+YLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSMSFLVDSAQRAVAGSRDYFEVLAEER
+ERAGGAGPQGRGAAAVAAGQPRADDDGGTDVRWGGAAPSRPAQPRADVVPGDGTGGMPAG
+PSADVVPAVRFDEVSFAYDPDASRPVLDRVSFEIPQGQRVALVGESGGGKSTIAHLLMGL
+YPVTGGRIEVFGQDVAELDLAELRERIAAVFQEPSLFSGTVRENIAYADPAASDERVRAA
+AEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSALDT
+KSERLVQGALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGRVQEVGTPAELAESGGIYA
+QLLRLQKAGTKEARKMLKEYGLSG
+>GCF_020097155.1_00512
+MRALLRILRFAPQLNPLYLGIAVCSVLAAALSLATPFLIGAATNRIVDAIAGRSTLDDAV
+AAVTWLALAFLAVEVATTAVVSVGGYWGDVMAARMRAALSGRYYDHLLHLPQRYFDTAIT
+GRIVNRLNRSITELTQFLQFFSNNAFTMLITTAAVLVITAFYWWPLAVLLAVVFPVYMWL
+TAKTSAKWQGWEGEKNTEVDIASGRFAETVAQMNVVRAYNRQDHELAGFTERFRRTVGIT
+RKQSRFWHGMDAGRRLALNLVFGVMYLIVFVRTARGLFSVGDMVILLQLMNMARQPIFSM
+SYLVDSAQRAVAGSKDYFGVLAEERERSGGAALPAGLGSAEAPTTTTATGVVVRDRAEAP
+TGAPVRAGADVPAVRFADVTFAYDPEAERPVLDGVTFDIPQGAKVALVGESGGGKSTLAH
+LLMGLYPVGSGRVEVFGRDVAGLDLAVLRGQVAAVFQEPFLFSGTIRENIAYADPDASGE
+RVRAAAKAAFADGFVEEFEHGCEQLIGERGLRLSGGQKQRIAVARAVLKDAPVLVLDEAT
+SALDTKSERLVQSALDDLMVGRSSLIVAHRLSTIASVDRIVTLRGGRVQEVGTPAELAQS
+GGIYAQLLRLQKAGTKEARKLLKEYGLSG
+>GCF_023573625.1_02112
+MTSLLRILRFAPQLHRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAIAGETGVAEAV
+TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT
+GRVVNRLNRTINELTQFLQFFANNAFTMLITTAAVLVITAFYWWPLAVLLAVVFPVYMWL
+TARTSAKWQVWEGEKNTEVDIASGRFAEVVSQMGVVRAYNRQEQELSGFRDRFLRTVGIT
+RQQSRFWHGMDAGRRLALNAAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM
+SFLVDSAQRAVAGSKDYFEVLAEERERAGGAVLAVASADAPRVPAEPRADVVAGAPDVPA
+DVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGAKVALVGESGGGKSTIAHLLLGLYPVT
+SGRIEVFGQDIAGLDLAALRGRIATVFQEPSLFSGTVRENIAYADADASDERVRAAAQAA
+YAHRFVAAFDDGYDQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSALDTKSER
+LVQAALDELMVGRSSLIVAHRLSTIASVDRIVTLRAGRVEEVGSPAELAESGGIYAQLLE
+LQRAGTQEARKMLKEYGLSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001695.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001695.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97011909f7096e39dcf266bae24abcb8fc34a67e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001695.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_02169
+MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLGFAAGALRSAWRGDRTLSTAAADVEGTG
+HGPDRIDLAVLTGELPLIDPVTGRLAEREPAGAGVGHHDDGAPGFGAPSGGGSVTVRQRV
+QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWAYVGGAVAA
+SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL
+>GCF_003691675.1_01883
+MARTWGDSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADAAGTG
+HGPDRIDLAVLTGELPLIDPATGRLAEREPAGAGVGQHDDGAPGVGAPSGGGSVAARQRV
+QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWTYVGGAVAA
+SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL
+>GCF_005280335.1_00583
+MTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLIVCFLGDVALLALGAAGIGVV
+AERWPWLVTALTVAGVVYLVWFAAGALRSAVRGQRTLAAAAEAEGPAVGLTDGEIAALTG
+ELPLIDPATGRLSADFTGRTAEGRAVPVGAGVGMGRGHDPLGDESRTVGGIPVGNPRLCG
+TRPGERGADGRSGGVAVKQRVQPRRVVLSAPQTPLPRIVLLALSVSFLNPHAVLDTVVMM
+GTFAQTYGPGKWVYVGGAVAASLVWFTALGWGGTRLAPYMNTPRTWRIVDAAVGVLMLVI
+AAKVGLTLL
+>GCF_020097155.1_00509
+MTVFSAGFLTYLALIVAIGAQTLFLLRQVVRGDRAWTAIGVCFLSDIVLLLAGAAGVGAA
+AERAPWLVPALTVAGVAYLVWFGVSALRSAHRGDRTLAGAAAEVEDDAWAPTAEEVAAMT
+GSLPVVAAGPDAGADAATAPAGTGGGVALRTRPVSTTAPASAAPRPALTPLPRLVLLCLS
+VSLLNPHAILDAVVMMGTFAQGYGADKWLYVAGAVASSALWFLVLGWGGAKLAPLMNTPR
+TWRIVDGAVGVVVLGIAGKVALTLF
+>GCF_023573625.1_02114
+MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGVGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADGAGTG
+HGPDRIDLAVLTGELPLIDPATGRLADREPAGAGVGRHDDGAPGVGAPSGGGSVAVRQRV
+QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWVYVGGAVAA
+SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001696.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001696.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f7051f6bca9fd32f806152e6b4640b5bcfc7471
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001696.fa
@@ -0,0 +1,33 @@
+>GCF_002008305.4_02170
+MATPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV
+PVRPTAAGERMLRLARQTLALEDETLAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA
+TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE
+LHRDARGRVDFGSLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG
+LGWGMLPSVQIPPGVLEGRHPDLETIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP
+SAGDTAD
+>GCF_003691675.1_01884
+MATPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV
+PVRPTAAGERMLRLARQTLVLEDETLAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA
+TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE
+LHRDARGRVDFGTLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG
+LGWGMLPSVQIPPGVLEGRHPDLEPIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP
+SAGDTAD
+>GCF_005280335.1_00582
+MNSDHLRALVSAVDHGTFDAAADALRISGSAFSQRVKALERQVGQVLLARTVPVRPTPAG
+ERMLRLARHTLALEEEALASLGRGDGGRVPVRVAINADSLDTWWELVLREAATWDDVVLQ
+LRTEDQEHTAALLRDGTVVAAVTDDPTPVSGCTSTPLGTMRYHAVCASFLLEMHRDERGR
+LDLATLPRVDYGLRDGLQRTVLRRAARGRAAFDPPHHLVPSVQSYLRAVELGLGWGMLPS
+AQLPPGVLEGRHPDLEPVPSLGTVDLTLHWQRWSAGTAALDRLTDAVLRAAPSVADAAD
+>GCF_020097155.1_00508
+MNSDHLRALAAAVDEGTFDAAAAWLGISGSALSQRIKALEGQTGQVLLTRTVPVRPTEAG
+ERMLRLARQTLPLEEEALAALGRGTGRRAPLRVGVNADSLETWWTPVLREAATWDDVVLH
+LHAEDQGHTPELLRQGTVVAVVTDDPTPVTGCTVTRIGTMRYHAVAASFLLDLHRDAHGR
+VDVATMPVVDYGPRDGLQRTMLERAARGRVSVPRPPHHLVPSVGAYASAVGMGLGWGMLP
+TGQVPPELAAGSHPDLELVPELGTAEVPLYWQRWSAGTPALDRLTAAVTAAAPAG
+>GCF_023573625.1_02115
+MTTPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV
+PVRPTAAGERLLRLARQTLALEDEALAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA
+TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE
+LHRDARGRVDFGSLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG
+LGWGMLPSVQIPPGVLEGRHPDLEPIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP
+SAGDTAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001698.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3740bfbf856a5ed4b550c0926e547e211da983d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001698.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02175
+MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH
+VYGTTEIPQRPTRVATVSWVNQDVTLALGVVPVGMAAVEFGGNAEKSTDWFDAKLAETEG
+AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS
+WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHADLQGASFVYGTIDPAAADQISIY
+TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA
+IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG
+>GCF_003691675.1_01889
+MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH
+VYGTTEIPQRPARVATVSWVNQDVALALGVVPVGVAAVEFGGNAEKSTDWFDAKLAETEG
+AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS
+WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHAGLQGASFVYGTIDPAAADQISIY
+TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA
+IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG
+>GCF_005280335.1_00577
+MATVSWVNQDVALALGVVPVGMAAVEFGGNAEKSTDWFDAALEKVEGAERPVTWSEAAGI
+DAEAVASVRPDVILAAYSGLTREDYDRLSKIAPVVAYPKDVPAFGTPWQQSTRMIGQALG
+KDAEAEALVEDVEGRIAAAAQKHPDLKDATFVYGTVDPTAADQISVYTLVDNRPRFLESL
+GMKQAPVVAENSPKDQAFFFTWSPERADELESDVLVSWALDASVADAIEADPLLSALPAV
+QKDGLVLQVDQQEVLSVSAISPLSIPFALERIVPPIAEAAARSRG
+>GCF_020097155.1_00504
+MPQSPSRRSVLAAGGSGLALLLAACSTGPAGSSVPSSSPASSAGSAAASSSASGSAAYPL
+TVEHVYGTTEIPARPERVATVSWVNQDVALALGVVPVGVPAVEFGGNADKSTDWFDAKLK
+ELGGPTPVQWSEADGIDAEAIAAVKPDVILAVYSGLTREDYDRLSKIAPVVAYPKDVPAF
+GTSWQQSTEVIGRVLGKEREAAALVADLERQIADAGAEEDGLAGASFIYGTLDPAAADQI
+SIYTAADNRPKFLELLGMELAPVVAENAPEDGAFFFTWSPERADELESDVFVSWAASADV
+ADAIEADPLLGAIPAVEKGGLVLQVDQQEVLSVSAISPLSIPYALEKVVPPIAEAARAAK
+G
+>GCF_023573625.1_02120
+MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH
+VYGTTEIPQRPARVATVSWVNQDVALALGVVPVGMAAVEFGGNAEKSTDWFDAKLAETEG
+AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS
+WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHAGLQGASFVYGTIDPAAADQISIY
+TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA
+IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001699.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a88ef26138d19a4bf9171ad66b7c9559bdd257f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001699.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02176
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAILTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRSGRTPGAPSPMALVLAGAALTAGAT
+AGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALALG
+DDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALMV
+GCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
+>GCF_003691675.1_01890
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAVLTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGRTTPGAPSPMALVLAGAAITAGA
+TAGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALAL
+GDDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALM
+AGCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
+>GCF_005280335.1_00576
+MPRALLLIAPAVLAVLAALASLALGARPVPVDAAVGALTEAALHGPAAVTGMDGAAVLSR
+VPRTLAAILVGAGLAVAGAALQGATRNPLGDPGLLGLTAGAVLAFALGIALGVAGSLPAV
+MALAILGTLAAAALVTAVAAGAARVSGVPGPPSPLSLVLAGAATTAGATAVTSALVVLHP
+AVRDRLRLWTVGSVARADLGDALWLAPVVLAAVAAVVVLGPGMDALALGTDLAHGLGARP
+ERVRALLLAAAVVLTAAAVALAGTVGFLGLVIPHAVRRLRPPDARTLVLACALWGAVLVL
