diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000007.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20c049fc02ebad765aaaf54cc1e6e7f9865f4c33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000007.fa
@@ -0,0 +1,48 @@
+>NZ_CP042169.1_151
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP042169.1_996
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKAEDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP042169.1_1250
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP042169.1_2020
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP033200.1_983
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP033200.1_1070
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP033200.1_1078
+MRVVLLPAVADRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP033200.1_1082
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP033200.1_1976
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP040019.1_1191
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP097650.1_566
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP097650.1_568
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP097650.1_1207
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP097650.1_1294
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP097650.1_1832
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
+>NZ_CP097650.1_2150
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000008.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..209b424df842695e58debbb9d79137b414934a28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000008.fa
@@ -0,0 +1,83 @@
+>NZ_CP042169.1_688
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN*
+>NZ_CP042169.1_1355
+MEGSLEGSHGDRVRLEDGRGHRGGLHHYPGLNSFTTWDPGASSIPAPTQQSLRTLEWLSR
+RENLVVCGPSGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARI
+LRADLIVIDDIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATAT
+VDRLLHHAHVCQTTGDSVRMTQAMAGKGVMPLN*
+>NZ_CP042169.1_1454
+MAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIGLLPVADDAAEGLYRIVDAA
+YEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQTTGDSVRMTQAMAGKGVMP
+LN*
+>NZ_CP042169.1_2169
+MLWKVRSKAPTVTASVSKMVVATGEGYTTIRDSTPKTLATATVDRLLHHAHVCQTTGDSV
+RMTQAMAGKGVMPLN*
+>NZ_CP042169.1_2171
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTVKSLEVV*
+>NZ_CP033200.1_81
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN*
+>NZ_CP033200.1_330
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN*
+>NZ_CP033200.1_980
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN*
+>NZ_CP033200.1_1356
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN*
+>NZ_CP033200.1_2232
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN*
+>NZ_CP097650.1_583
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN*
+>NZ_CP097650.1_974
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN*
+>NZ_CP097650.1_1114
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN*
+>NZ_CP097650.1_1305
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN*
+>NZ_CP097650.1_2109
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000012.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a876ad71409e7a9c1f213ab3de105739bbbdab54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000012.fa
@@ -0,0 +1,42 @@
+>NZ_CP042169.1_149
+MKGAAQLDFIRRGQAVGLTLAQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQ
+LRTTIADLREDAAAGDPATCSPEDVCRYL*
+>NZ_CP042169.1_152
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLGPAVG*
+>NZ_CP042169.1_1034
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAVGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC
+SPEDVCRYL*
+>NZ_CP042169.1_2007
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL*
+>NZ_CP033200.1_284
+MRIGELAERAGTTAKTLRFYEEQGLLPPAERTPSGYRDYAPETAARIDFVHRGQAAGLTL
+AQIRQILDIRDDGAAPCEHVRDLLDARLAEIEQQIAQLAALRDTITELRRDAAQPDPDSC
+SADQVCRYL*
+>NZ_CP033200.1_325
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL*
+>NZ_CP033200.1_332
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL*
+>NZ_CP033200.1_763
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL*
+>NZ_CP040019.1_704
+MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATCSPEDV
+CRYL*
+>NZ_CP040019.1_706
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGSSPMKWC
+SG*
+>NZ_CP083691.1_2174
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL*
+>NZ_CP097650.1_982
+MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATCSPEDV
+CRYL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000017.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e1d9a37d6cc88e96907158bd44cf7758dcf4dc5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000017.fa