+VADTLGRLVIAPAEVHLGVTTAVLGVPVLLALLRRRGVAA
+>GCF_020097155.1_00503
+MPSSPTRGALLFGLLPLALLLTAGLAALALGARPVPLTTTATTLQAMLAGEGVPAGVDAA
+AVASRVPRTLTAALVGAALAVAGAALQGATRNPLGDPGLLGLSAGASLATAIGLALGVSG
+STFWVLALAAAGTLAAALLVYAVAAAASRGAGAGGAPTPIGLVLAGAAVTAGAGAVTTAL
+LVLSPVVRDRFRFWAVGTVARADLGEAALLTPVIGLGIVLALAAARGLDALALGDDLAHG
+LGARPGRTRALLLAAVVLLTAAAVALAGPVGFVGLVVPHALRRLRPGGTRTLLIGSALWG
+AVLLVAADLLGRLVIAPAEIHLGVTTVLLGVPVLLVLLRRTGLGS
+>GCF_023573625.1_02121
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAVLTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGRTPGAPSPMALVLAGAAITAGAT
+AGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALALG
+DDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALMV
+GCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001700.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001700.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d03f86ed29acb4531607300df15c2608ea486985
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001700.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_02177
+MSLQCTAPDDVVARLRRADRRRLGGACAGLAVAVLVLALLRVVWGTYQVTVPDLVRILGG
+ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAAAVV
+LGMLATAGQTGGGSDLMRAATALIGGLAAVVAVFATARSVGGERFVVAGIAVAAAGQAVV
+AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLVVALPLAGVLHARLAPADVGPD
+LAHALGARPRPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL
+TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLCQGRTPGGVRSA
+>GCF_003691675.1_01891
+MNLQHTAPDDVVARLRRSDRRRLGRACAGLAVAVLVLALLRVVWGTYQVTVPDLVRILGG
+ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAAAVV
+LGMLATAGQTGGGSDLMRAATALIGGLVAVAAVFATARSVGGERFVVAGIAVAAAGQAVV
+AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLAAALPLAGALHTQLAPADVGPD
+LAHALGARARPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL
+TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLRQGRTPGGVRPA
+>GCF_005280335.1_00575
+MSGRGSATLEHAVARVRAARRRDARRVGTALAVLTAAVLALVLLRLTWGAYMVAVPDLVR
+ILTGTTIPGASFIVTEEKLPRAAAAVLAGAALGAAGALYRRGLGNPLASPDVLGVTSGAA
+AGAVLWQAAATGTGGTTDAARAAAALAGGLIAALAVLLAARGTGGERFVVAGIAVAAGAQ
+AVVAGTMVTLAEHDLQAAALWVSGSLTGVTWGRIGLLAAAVALALPLAAWLHGRLEPADT
+GEDLAHALGARPRRTRPAALLLGAVLAAAATAAVGPLAFVALLATPLARGLAGGRPSLAA
+AALAGAVLVLAADLLAAEAVALLADGTRLPTGVLTGAAGAPLMMTLLIRAGRRGERTA
+>GCF_020097155.1_00502
+MSARRETTTPGRRDAAPGGDAPETVRALRRADARRVAGVVLGLAVLTAGLMLLRVTWGTY
+QVTVPDLVRILGGERIAGASFIVWEEKLPRAVAATLTGAALGAAGALYRRTLRNPLASPD
+VLGTTAGAAAGVVLTLTASAGQAGGSSDLARAGAALLGALAAGAAVLLAARSVGGQRFVV
+AGVGVAAAGQAIVSGAMLSLSEHDLASATRWIAGSLNGVTWGRIGLLAAVLALALPAAGW
+LHRRLAPADVGDDLAHALGARPRTTAALALTVGAVLAAAATATVGPLSFVALLATPLALG
+LTRGRPSLPAAALTGAGIVLLADVLGTEALGLIADGAALPTGVLTGAAGAPLMLALLLRA
+GRSSEGTR
+>GCF_023573625.1_02122
+MSVQRTASDDVVARLRRSDRRRLGGACTGLAVAVLVLALLRVVWGTYQVTVPDLVRILAG
+ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAATVV
+LGMLATAGQTGGGSDLMRAATALIGGLVAVAAVFATARSVGGERFVVAGIAVAAAGQAVV
+AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLAAALPLAGALHTQLAPADVGPD
+LAHALGARARPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL
+TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLRQGRTPGGVRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001701.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001701.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5999b47e24696f806471da637c9680ecfea8102
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001701.fa
@@ -0,0 +1,32 @@
+>GCF_002008305.4_02178
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVADLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTDLVELADREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIVPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR
+>GCF_003691675.1_01892
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVEDLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTDLVELADREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIVPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR
+>GCF_005280335.1_00574
+MTPPHPAAAPAERPGADPATGPAQDPALRLRGVRLGYGRPDTPDTVGPVDLDVPAGRVTA
+LIGANGCGKSTLLRGLTRQLPLRGGSAEVLGRDLGAYSAREYARTVALLPQHPVAPEGMT
+VAQLVQRGRHPHRGLFGTTGADDDAAVARALRHTDLEKLADREVAELSGGQRQRAWLALV
+LAQRTPVLLLDEPTSYLDLAHQVEVLDLVRGLTRPDGDEEPVTVVAVLHELSLAARVADR
+LVALRDGRVAAAGTPAEVLTPAVLAEVFDLDADVRPDPLLGHPVVLPRGAADRGAPLPSP
+TTQETR
+>GCF_020097155.1_00501
+MTSSPPTPAAPSTAPAPALRLRGVELSYGPASAPPTVGPVDLDVPAGQVTAVIGANGCGK
+STLLRGLTRQLPLRAGTVDVLGRDAAGMSARDYARTVALLPQQPVTPEGLTVAQLVERGR
+HPWRGLLGGRAAGDDAAVAAALARTGLVDLAARDAATLSGGQRQRAWLALVLAQQTPVVL
+LDEPTSYLDLAHQVEVLDLVRTLPDPRAVGARTVEAAGGVVGGGAGTEAGPPPRATVVAV
+LHELSLAARAADHVVAMAGGRVVATGTPAEVIVPEVLAEVFGLDADVVPDPLLGHPVVLP
+RGRGDRA
+>GCF_023573625.1_02123
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVEDLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTGLVELAEREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIAPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001707.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001707.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2078c269cfbe098f749ecd15bd2c211de118e34d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001707.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02185
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED
+>GCF_003691675.1_01899
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED
+>GCF_005280335.1_00565
+MNGQDGGQGRTTTDGATGREAPVPFETEIQVRWSDEDRYGHVNNARLLTLTEEARVRATR
+AWSGVTPGRDVHRVVRAMEVQYEAPVVYGPELTAKVWIARIGTSSYTLRHELWQDGRRCV
+LCDAVFVHVDPETGRSVALAEDERVTLERVLIPAEADAT
+>GCF_020097155.1_00490
+MSDSQPRPYEGVLDLRWSDMDLYGHVNNVRILTLTEEARVRALKAWDEGDVGRDVMRVVR
+AMTTEYERPVEYGPELTAKVWVRALGRTSYTLHHELWQEGVRCVTCDAVMVHLDPETGAP
+LPHDDARRARLQAVLVPAEG
+>GCF_023573625.1_02130
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLTEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001708.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001708.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6efaa969f100355e408d0abfd030cb256b7b4949
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001708.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02186
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPAFEDEPTVEPGEARPGDAPGASTA
+>GCF_003691675.1_01900
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPVFEDEPAAGPGEARPGDDAPGASTV
+>GCF_005280335.1_00563
+MEQDRDPEESSQSTAIETLRGTPVSELTHLPPAMAGALDRLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKTPESILRKAASRGLSMDLDALRSNVTDIAGARV
+IVSFARDVYEVFRLFTRQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPVHLSTGSIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGAVPPDITTELIAAARVAADLDTRMERLSDQVRQTD
+KDDDAAASWEDDGGPAFEDEGDDDGPDGDAPGTSTG
+>GCF_020097155.1_00489
+MPRDVDHPPPADDPAPVERPAPGGRGVTSASTALEALRATPLTDLTQLPGEVADALASLR
+TDFERFDLEYRSALLQVETRLETLQDEFTHLHEYNPIEHIATRVKSPESLLRKAASRGLS
+LDLDALRSGVTDIAGARVIVSFTEDVYRVFRQFTSQPDIRVLEVEDYIRDPKPSGYRSLH
+CLVQVPVHLTTGTVPVTVELQFRTIAMDFWASLEHKINYKFAGHVPPAITTELAAAARVA
+HDLDARMERLHQAVHDAGAGPDEHDDEDDWVGHA
+>GCF_023573625.1_02131
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIQVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPAFEDEPAAGPDGTDPGEARPGDDAPGASTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001709.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001709.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed0253da9ff6d696db5f9fe16a85ef06b16f70a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001709.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02189
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG
+>GCF_003691675.1_01903
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG
+>GCF_005280335.1_00557
+MSIPATEVEARWNEASEPFTAVVRAVRDWDAATPCEGWDALDLLDHVVGAERDFAARQGR
+EVPLFDGSRQQTANQWTKHSAALSALAGDEEFIMKPMHTALGEMTVGEAMIRFHAFDLIV
+HRWDLARSQGVDERFTDAEMDCIEESLDLFGDAAYTPGILAQPVPVADDADRQARLLGRL
+GRRA
+>GCF_020097155.1_00484
+MSTQTDVEQYWMDCVEPFTDVVRAVEDWDASTPCKGWSAQDLLDHVVVAERDFAARQGRE
+IPVFDGSRNELWTQWVKHASAVTALAGDETFIMQSLHTATGDMTVGEALLHFHGFDLLVH
+RWDLARSQGRDEQWTDEEMDRIERALDSFGEQAYQPGILADPVPVADDAPRQVRLLGRLG
+RRA
+>GCF_023573625.1_02134
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAALSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001712.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001712.fa
new file mode 100644
index 0000000000000000000000000000000000000000..758d03440fd2a9b4abeccbd5d9da0ff4569a719e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001712.fa
@@ -0,0 +1,75 @@
+>GCF_002008305.4_02195
+MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR
+GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPQQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGTASAEDGASRLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGAASAQDGAGRLADGLDQAREGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVVPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA
+EDGAGARIADAQTALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDGGLAQLQDGAGELRAGLGTLDDGAHELASGLSDGADRVPALTEDERDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLVLQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGPDQRF
+WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA
+>GCF_003691675.1_01908
+MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR
+GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPRQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGTASAEDGASQLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGAASAQDGAGRLADGLDQARGGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVIPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA
+EDGAGARIADAQAALAELAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDGGLAQLQDGAGELRAGLGTLDDGAHELASGLSDGVDRVPALTEDERDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLVLQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGPDQRF
+WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA
+>GCF_005280335.1_00549
+MLFRYELRRFRRGLPLLALLFILLVPAIYGALYLSANWDPYGAMNRLPVAIVNEDEPVQR
+GDTTLRTGADMTARLKEDHAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPQQAQITLRRDDANGFVIGSVTASSQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGSASAVDGASQLEDGIVQAHDGSGRLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGATSAQDGAGRLADGLDQAREGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVVPGLDRVIERQDAVAADVAAVDEDVQRVAEVAGTA
+GDGAGARIADAQAALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDDGLAQLQDGAGELHTGLRTLDDGAHELASGLSDGVDRVPALTEDQRDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGHRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLILQLASTGGTYPAEVLPGFFRALHPFMPMSYSIEAFRNAISGGLDQHF
+WVPVVVLMGVGAAALALDVLVVRRRRRFRMKDLHPALQA
+>GCF_020097155.1_00478
+MLFRYELRRFRGVLPTIALLFIVLVPTIYGALYLSANWDPYGNLSSLPVAIVNEDRPVES
+DGKTLTTGADITEELVDQHTFDWHETTRDDAEAGLRDGRYYLVMEIPEGLSADLVSANTS
+DPQQAHITLRRNDANGFVIGSVTSSSQSKIENAVDKAAVEAYFKAVFENLATIRQGMADA
+RDGAGRLADGAGQADDGAAQLADGIVQAHDGSGQLAQGASDAQDGAGQLADGAGQLKDGA
+DQLAAGATSAKDGAVQLQTGIGQAREGSQKLADGAGQIAAKVPDLRDGATALSNGLTQLD
+TGSADLADGAHQVADGTQQLYDTVIPGLDAVIERQDKVASDVATVNQDVQTLNDAVATAG
+SGAGGDIDTASEQLQALAESNPDIAVAPEYAALQQSLTDAKEKAGSATSTAQDVADRSAA
+VNSRVQGFVSEDVAGNAKADITKLNDGAHAVAEGADTLHAGIGQANTGAQALADGVGRFA
+DALDQLAAGATALDDGLAQLEDGSGRLVDGLGKLETGAGDLADGAGRLDQGAGELQTGLG
+KLSDGATSLDSGLAQLETGSGDLKTGLDSLSDGATQLHDGLASGTDKIPALSEDAADEAA
+LVMSRPVQVDMDVLNPAGVYGRGVAPLFFSIALWVFGIAAFNVMRPVNGRLLAGRRNPLL
+LALSAWLPVGLLSVVGSLVMLAATVPLGIDPVHPWHLVGLVVFTALAFSLFAHLVMTALG
+TPGSAVLLVTLILQLGSAGGTYPADVLPPFFRWVSPLMPMTHSINAIRYALSGGQPAQFW
+GAVAFLAVFGAACLFLDMAVVRRRQRFRMKDLHPALEK
+>GCF_023573625.1_02139
+MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR
+GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPQQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGTASAKDGASQLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGAASAQDGAGRLADGLDQARGGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVVPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA
+EDGAGARIADAQAALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDDGLAQLQDGAGELHTGLGTLDDGAHELASGLSDGVDRVPALTEDERDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLILQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGLDQRF
+WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001715.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001715.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8f5dd73361db57138c450531b1e5d564148ae01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001715.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02198
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVVGGPLGVLLGSVVARRVDPAKARVLAICLAGV
+GGTVALVRGVAGTLG
+>GCF_003691675.1_01911
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVVGGPLGVLPGSVVARRVDPAKARVLAICLAGV
+GGTLALVRGVAGTLG
+>GCF_005280335.1_00545
+MSVVVLTGADGGARLGHTAPMDMSLVMLVPALVALAALMVGGALQRVSGMGVGMIAGPTL
+SLLLGPVAGVSLANVAAVVSAVLLFALLRRHVDWGRFLRLAPLLIVGSFAGAWAVRSLDV
+HALEVLLGGSVLVAIAASLGLQRRFTASGSAPAALAGTAAGFMNTTAAVAGPALAVYAVA
+SRWEQRSWAATLQPIFLLANLTSLATKSLFGTAVPASVDVHWTVWTAVVVGGPIGVLIGS
+RIAPRVNPSRARLLAICVAGVGASVALLRGIVGLLA
+>GCF_020097155.1_00481
+MAATAAAAVRTAERARSGGGVTVPVWHAPAVASRRRGARAHTAGVSISLAAVVFLCVAVG
+GVLQRISGMGVGMVAAPTLSLLVGPVAGVTMSNAAASVSALILFWMLRRHVDWPRFLRLA
+PLLVVGALAGAWTVRVMDHAWLEVVLGACVLVAIAAVLGLQDRLTLRGSAAVFGSGAVAG
+FMNTTAGVAGPALAVYAVASKWEQRSWAATLQPIFLTANVTSIVLKASLGATAGAAAVPW
+WAWAAAVAGAPAGIAVGSRLARRVDPGRARRVAVTLAGVGAAVTLVRGLASL
+>GCF_023573625.1_02142
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVAGGPLGVLLGSVVARRVDPEKARVLAICLAGV
+GGTVALVRGVAGTLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001716.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001716.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c03ca745ca2af039dc36c4cc443504bfda90ab7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001716.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02200
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
+>GCF_003691675.1_01913
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
+>GCF_005280335.1_00542
+MLAAVLAFALIGAVLWAALALGPDGVPGQQGSRRPAASTPAPPTVSAEGFAEPVRGRVTS
+RFGPRPNPFGEGSAPPSTDTDALTDHTGVDLGGVPEGTPFHSVSDGRVLFVEAGEDAGGN
+LLAVDSGDGHVWRYLHAAPDSTVVNAGQRVSAGDALAGVGQTGTATGVHLHLELRVDGTP
+VDPEPYLRERGVELGSSWERPRRR
+>GCF_020097155.1_01787
+MKKLAVIAAVLVLFSPALLLLGVGMIFSPGANASCTTSTTGPSVVGPVPDSLDVTTADGQ
+TFTLNTTQLTHAATIIQTGSQIEGVTRDGLQIALMAALTESNLRMLANTSVYPDSGNHPN
+DGDASDHDSLGLFQMRPQAGWGTVPDLMDPGYQARAFFGGPTGPNHPSPRGLLDIPGWQT
+LSKGEAAQAVEVSAYPDRYANYEPVAEQILTTLTTPTADSPQLPETGRVVFPLPEGTWVA
+TSPFGMRVHPITGENKLHTGADYSAPDGTPVLAAADGIVTHASMSGGYGGLIIIEHTTGG
+QKIATAYAHLWETGIHVNVGDQVTAGQHIGDVGSAGYSTGAHLHFELRQGGSDGEFTDPQ
+PWLDQHTSGNLPAPTTPVEQEGCNPVATQPAPPQGPDAGDPDRKVDDPTTDGQITARMLH
+VYTQALTAYPDSSWACYSPRPGTKSEHPLGRACDVTFGNAIGSRPTPQQLEAGWALTNWL
+QDNAETLGVEYLIWQGQIWSLARDAEGWRPYNGGGMHDPTDVTGGHYDHVHITVKEGS
+>GCF_023573625.1_02144
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001718.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001718.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8adeb9d444e656c24ab4188c44899f1de847240
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001718.fa
@@ -0,0 +1,27 @@
+>GCF_002008305.4_02202
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A
+>GCF_003691675.1_01915
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A
+>GCF_005280335.1_00541
+MLPAPTARLRFREMTEADLDAMAALLGDPAVMRFYPAPRTREQAAEWIAGNRRRYAQDGH
+GLWVIETLPEHSDDGEPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACR
+DHARDALGHHELVAIIHPENSVSRRVAEKIGLREAEQDFTGAAEARETMGLASRTVMAMR
+F
+>GCF_020097155.1_00472
+MTQPIPRHPDPGNTGTDALDDVVREHMLLLRRAVHGLGAYRRPEALDRSAVLLLARLEAQ
+GPMTMAELAAAFGLDVSTLQRQIGAAQRAGFVERFRDPAGGQARLHRATDAGRAALEGEL
+AARRAAVAEVTRSWPAPDVAALARLLRRFNEGSEELREQPWPRERPEAPGAAAVPAGTAR
+LRFREMTEADLDVLVGLLGDPEVMEFYPAPKTRAEVADWIAWNRRSYAEHGHGLWIVETH
+AGAFVGECGLTWQRVNGERRLEVGYHVAPVLQGRGYATEAAAACRDHARDVLGAPELVAI
+VHPENTASRRVAEKIGMEVLEEDRTGVDASYLEAIGAEARTVLGMRLA
+>GCF_023573625.1_02146
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001719.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001719.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fce12485c1706e0fdcd61dc94bd4327a6496dff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001719.fa
@@ -0,0 +1,37 @@
+>GCF_002008305.4_02206
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG
+>GCF_003691675.1_01919
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG
+>GCF_005280335.1_00539
+MTSPRPESDWRPPWQDLPADLPGRLAHALPGIMERIIQTVPDQIPAYAAARDGRYGKNLT
+LGVTTALEQLMSLPGTSRPALSAQSRELMARLGAGEFREGRSMDALLGAYRTSARIVFRD
+LSAECARLGMDMSVVIELGESIWAYIDELSAVSAQAYAEAQSAQAGVRELHRTALAAALV
+RGGAEEKEVERLAALADWRVPARLAVVALPPDAGQAVRARLGRGGLVVERDSEVVAVVGA
+DAPARRRRLLRILAGTAAVVGPAVEWPLAPHSYRVARTLAGQEAARRAAEQRAAARPEGD
+GSAADGPGAEEAVGFEPVGGADPAPGTPILAEEHLARVVLGAEPRVVAELAERVLAPLAE
+LTDAKRAVLEQTLLSWLVHWGQRAPIAAELSVHPQTVGYRVARLRELFGDALEDPDARFD
+LELVLRARAGGMAA
+>GCF_020097155.1_00469
+MVLSAPPRSPVVTRRLLAALQGTGAVVGPEVDALEVARSLHVARAVLARRDALSGVAPGA
+AVLAEEHLADVVLGAEPEALRRLSERVLAPLDGLSDAKRATLEATLAAWLAHRGARGPMA
+AELNVHPQTVGYRVGRLRELFGGALDDADARFDLELALRSRRGQG
+>GCF_023573625.1_02150
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001720.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001720.fa
new file mode 100644
index 0000000000000000000000000000000000000000..272df66667582f9965ad1f8eab3e5c14059875e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001720.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_02208
+MTQTPTAPDRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPRTAESRAAATTP
+GLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRVIRWQRRL
+ELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIHSTTWEWD
+FVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWRPRHLLNPVINAGLAPIF
+EWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVLTGSGKAA
+LVGTLLANGLRNIWAHAVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSANISGSKL
+MHFMTGNLSHQVEHHLFPDLPSSRYAEVAPRVREICARYGLPYTTGPLLRQVGSAWKKVF
+RLALP
+>GCF_003691675.1_01921
+MTQTPTTPSRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPHTAESRAATSRS
+TAAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRV
+IRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIH
+STTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWQPRHLLNPVIN
+AGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVL
+TGSGKATLAGTLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSA
+NISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPQVREICARYGLPYTTGPLLRQVG
+SAWKKVFRLALP
+>GCF_005280335.1_00537
+MTQTLPATERTGATAPDDLSLAIPGTTVRGRTARVLPEDRPDTTSWAPQTADAGTDAAAP
+AASETPEAPTADAATRPAANAKPGLLGVVGSPAVRPPGAAHLTDEQVAELGRELDAIRDD
+VLSRRGASDAAYIRRVIRLQRWLEIGGRAALLNARHPAAFVAGTTMLTVAKIVENMEIGH
+NVLHGQWDWMRDPDIHSTTWEWDFVTPSRAWQNTHNDLHHRWTNVIGKDRDVGYNVLRMD
+ESEPWRPRHLLNPVINAGLAPIFEWGIALYDLELDRVHAGEKSRKELMTDLRSVGVKASR
+QFAKDYVATPAVAEFLTGSGKAALVAGLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVD
+GETRGDWYVRQMIGSANISGSKLMHFMTGNLSHQVEHHLFPDLPSNRYAEVAPKVREICA
+RYGLPYTTGPLLKQVGSAWKKVFRLALP
+>GCF_020097155.1_00468
+MIRSATAGKIIENMEIGHNVLHGQWDWMRDPDIHSTTWEWDFVTPSSAWQHTHNDAHHRW
+TNVTGLDEDLGYNVLRMDEAEPWEPRHLLNPVINAILAPFFEWGIAIYDLELAKVRAGEK
+PVADLRRDLASVAVKAVRQLAKDSLATPIAAELVSRSGSAWRKVFRLALP
+>GCF_023573625.1_02152
+MTQTPTTPSRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPHTAESRAATSRS
+TAAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRV
+IRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIH
+STTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWQPRHLLNPVIN
+AGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVL
+TGSGKATLAGTLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSA
+NISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPQVREICARYGLPYTTGPLLRQVG
+SAWKKVFRLALP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001721.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001721.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dfb495289d80ad00c09e878554e1a06ea32afdc8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001721.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02216
+MPAQPSPSGHTVHLSTSGVDARITPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA
+HVLDAASPAGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLALDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL
+LVNIGDDAGLRFLGAELGALEEAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLGEA
+GCTERLAAAGPHPAAVLDPAESAALADRIRRA
+>GCF_003691675.1_01929
+MPAQPSPSGHTVHLSTSGVDARIAPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA
+HVLDAASPTGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLALDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL
+LVNIGDDAGLHFLGAELGALEEAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLGEA
+GCTERLAAAGPHPAAVLDPAESAALAARIRRA
+>GCF_005280335.1_00525
+MRAHPSPTGRTVHLSATGEDARILADELGGSVLEIGGAVQSHVDPADPTALRYEYLRRMA
+NVLDGVAPAGAPLRVLHLGAGALTLPRYVQATRPGSEQTAVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLLMDGERFDAVVLDIGTGEDGAAHLTGAEFYGELLGLLTAAGVL
+LVNIGDDDGLRFLGAQLRHMEAACAEAGVPGPWTLASAAMLERLELGNAVLAAGPALRGD
+GAAAGGDAGPEEDGGPLTPAALLARGPHPGAVLDEAASADLARRVAGR
+>GCF_020097155.1_00467
+MPTQPQDDASSPAPSPTARTVHLAASGVDARILPDPHAGGWMLEVGGAVQSHVDLADPTQ
+VRYEYLRRIANVLDALAPAGEPLRVLHLGGGALTLPRYVAATRPGSVQTVVDLDRELMGL
+VLEELPLPADADVYVVVADARAVVDDLLDPLEGESQAGAWDAVVLDIDTDAGAVAHLTGA
+AFHAELLELLAPGGVLCVNIGDDDGLAYLATQLTALEAACADAAEGAGVPGPWTLGPNSV
+LERRELGNAVLVAGPGLAGMDAAALHAAGPHPAVVLDAHESAALAERITAAP
+>GCF_023573625.1_02155
+MPAQPSPSGRTVHLSTSGVDARIAPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA
+HVLDGVAPAGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLAMDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL
+LVNIGDDAGLRFLGAELGALEKAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLREA
+GCTERLAAAGPHPAAVLDPAESAALAARIRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001722.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001722.fa
new file mode 100644
index 0000000000000000000000000000000000000000..add9483c8a0d6e731de79b61773340759d7cef1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001722.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02219
+MPPEPSAPSGERGPARPHPADVAARPDAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEAGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPARRR
+>GCF_003691675.1_01932
+MPPESSVPSAERGPSRPRPAAVAARPEAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLAVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGMIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEAGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPARRR
+>GCF_005280335.1_00527
+MSARAARAARAGEGRQGSDAPAGADARPGAAGSALLFAMAIVAGSTIPVQARLNSALAER
+SGDPTLAAVASFAAGLVLVAAVTVLTPAGRRGLRAVRPALAAGRVRWWYLLAGTIGGAMV
+FSQATTVGLIGVAVFTVAVVTGQLIGGMVVDRLGLTPAGVRRMTPRRLAGAALALACVVL
+VVAPQLGARGDGGPPLWLLVALAPLAVGLATSIQQTLNARQAAAYGSVLPVTTVNFVAGT
+GILALVHLGGRLGGGVGGTLPGDWWLYLGGPMGVVFIAFSAYLVPRVGAFLTMLGLVSGK
+LLGSLAVDALAPVGEVAASPWTVVGTLGALAAVVLASGAARPARKG
+>GCF_020097155.1_00465
+MPASSPALTPAPRSGATTALLFLLALVAGLAMPVQGRVNSALSLAVGSPALAACASFATG
+LAVLVLATLLLPSGRRGAARIPAAVRNGDVRWWQLLAGTIGAAFVLTQAWTIPLIGVAVF
+TVAVVTGQMLGGMLWDRLGWTPAGVQRISRRRLFGALLAFCAVTAVVWPRLQESGSPGAW
+LALAVLPLAAGVATSGQQAMNGHQTAHFGTPLPPTLVNFAAGTAVLAAATAVAAGTGAGM
+GPLPAAWWMYLGGPLGTVFVGLGAFLIPRVGAFLTTLGMVAGQLVGSLLLDVVAPAPGAQ
+VTWLTVVGTLGALAAMVVASSPQVPAGLRASRRRARRG
+>GCF_023573625.1_02158
+MPPEPSAPSGERGPARPHPADVAARPDAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEVGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGMPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVTLASWPARRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001723.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001723.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20decdd2c519f02d84f9b3af20cc95a0c60b4bcf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001723.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02220
+MKHEIVLTRGDLTLRPLTPDDGPALRELVDAAMWAGNSAPLPVDGAAMSAHLAELSEREG
+TFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRGG
+LEARLAA
+>GCF_003691675.1_01933
+MKHEIVLTRGDLTLRPLSPTDGPALRELVDAAMWAGNSAPLPVDGAAMSAHLAELIEREG
+AFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRAG
+LEARLTA
+>GCF_005280335.1_00515
+MSHDLHLTHGPIRLRPLTPDDAPRLRAIVDEASWAGMSTPLPETDAAMAEHLRELMGRPG
+LQAFAVERDGEFVGRTALYDPVPTVRVDVGHTVYARPVWGTEVNPACKLLLLGHAFEELG
+VARVGLRCDHRNTRSHRAILRLGATFEGTLRAFRRAADGTVADADHFSVTAPEWPAVRAG
+LETRLGA
+>GCF_020097155.1_00462
+MPAAQLPADLLLEHGAVRLRPLTLDDAPRLRALVDAGSWAGMSSPLPTSDEAMAAHLAQL
+MAREDLTAFAVERDGEFVGRTAYYEHVPGVRVDVGHTIYAREVWGTEVNPACKLLLLRHA
+FEALGVERVGLRCDHRNTRSHRAILRLGATFEGTLRAFRPAADGTVADVDYFSVLAAEWP
+AVRAGLEARLAGSAPAD
+>GCF_023573625.1_02159
+MKHEIVLTRGDLTLRPLSPTDGPALRELVDAVMWAGNSTPLPVDGAAMSAHLAELIEREG
+TFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRAG
+LEARLAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001724.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a1ef855c490801fcd6ca4127e4f5538046254d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001724.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_02239
+MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLAARERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD
+RDGLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAEGRPTGLL
+EETAMSLVTRLLQSESHEHIGACLARASQGYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQTMVTLDALHSVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV
+IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER
+AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA
+LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRVVPSDQIAAIDVVATAVGGEFVH
+GGL
+>GCF_003691675.1_01941
+MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLTARERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELGPGAWVTCTGFDPGHLTGPQPD
+RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL
+EETAMSLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQTMVTLDALRPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV
+IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER
+AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA
+LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH
+GGL
+>GCF_005280335.1_00506
+MQLDLIVENAHLLTGDPARPEATRLGVWRGAVVGVDEELDGLGARERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGAHTAQEVYDRIRARAAELTPGAWVTCTGFDPGHLTGPQPD
+RDGLDAAAAGRPVLIRHNTGHAFTVSGAVLFLAGVGEQVMQQPEGGRIITDAADRPTGLL
+EETAMNLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGIAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQAMVTLDALRPVDGHADDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTADYCGHGHGRGYLQQDAGEMRRECLGAAAAGWSLALHAIGDAALDFALDV
+IAEARARFGRPVMPHRVEHGGVVRDDQVARLAELEVVMATQPNFISAFGGSVRERIGPER
+AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLDVIQDFVLRRTETGEQYGPDLERLTVAQA
+LQAYTVGSAEATGWGGRKGRLVAGQLADFTVLSADPRAVPSEEIAAIDVVATAVGGEFVH
+GGL
+>GCF_020097155.1_00442
+MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLAAGERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD
+RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL
+EETAMSLATRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQTMVTLDALRPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV
+IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER
+AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA
+LHAYTVGSAEATGWGGRKGRLAAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH
+GGL
+>GCF_023573625.1_02171
+MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEQLDGLATRERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD
+RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL
+EETAMSLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQTMVTLDALHPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV
+IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER
+AVLSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA
+LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH
+GGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001729.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001729.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45d030055fa05893635982b3efbf34a77d981df1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001729.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_02247
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLTDMVGQLARGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGPDGESLLAEHVPGVEEGPAWVQIAIDEALPAFGPSFVA
+IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQTSAFVWS
+LADFGVGLYTWVNIVALILLSPVAIRLFKDYDRQRRAGQDPVLDPAAIGVRNARLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG
+>GCF_003691675.1_01949
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLRDMVGQLVRGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGTGEGPPIVEHLPGVEEGPAWVQIGIDVVLPSFGPSFVA
+VAVFLFAFTTLLSFAFYAETNLAYLIPNKKAQRICIAAARLLLAASMVIGSVQTSAFVWS
+LADFGVGLYTWVNILALVLLSPVAIRLLKDYDRQRRAGQDPVLDPAAIGVRNAHLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG
+>GCF_005280335.1_00499
+MEQFLAGANAIMWSLPMVFGLLALGLYFTIRMGAPQLRRIPDMIGQLVRGGSSSAGISSF
+QAFAMALGGRIGVGNIAGVATAISLGGPGALFWMWVTALLGAPVALAESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVITGPQIQANAVTAATTQAWGWDPLW
+VGLAMAVLFCVIVFGGMHRLGRTVGLVVPFMAAAYIIVGVVVVALMWQQVPAMFGLIFTS
+AFAADSLYAGMLGAAISWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAFVD
+TLFVCTVTGLMILSTNSFNVLGPDEETVLVEHVPGIEAGPAWVQTAIDSVIPAFGPAFVA
+VAVFLFSFTTLLSFAFYAETNLAYLIPNKSVQRACIAVARLGLAASMVFGAVQTSTLVWS
+FADFGVGLYTWVNILALVLLSPVAIRLMKDYDRQRRAGQDPVLDPRAIGVRNATLWEQIH
+DEYERTGDVTAALDHVADTAPDTRAISVVRSHGERGQG
+>GCF_020097155.1_00437
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLKDMVGQLVRGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGPDGESLLAENVPGVEEGPAWVQIAIDAALPAFGPSFVA
+IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQSSALVWA
+FADFGVGLYTWVNIVALILLSPVAIRLFKDYDRQRRAGQDPVLDPAAIGVRNARLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVRGGPERGEG
+>GCF_023573625.1_02179
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLTDMVGQLARGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQIPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGPDEESLLAEHVPGVEEGPAWVQIAIDEALPAFGPSFVA
+IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQTSAFVWS
+LADFGVGLYTWVNIVALILLSPVAIRLLKDYDRQRRAGQEPVLDPHAIGVRNARLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001730.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001730.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2d4c3976afc52e881c64110a2b9391368f7dca8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001730.fa
@@ -0,0 +1,29 @@
+>GCF_002008305.4_02254
+MMGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA
+LPPLTEWLSRGIRHVAGGHRRGTHSLVGVAAFTAIATAAASIQVPIAGHVYTPGQGVIAA
+FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT
+NNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLVP
+LAARGVAALF
+>GCF_003691675.1_01954
+MMGPSHAATGAAAWLALTHWQSPIAALHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA
+LPPLTEWLSRGIRHVAGGHRRGTHSLVGIAAFTAVATAAASIQVPIAGHVYTPGQGVIAA
+FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT
+NNGVALLWPLSPEPPTRLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLIP
+LAARGVAALF
+>GCF_005280335.1_00477
+MGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHAL
+PPLTEWMSRGIRHVAGGHRRGTHSLVGIAAFTAIATAAASIQVPIAGHVYTPGQGVIAAF
+LAAVAAKALRLLPNRGWRAAWALGILVAGAATVLSDGLWWIPASVAVGVSVHILGDALTN
+NGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWAFVSVVTAFTVVRAVRLVPL
+AARGVAGLLGAGAPS
+>GCF_020097155.1_00432
+MSTPPAALALFLPRGPPAGPRGCGDAAWLALTHGQSPVGVRHLPAELQLLGAVTTAGAAM
+ISDWDYPRATAIATAAASIHVPIAGHVYTPGQGVIAAFVAAVAAKALRLLPNRGWRAAWP
+LGILVAVSATVFSDGLRWIPVSVAVGVSVHILGDALTNNGVALLWPLSPEPPARLWWWQS
+SGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLVPLAARGAALF
+>GCF_023573625.1_02185
+MMGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA
+LPPLTEWLSRGIRHVAGGHRRGTHSLVGIAAFTAIATAAASIQVPIAGHVYTPGQGVIAA
+FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT
+NNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLLP
+LAARGVAALF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001731.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001731.fa
new file mode 100644
index 0000000000000000000000000000000000000000..daa9e06aa12113d3a0a6af58152488d6c550c322
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001731.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02255
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMNGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>GCF_003691675.1_01955
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>GCF_005280335.1_00476
+MNGAELADSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPIAVGVTVGSLTAM
+VSAVLIVRLMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVFAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>GCF_020097155.1_00431
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTAGSLTAM
+VSAVLIVRVMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>GCF_023573625.1_02186
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001732.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbf3bd380a6112c8f1bf738392022a81b9e2fced
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001732.fa
@@ -0,0 +1,17 @@
+>GCF_002008305.4_02256
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
+>GCF_003691675.1_01956
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
+>GCF_005280335.1_00475
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTTSHHLLQ
+HLPLLFVPAGVGVVAVLGLIGEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKENA
+Q
+>GCF_020097155.1_00430
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVITASHQLLQ
+HLPLLFVPAGVGVVAVLGLIQEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKEDA
+Q
+>GCF_023573625.1_02187
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001733.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001733.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40bd46c168d4c1422558c5f81ef8a5e9c7bfdc67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001733.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02257
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR
+>GCF_003691675.1_01957
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR
+>GCF_005280335.1_00474
+MHLIILARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVRLSTEAGISRT
+PAREALLQLESWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGCAADAQRALQAHLDAAGTGVVVPGLPTVSQPEA
+GEPR
+>GCF_020097155.1_00429
+MHLIILARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTDAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIAMCGNAAFDEIMGTFAPRLARLIH
+AATGGSVDAARRLLDGHVQICAQLAAGRAADAQRALQAHLDAAGAGVVVPGLLPVGSSEA
+GEPR
+>GCF_023573625.1_02188
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001734.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001734.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b05a2c171a0d19edecbafbff2e1611246ff2143
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001734.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_02268
+MPTLRTVPLSAATREDHLARLRATSPEAPLDILVVGGGSTGVGAAFDAATRGLDVGIVEA
+RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH
+KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ
+FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAGADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD
+EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVVATYAGLRPLLQPV
+TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTERI
+PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI
+AGEIRAYKNLVAARLRGETAHDDVTAAAALAAADADAAPTP
+>GCF_003691675.1_01961
+MPTLRTVSLSAATREDHLARLRATSPEAPLDILIVGGGSTGVGAAFDAATRGLDVGIVEA
+RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH
+KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ
+FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAGADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD
+EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVIATYAGLRPLLQPV
+TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTEHI
+PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDGDPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI
+AGEIRAYKNLVAARLRGETAHDDVTAAAALAAADAAPVHGKEPVHGHDLPA
+>GCF_005280335.1_00462
+MGGGSTGVGAAFDAATRGLDVGIVEARDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEAL
+RERDLLLTQTAPHLVRPLRFVFPFFHKVIDRGFIGAGVTMYDAMQSLGRRRAMSAHRHLS
+RRSMAATFPSLDDEKIVGAVEYADAQFDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGD
+DGRVQGVRVREETSGEEFDVHARAVILAGGVWTQEQQELAEADGGLEVLASKGAHITVPR
+DRIRADAATGVITKTEKSVLFLIPWDEYWVIGTTDTPWAEDVAHPAATADDIDYILEHAN
+AVLKEDLTRDDVIATYAGLRPLLQPVTGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTY
+RAMAEDVVDFVVRETHPTRPSLTERIPVLGGLGYSEIEAEADRIAADYGLDEARVDRLLF
+RYGTVLRHVLDLIDADPSLSVPLAEAPRYLRAEIVHAARAEGVVHLDDVIERRTRLSTEV
+RDRGVAAAEEIASLVAPELGWDEERIAGEIRAYKSLVAARLRGETAHDDVTAAAALAAAD
+AASTH
+>GCF_020097155.1_00493
+MPTLRTVELSPATRADHLARLRAADADHPLDVLVVGGGSAGVGAAFDAATRGLDVGIVDA
+GDWAGGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTRTAPHVVRPLRFVFPLEH
+ARDRGWIGAGVGVYDAMQSVGRRRAVGGHRHLGRKALAETFPGLDPEAAVGAVEYADAQF
+DDARLALLLVRSAVDLGAAALNHAPVVGYLKDGAGAVVGARVRESLTGEELQVHARAVIL
+AGGVWTQEQQELAGVDGGLEVLASKGVHVTVPRERIAAEPGVGVITRTEKSVLFVIPSDE
+HWIIGTTDTPWRQDVDHPAATAADVDYVLEHANAVLSEDLTRADVVAVYAGLRPLLQPAA
+GADDASTKVSREHTVTELAPGLTAVAGGKWTTYRAMAEDTVDFAVRDLFPTRPSLTAHTP
+VLGGLGYAEIAARAAEIAAERGFDAARVDRLLRRYGTLLPHVLALVDADPALGEPLPGGE
+AYLRAEVVYAARAEGAVHLDDVLERRLRLSTEVPDRGADAASEAAALVADVLGWDAARRD
+AEVAAYRALVAARRRAEGLDDDAAAAAELAAAGERAGVVPVTSRETVTPEEKGGAR
+>GCF_023573625.1_02200
+MPTLRTVSLSAATREDHLARLRATSPEAPLDILIVGGGSTGVGAAFDAATRGLDVGIVEA
+RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH
+KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ
+FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAEADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD
+EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVVATYAGLRPLLQPV
+TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTEHI
+PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI
+ADEIRAYKNLVAARLRGETAHDDVTAAAALAAADAAPTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001737.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22a625e1956923db28b5a83b2d59fc62a54e8efa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001737.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_02285
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTCVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRRLPATPILASVAEEAPAPEAPADDA
+>GCF_003691675.1_01976
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA
+>GCF_005280335.1_00452
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+ILPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGKDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA
+>GCF_020097155.1_00405
+MKLAILSRSLRAYSTQRLKSAALDRGHDVKVLDTLRFGIDLAGDEPDMMFRGKPLSSYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRASQILSRHGIAQPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGKDVRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVEQVELSEEYAETAVRAAHIM
+GLRVAGVDMLEGEDGPLVMEVNSSPGLEGIERATTLDVAGAIVDYIADQAGFPEVDVRQR
+LAVSTGYGVAEIAVLAGSDMAGQSIEDSGLLEKDLQVLTLHRGASVFPNPADSKVLEEGD
+RLLCFGKTENMRALIPARSQRPKRVKKLPKNPIIEAPPAEPAVRPDAESGES
+>GCF_023573625.1_02224
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001738.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001738.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5a749e837948468b5d08e299f7492d10ade6a9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001738.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_02286
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVIVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA
+>GCF_003691675.1_01977
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVVVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA
+>GCF_005280335.1_00451
+MSESKHTATAPHGVPPIDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGKAQERVVVVMPLTLAG
+RTFEAEVTLTHRDEMGFRMLVGRTALAAGGFHVDPAASYVGGQPPRGVRRRNRGRA
+>GCF_020097155.1_00404
+MGHVTESNHTPGRAAARPPHGDAHDAAPRPAQADADARPVREAATGVVVGWREWVGLPEA
+MTPWIKAKIDTGARTSALHAFGIERYTGADGAARVWFEVHPWQASAADARTVDLPVADLR
+AVRSSNGEVQERVVVMMPLRLAGRTVDAEVTLTHRDEMGFRMLVGRTALAKGFLVDPGAS
+YLGGQPPRGVRRRNRGHA
+>GCF_023573625.1_02225
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFARDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVVVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001739.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001739.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e8240621497a16728fd4199ac90f7e34435285f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001739.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_02287
+MSRRPARAPFAFGGVEVAAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIARCTVGIDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADVGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLHVALGERVSAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
+>GCF_003691675.1_01978
+MSRRPARAPFAFGGVEVPAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPTQLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIGRCTVGIDLHTGADRRSNLPQIRCDLEDSQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADIGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLDVALGERVNAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
+>GCF_005280335.1_00450
+MSRRPARAPFAFGGVEVPAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGNEVAGIEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIGRCSVGVDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAAREAGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALGMVDPAEVGL
+TEPGPAAVVDAPGPLPGEVPGDATTDVPEATDATGEDTEAVHADVVDGGQDAPHLVWHSS
+WVRARADGLVHLDVSLGERVAAGDRIGALYNSFGRRVAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
+>GCF_020097155.1_00403
+MSAPQKDPDRGGRTGDEAAAEKATGRRRASRAPFELAGVEVRPGRRHEVSLPVSRLVTGA
+EVTLPVHVLHGREDGPTVWVSAAVHGDEVAGIEIVRRVLERLKPSRMRGTLLALPIVNVL
+GVMTGDRYLPDRRDLNRSFPGAARGSLAARIAHLMMSEVVRRCEVGIDLHTGADRRSNLP
+QIRCDLEDPRTRALAESFGAPVLFHARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAI
+SPGVEGVLRVLAALGMVAAEDVGLATPVDAPAPLPGEVPEDRTTEVPEALDATGRDTGGV
+HADVVDGDLAAPHRVWHSRWVRARADGLVHLDVALGEQVTAGDRIGALYDSFGRRRSDVK
+AELTGVVLGRTEAPLVHRGDALVHIGELDGRPAGTFPAPSPGRRTAPSVAEGDPEAEAPP
+AATP
+>GCF_023573625.1_02226
+MSPRPARAPFAFGGVEVAAGRRHELSLPISQLVTGADVTLPVHVLHGRDDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIARCTVGIDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADVGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLDVSLGERVSAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001741.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001741.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98f4554b234afb37388f0c2d19d55685ec468e11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001741.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_02290
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG
+>GCF_003691675.1_01982
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG
+>GCF_005280335.1_00448
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG
+>GCF_020097155.1_00400
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AIKNAREVALLPYAGAGRG
+>GCF_023573625.1_02230
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001742.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001742.fa
new file mode 100644
index 0000000000000000000000000000000000000000..627de632d1ccc312f92f13db8cf8b3a07b3ec379
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001742.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02291
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGFGGAPAGGGFGGNSDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF
+>GCF_003691675.1_01983
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGFGGAPAGGGFGGNNDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF
+>GCF_005280335.1_00447
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLKARSYDDRDGNRRTSWELDVDEVGPALKFATAKVTRA
+QRSGGGGGGGFGGGQQGGGFGGAPAGGGFGGNNDGGFGGAPQGGGWGGQQQGGGQAAPQD
+PWSGGGGGGGWDTPSSNEPPF
+>GCF_020097155.1_00399
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDEEALFVRCSVW
+REAAENVAESLTKGMRVIVQGRLKANSYQDREGNKRTSWELQVDEVGPALKFATAKVTRS
+QRGGGGGGGFGGGQQGGGFGGSPQGGGGFGGGQQQSGGWGQPSGGGQSAPAQDPWSGSGG
+GGWDTPSNGEPPF
+>GCF_023573625.1_02231
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGVGGAPAGGGFGGNNDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001743.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001743.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f561b8c9711ec40b51e09d4ce6b5e1a206f02bf4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001743.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_02292
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY
+VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE
+>GCF_003691675.1_01984
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY
+VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE
+>GCF_005280335.1_00446
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDKVDVWGRRKTAYEIQKKSEAIY
+VVVDFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE
+>GCF_020097155.1_00398
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVEKIDVWGRRKTAYEIQKKSEAIY
+VVVDFTAEPAATQELDRVLNLNETILRTKIIRPEEQKISAE
+>GCF_023573625.1_02232
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY
+VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001744.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001744.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b0f8b04de32f4a0e8a9169ee266ddc7b94ba5d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001744.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_02293
+MTPVTRDTVAELHAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGARALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALVPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA
+IAYEGTVAGGVAGVAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLTAAVREFFRGV
+>GCF_003691675.1_01986
+MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGPSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLAALEELAREHGGAEGA
+IAYEGTVAGGVAGEAADAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLAAAVREFFRGV
+>GCF_005280335.1_00443
+MTAVTRDTAPAPEMSAHVQDLAAFVTASPSSYHAAAEVARRLVAVGFTCLDEAADFPAAP
+GGYVVVRDGAALAWVVPTGAGSDVSDGAGAAGGSGAGAAVPVFRVLGAHTDSPGFKLKPN
+PATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQLAIH
+LDREVNDGLKLQRQRHTNPVVGALAPRGEGAGEAVADVSEGVDGRSAPLEQAAGAGAGVG
+AGAGEGAGAREGDGAGLEARAPGDVLSALAAAAGVDPAAVRGHDVMVADAQAPGLFGLAG
+EFFASGRLDNLSSVHAGLVALEELARANGGASGAIAYAGTVAEGVAGEAAGAPVIPVLAA
+FDHEELGSASRSGAAGPLLEEVMGRVLEALGVAGQGRARAIAGSWLLSADAGHLVHPNYA
+ERHDPVNHPRVNHGPLLKINANQRYATDAGGEAAFARWCGVAGVPFQEFVSNNDMPCGST
+IGPISATRLGIRTVDVGLGLLSMHSAREMCGVRDVEHLTAAVREFFRGV
+>GCF_020097155.1_00396
+MSTVTSESTVTAAVPGAPALSAHLQDLAAFVQASPSSFHAAAEVARRLEAVGFTRVDPAQ
+DLPAAPGGYVSVTDGAVLAWILPEALAERAADAVPVFRLLGAHTDSPGFKLKPQHLTVTA
+DGWVQAGVEVYGGPLLNSWLDRELRFAGRLALADGRQVLAATGPVGRIPQLAIHLDRSAN
+DDLTLGRQRHTQPIVAAVAGAPDAAGTDAADGASADPVVRLTGDILELLAAQAGVDPAEV
+RGADVVVADAQQGGAFGANGEFFACGRLDNLSSVHAGLRALESLAADADRAGRGVVVAEG
+VAGEAAGAPVIPVLAAFDHEEVGSATRTGAGGPLLEELMGRLLSACGVTGQGAARSRAGS
+WLLSADAGHLVHPNYTERHDPVNHPRVNHGPLLKINANQRYSTDAAGEAAFARWCAAAGV
+PFQRFVSNNDVPCGSTIGPISATRLGVRTVDVGIGLLSMHSAREMCGADDPARLAAVARA
+FFAGV
+>GCF_023573625.1_02234
+MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA
+IAYEGTVAGGVAGEAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLAAAVREFFRGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001745.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001745.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b3e6e4dabe1ac02a5ff38b8cf4a949070c62d23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001745.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_02294
+MDIMIAVAVGVFLLVAWTVGGWAIVRMGFTRDGDAARTPAHDDGAARPAHPGAAADPATD
+PHVIWREQMKAATAASGAPCVCPPPPREGGAAEAGTSAPPSSPDCPIHRWDYA
+>GCF_003691675.1_01987
+MDIMIAVAVGVFLLVAWTVGGWAIVRLGFTRDGDAARAPAHDDGAARPAHRGPAADPATD
+PHVIWREQMKAATAASGAQCVCPPPREGGAAEAGTSAPPSSPDCPIHRWDYA
+>GCF_005280335.1_00442
+MEIMIVVAVGVFLMVAWTVGGWVIVRMGFTRDSDAASRAGSQDDDGTRPVPDGPVPVDPA
+SDPNAIWREQMKAATAASGAACTCPRRPVGTPSESPAGSGEQGAAVDSAVDRALDPAADH
+AAVDPSPDCPIHRWDYA
+>GCF_020097155.1_00395
+MPNEVLLVAGVGAALFVLWAVGGWLIVRMGFTRDRDRLPDGPGHASALPDGDGAPSPGRL
+PADPAQDPHAAWREQMKAATVASGARCTCEDGAVPDPDCPVHRWDYA
+>GCF_023573625.1_02235
+MDIMIAVAVGVFLLVAWTVGGWAIVRMGFTRDGDAARTPAHDAHDDGAARPAHPGAAADP
+ATDPHVIWREQMKAATAASGAQCVCPPPREGGAAEAGTSTPPSSPDCPIHRWDYA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001747.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001747.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16dc9271936b5b172c58d03663e525e1c0614ca0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001747.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_02296
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESDVEPVDV
+AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFQDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R
+>GCF_003691675.1_01989
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGVYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV
+AQALRDAEVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R
+>GCF_005280335.1_00440
+MATTPIRVAIAGVGNCATSLIQGVEYYRDAKATDTVPGLMHVQFGDYHVSDLQFVAAFDV
+DAKKVGLDLSEAILASENNTIKLADVPHADVTVQRGPTLDGLGKYYAETIEESDAEPVDV
+AQALRDAQVDVLVCYLPVGSQLATEHYAQTAIDAGVAFVNALPVFIAGTPEWADKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAKLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGTGGPILSASSYFMKSPPVQHNDDEARELVEAFIRGDIE
+R
+>GCF_020097155.1_00393
+MAENPIRVAIAGVGNCATSLIQGVEYYKDAQASDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAILASENNTIKISDVPATGVTVQRGPTLDGLGKYYRETIEESSAEPVDV
+VQALKDAKVDVLVSYLPVGSEEADKFYAQCAIDAKVAFVNALPVFIAGTQEWADKFTEAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAELAEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHADDEAHELVEAFIRGDIE
+R
+>GCF_023573625.1_02237
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV
+AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001748.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001748.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa8134b39e38553fc9b5a796b719220e70f1fe41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001748.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_02299
+MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRPSPDLDFT
+TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR
+AARFASQLGFAVAPEVEQAMTAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL
+ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV
+GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEITEAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYTHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA
+QQD
+>GCF_003691675.1_01992
+MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRTSPDLDFT
+TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR
+AARFASQLGFAVAPEVEEAMAAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL
+ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV
+GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEIAEAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYNHLLEWRLDEGPHEQAEAEAELRRWWAEQPEA
+QQD
+>GCF_005280335.1_00437
+MDLTTATLALPAGFPADAALPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRVSGDLDFT
+TDAGPDAAEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEEDLLRRDFTVNAMALRLPGLELVDPYGGVQDLAAGVLRTPGAPEDSFSDDPLRMLR
+AARFASQLGFTVADEVEAAMTAMAERIGIISAERVREELVKLVCGAHPRRGLDLLVRTGL
+AEHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEAEYSPSAPDPVLRLAALLHDV
+GKPATRRFEKGGAVSFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGEA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNKRKAERLAHAYDDLERRIAEIAEQEEL
+AAVRPDLDGEQIMALLGIRPGPVVGRAYRHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA
+AEG
+>GCF_020097155.1_00390
+MEPRTDTRPLPAGFPADAALPAVVVELGRRFEAAGHELSLVGGPVRDLLLGRPVVDLDFT
+TDADPDATERIGAGWAEAAWDVGRHFGTIGFQKGGWQLEVTTYRAEQYDPTSRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPAMELVDPHGGVRDLAAGVLRTPGAPEDSFSDDPLRMMR
+AARFASQLGFGVADEVEAAMTDMAERIGIISAERVRDELVKLVRGDRPRAGLDLLVRTGL
+AQIVLPELPALQLETDEHHRHKDVYAHSLQVLEQAMGEEERYSPERPDVVLRLAALLHDV
+GKPATRRFEPSGAVSFRHHENVGAKLVRRRLKALRFDNDTIKAVARLVELHMRFYGYGEA
+GWTDSAVRRYVHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIEEISAAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYAHLLEWRLDEGPHEQAAAEAELRRWWAEQPEA
+AGASSGGGARD
+>GCF_023573625.1_02240
+MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRPSPDLDFT
+TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR
+AARFASQLGFAVAPEVEQAMTAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL
+ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV
+GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEIAEAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYTHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA
+QQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001750.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001750.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ff46ee3b743204165d159be46997b1f68fd8e61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001750.fa
@@ -0,0 +1,61 @@
+>GCF_002008305.4_02302
+MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR
+ELATGERTDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF
+GESRTGDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA
+AAGASALAAADAATRKQQEERERAEREAAERAERERKEAAERAERERKEAAERAERERKE
+AEEKARAEREAAERAERERKEAAERAERERREAEERAEEERRAEAERARRQAEQEAEERA
+AREREAEQARLAAEREEAERRELERRAEARRRAEEERAREAAEREAEKRAAQEREAAERE
+AQAGTAALPAVAAGAAAAQAPDADADGATPPTEPVESVAAEKTDPPEPVAPDTEAIPVRR
+QRPVPRRAIVAESAPTAHEESRGTAAPVAAGAGVATAAGAAAAGSTAAAAAPDAQAAPAT
+TGGGDGATVADPGDGHGRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAASSE
+SESASSESASDTPSPSESTSPSPTPSSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNL
+IDGDPTTVWRTFAYARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADS
+PEGANAKEIGNGTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGE
+IAVR
+>GCF_003691675.1_01995
+MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR
+ELATGERNDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF
+GESRTGDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA
+AAGASALAAADAATRKQQEERERAEREAAERAERERKEAEEKARAEREAAERAERERKEA
+AERAERERREAEERAEEERRAEAERARRQAEQEAEERAAREREAEQARLAAEREEAERRE
+LERRAEARRRAEEERAREAERREAEKREAQEREAAEREAQEREAAEREAQAGTAALPAVA
+AGAAAAQATDADADGATPPTEPVEPVESVAAEKTDPPEPVAPDTEAIPVRRQRPVPRRAI
+VAESAPPVHEESRSTAAPVAAGTATGATAAAAGSTSAAAAPDALAAPATTGGDDGATVAD
+PGDGNGRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAAAASSESASSESASD
+TPSPSESTSPSPTPTSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRT
+FAYARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADSPEGANAKEIGN
+GTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEIAVR
+>GCF_005280335.1_00435
+MAPGAAETDTVETRADEPAAAEPESTATAPAEDVDPEPTAPAPVVPASTAPDSAPDTEAI
+PVRRQRPVPRRAMVVEPTTPDADRSPDAQRSRGAGAPLAAAGAGAVAAAGATAASAAAAG
+AAPSATSAPSTASAAPEATAAGTSPADGDGGAPVDPDQGGSRRGGWPLALLLLAVLVGAL
+VLGGVLLAQNLRGAPHRAGRPARLPHRDRRGARTRRQPPPTQSDEASPTEASPTESSPAA
+STSASPTESETAAAAPQPARALRMVPDLPAHESEHDGELPNLIDGDPSTAWRTFAYARPN
+FGGYVESMNLVVELEDRAEVNEVTLQSTGATGGAWFAYIADSPEGENAREIGNGTFDQDS
+VTVPVPFDGAEAEAEYVIVSLTSLPRLDGTTPDLPFGLRLGEIGVR
+>GCF_020097155.1_00387
+MPQPLAVGSVLGGRYRITDHVVTSADQNMVFQGADQVLNRRVTVLVASPENATQVAASAR
+ELATGERQDDVQVLDLGLSEGRTYLIAGGNPDPDVLLGLAYAQELYVEPFQTDSLGSEIF
+GESRTEQAHEYDDDDAYYADLDRRLRADQKQSQRRPGFLNRISEKLNERVRPADGTAAKA
+AAGASALAAADAATKAQLAEQERAEREAREAQERAEREEAQEAERREREAQERAERERLE
+RAAAAQAEKDRAAREAAEAEAAARREREAQRHAEAETRRREEEAAAAAALAAAAPAADAD
+PADAPTQAVPVTEPASTPEAVPAPVRRPRPAPRRALPAVASAAAVAASVSAEEGASAAEA
+APAESVAPEAVPTATATSSAAIAVAEAEPAVTEHREEAHAAPVAGGAGAGAPAAGATAAP
+ARSTSGKGWLMVLGLLALLALAGLAGLFLLGQNTRSVEPAPSASASSAAPSTAQASSAPP
+AASSSAAPTASSSAAPSTEPAPSTSAAAPAPTAAPQAVAVTRQVPEMPELEAPNDATLAN
+LIDGDPNTAWQSYTYARPNFGGYVGSMNLVVQLQERTTISEVQLENRGATGGKWIAYVAN
+TAQGGEGDARVIGQGTFDEDSITIPVDIAENQGQYVILSITGLPQLEGAGQRPYGLQLTE
+IGVR
+>GCF_023573625.1_02243
+MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR
+ELATGERTDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF
+GESRTQDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA
+AAGASALAAADAATRKQQEERERAEREAAERAERERKEAEERARAEREAAERAERERKEA
+AERAERERREAEERAEEERRAEAERARRQAEQEAEDRAAREREAEQARLAAEREEAERRE
+LERRTEARRRAEEERAREAERREAEKRAAQEREAAEREAEKREAQAGTAALPAVAAGAAA
+AQTTDADADGATPPVEPVEPVEPVAAEKTDAPEPVAPDTEAIPVRRQRPVPRRAIVAESA
+PPVHEESRSTAAPVAAGAATGATAAAAGSTSAAAAPDALAAPATTEGDDGATVADPGDGN
+GRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAAAASSESESASSESASDTPS
+PSESTSPSPTPTSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRTFAY
+ARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADSPEGANAQEIGNGTF
+DQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEIAVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001751.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001751.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cdb9a2e7b9fe73db16df5a0d5c3a4754740476e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001751.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_02304
+MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD
+ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG
+>GCF_003691675.1_01997
+MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD
+ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG
+>GCF_005280335.1_00433
+MSTINVTDTDFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLDEMAVEHEGKAVIAKLNVD
+ENPATAARFGVTSIPLVLGFQGGEKVAESVGAKPKAALEKEFSALLG
+>GCF_020097155.1_00385
+MSTINVTDADFQAKVLDSELPVLVDFWAEWCGPCRMLGPVLDELAAEHEGEVLVAKLNVD
+ENPASAARYGVTSIPLVLGFQGGEKVAESVGAKPKAQLEKEFAALLG
+>GCF_023573625.1_02245
+MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD
+ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001752.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001752.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7dd69149cca3f5de3d23dc5745dc625f903ff06c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001752.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02306
+MAQEQESRGGAWRALRQKWTGRTAEKGGADAEEPARLQRRRLTRPDRTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWRAEDGQERLDYVFID
+CPPSLGLLTVNAFVAAQEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM
+FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA
+AAEIAGRGAPSVKG
+>GCF_003691675.1_01999
+MAQEQESRGGAWRALRQKWTGRTAEKGGADVEEPARLQRRRLTRPDRTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREEDGQERLDYVFID
+CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM
+FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA
+AAEIAGRGAPTALKS
+>GCF_005280335.1_00430
+MAQEQESRGGAWRALRQKWSGRSAEQGAGEAEESSRLKARRLARPERTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVIDIDPQGNASTALNIPHTGDVASVYDVLLGEMEMHDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREENGQERLDYVFID
+CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPKLQVSTILLTM
+FDARTNLAVQVAEEVRAHFPEQLLGTAIPRNVRISEAPSYQQTVLTYDPTSAGAVAYREA
+AAEIAGRGAPAAKG
+>GCF_020097155.1_00383
+MAKDQDSRGGTWKALKQRWSGRASDKASPEEAARLKARRLPVPDRTRVFTTSNQKGGVGK
+TTTTVNLAAALARAGMRVLVIDIDPQGNASTALNVPHAGDVASVYDVLLDEMEIHEAVQD
+APDVDGLQVVPATIDLAGAEIELVSMVAREQRLARALDRYMAWRADQGQERLDYVFIDCP
+PSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPKLQVSTILLTMFD
+ARMNLAVQVAEEVKAHFPEQLLETAIPRNVRISEAPSYQQTVVTYDPASAGAVAYREAAA
+EIARRGAPQAR
+>GCF_023573625.1_02247
+MAQEQESRGGAWRALRQKWTGRTAEKGGADAEEPARLQRRRLTRPDRTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREEDGQERLDYVFID
+CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM
+FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA
+AAEIAGRGAPAVKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001753.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001753.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87a6e5004cffe45c53d5c944f44d5960f793df74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001753.fa
@@ -0,0 +1,29 @@
+>GCF_002008305.4_02307
+MTERGSAYERRPGLDPQDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ
+FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVAARAVSALKTLVPLT
+MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP
+R
+>GCF_003691675.1_02000
+MTEQGSAYERRPGLDPRDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ
+FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT
+MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP
+R
+>GCF_005280335.1_00429
+MPEQASPYERRPGLDPKERGDRPAPVGQPAPPLIDALRPAAVELFGEDLPRAERYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELIPEGALVADVGSGAGLPGLCLALARPDCR
+FLLIEPLERRVEWLDMVVEDLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT
+MPMLQGDGQLLAIKGRAAADEIAAARKVLRKYGGDEPEILTVGEGLLPETTTVVRVSARA
+R
+>GCF_020097155.1_00382
+MSAPQLTAELRPAAEDLFGEALPLAERYVDHLATTGIEWGLLGPREVPRLWGRHVLNCAV
+VARLLPEGSLVADVGSGAGLPGLCLALARPDCRFTLIEPLERRVAWLEMVIADLGLTNVE
+VVRGRSEQVADEIQVDIVTARAVSALKTLLPLTMPLLRSSGHLLAIKGRSAAEEITAAQK
+PLRKYGGGDPEIVTVGEGLLPEPTTVVRVPARRAR
+>GCF_023573625.1_02248
+MTERGSAYERRPGLDPRDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ
+FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT
+MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP
+R
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001754.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001754.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51f0d9dd45aa17182a89ea49af01b034a3b2ad9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001754.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02308
+MSAENVTPAPEAEDAVVETPAGQGSRVAEQDGAAVSEAVRRLEEEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL
+ILDVCGHRERRNVALRTAAQAAVERVRVGEGPVHLEPMGAYERKIVHDVVADAGLTSESE
+GEGARRHVVISADD
+>GCF_003691675.1_02001
+MSAENVTPASEAEDAVVETPVGQGSRVAEQDGAAVSEAVRRLEEEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL
+ILDVCGHRERRNVALRTAAQAAVERVRAGEGPVHLEPMGAYERKIVHDVVADAGLTSESE
+GEGARRHVVISADD
+>GCF_005280335.1_00428
+MSAENVNPAAEAEDAVVETTPAPDAPQAPAAEERTGSDAAVAAGEGAESSAAESASDGVR
+RLEEEGDVAADYVEELLDIADLDGDIDIEVRDGRTYVSVVSEDHDERLNALVGRDGKTLE
+ALQELVRLAVLAATGHRSRLILDICGHRERRDADLRETAQDAVERVRAGEGPVHLSPMGA
+YERKIVHDVVADAGLASASEGEGARRHVVISADA
+>GCF_020097155.1_00381
+MTAEHEGPLADAAEDSPAVEAPVEATAPDAAVDEQAEAVRRLEEEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVPGEDDEDDRLADLVGPDGKALEALQELVRLAVLTATGHRS
+RLILDIAGHRRRRDAELRTLAGEAVERVRSGAGEVHLDPMGAYERKIVHDVVAEAGLASE
+SEGEGPRRHVVISG
+>GCF_023573625.1_02249
+MSAENVTPAPEAEDAVVETPAGQGSRVAEQDDAAVSEAVRRLEQEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL
+ILDVCGHRERRNVALRTAAQAAVERVRAGEGPVHLEPMGAYERKIVHDVVADAGLTSESE
+GEGARRHVVISADD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001756.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001756.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ddc0d1d3cc04adb2622bd543d62c88b151323e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001756.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02310
+MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ
+ED
+>GCF_003691675.1_02003
+MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ
+ED
+>GCF_005280335.1_00426
+MAVTPSPFTVLEPSREWGPVRALPSALLAGLLTVYRAVVSPLYGQVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ
+ED
+>GCF_020097155.1_00379
+MPASSPYTVLEPSHEWGPLRALPSTLLAWLLTAYRAVVSPLYGPVCRFFPSCSAYGLEAV
+HVHGAVRGSWLTARRLLRCHPWNDGGVDPVPPGRRRWPPGREPRIFALNHPPIPPDPSQE
+D
+>GCF_023573625.1_02251
+MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILALNHPPIPPDLPQ
+ED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001757.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001757.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8be7ec2e7b92d7b093a129929175e162e52aa430
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Single_Copy_Orthologue_Sequences/OG0001757.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02311
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTPPSAPRPRAGFVVSKAV
+GNAVTRNRVRRRLRAVVADQMRTAPLRELPVLVQVRALPAAAEADFALLRRETVGALGKA
+LKPHLPAASEHA
+>GCF_003691675.1_02004
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTSPSAPRPRAGFVVSKAV
+GNAVTRNRVKRRLRAVVADQMRLPPLRDLPVLVQVRALPAAAEADYALLRRETVGALGKA
+LKPHLPAASEHA
+>GCF_005280335.1_00425
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDHTRSTSPSVPRPRAGFVVSKAV
+GNAVTRNRVKRRLRAVVAEQMRAAPLRELPVLVQVRALPPAAEADHALLRRETVGALAKA
+LRPHLPAVPRDEA
+>GCF_020097155.1_00378
+MLPRDRRVRTPEEFRRIRRTGSRAGRSTVVVSVAADTDPARPGATSQPRRPRAGFVVSKA
+VGNSVVRHRVTRRLRALLRAELDSPALRDRALLIQVKALPAAVDADHATLRRDVHGALGA
+AVRKLDQADRSR
+>GCF_023573625.1_02252
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTSPSAPRPRAGFVVSKAV
+GNAVTRNRVKRRLRAVVADQMRLPPLRDLPVLVQVRALPAAAEADYALLRRETVGALGKA
+LKPHLPAASEHA