@@ -0,0 +1,102 @@
+>NZ_CP042169.1_520
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDA
+LHVTLADEAVALGGETAADSYLVIGKILDAAERAGADAVHPGYGFLSENADFARAVTDAG
+LVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEFGLPVAIKA
+AYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVSEEITGIDLVREQFRLARGEALGYTDPQPRGHSIEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGEAVSGAFDSMVAKLIVTGADRRQALQ
+RAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPSA
+LTPAEPAPREARHTVTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGKRGAPV
+AAAVSTDALTAPMQGTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVE
+PGQTVTAGTVIATIADAE*
+>NZ_CP042169.1_1861
+MTTTPAARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLP
+GASSADTYLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRA
+LGDKITARSLAQQAGAPLVPGSDGPVPDAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVR
+ELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGHVAVLGTRDCSLQ
+RRNQKLVEEAPAPFLTDEQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTR
+LQVEHPVTEEVFGVDLVREQFRIAAGELLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPG
+PIDAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVWGEDRAQAIARARDALAELRID
+GVPTVVPFHRAVLEQDAFTSGDRLGVYTTWIESEFAEPLAESPYLGAEVPAGGRTSVTVE
+LDGRAVRLGLPADLYAALLGGGGAGAAAPADAAGAGKPDDDGAVASPVTGTLASWKVEDG
+AEVAEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAISRLGA*
+>NZ_CP033200.1_254
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDA
+LHVTLADEAVALGGETAADSYLVIGKILGAAERAGADAVHPGYGFLSENADFARAVADAG
+LVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEFGLPVAIKA
+AYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVSEEITGIDLVREQFRLARGEALGYTDPQPRGHSIEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGETVSGAFDSMVAKLIVTGADRRQALQ
+RAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPSA
+LTPAEPAPARRATP*
+>NZ_CP033200.1_1568
+MTTTPAARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLP
+GASSADTYLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRA
+LGDKITARSLAQQAGAPLVPGSDGPVPDAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVR
+ELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGHVAVLGTRDCSLQ
+RRNQKLVEEAPAPFLTDKQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTR
+LQVEHPVTEEVFGVDLVREQFRVAAGEPLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPG
+PIDAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVWGEDRAQAVARARDALAELRID
+GVPTVVPFHRAVLEQDAFTSGDRLGVYTTWIESEFAEPLAESPYLSAEVPAGGRTAVTVE
+LDGRAVRLGLPADLYAALLGGGGAGAAAPAGAAGAGKPDDDGAVASPVTGTLASWKVEDG
+AEVVEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAIARLGA*
+>NZ_CP040019.1_2361
+MSIADAPQASVIPPRDPKAERRFSRVLIANRGEIAVRVVRACQDEGLTSVAVYAEPDRDA
+LHVKLADEAVALGGETAADSYLLVEKILDAAERSGADAVHPGYGFLSENADFARAVEAAG
+LVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEHGLPVAIKA
+AYGGGGRGIKVARSREEIPELYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+GVVVMSTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILKEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVTEEVTGIDLVREQFRLARGEALGYEDPVVRGHSFEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDTGVVEGETVSGAFDSMVAKLIVTGADRRQALQ
+RAARALGEAEIAGMPSVLPFHRAVVTDPAFAPEIAGAAEPFTVHTRWIETEFANHIEPSE
+HAPADPTSREPRRTVTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGRRGAPV
+AAAVSTDALTAPMQGTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLTAHRAGVVSGLEVE
+PGQTVSAGTVIATIADAD*
+>NZ_CP083691.1_862
+MSTPSTTASRPVTRVLIANRGEIAVRVARACRDHGIASIAVYSDPDAQAMHVAVADEAYA
+LPGSTSAETYLDIAAVLDVARRSGADAVHPGYGFLSENADFAQAVIDAGLTWIGPSPQAI
+RDLGDKITARAIAQRAGAPLVPGSDGPVPDAAAARAFAQEHGLPIAIKAAFGGGGRGIKV
+VRELSEVEDAFESAVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGAVAVLGTRDCS
+LQRRNQKLVEEAPAPFLTDEQRQRIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVN
+TRLQVEHPVTEEVFGVDLVREQFRIAAGEPLSIPEDPAPRGHAIEFRLNAEDPAHGFLPV
+PGPVEAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVVGEDRSQAIARARDALAELR
+IEGVPTVVPFHRAVLEEEAFTSAEALGVYTTWIESEFAAPLAASPHLGASVPGGGRTTVT
+VEVDGRAVRLGLPADLHAALLGGGGARTGASAPAEQSVDEGAVTSPVTGTLASWKVEDGA
+QVAEGDTIAVVEAMKMETPVRAPRAGRVERAAGDAPAAVTRGQVLASVRA*
+>NZ_CP083691.1_2238
+MTNASAPQASADIAEAPGRPFSRVLIANRGEIAVRVIRACQDEGLTSVAVYAEPDRDALH
+VKLADEAVALGGETAADSYLVIQKVLDAAERSGADAVHPGYGFLSENAEFARAVEAAGLV
+WIGPPADAIDALGDKVSARRIATKVGAPLAPGTTSPVNGTDEVVAFADEFGLPVAVKAAY
+GGGGRGIKVARTREEIPELYESAVREAVAAFGRGECFVERFLDRPRHVETQCLADAHGNV
+VVVSTRDCSLQRRNQKLVEEAPAPFLTDEQNTRLVESSKALLKEAGYVGAGTCEFLVGQD
+GTLSFLEVNTRLQVEHPVSEEVTGIDLVREQFRIARGEALGYGDPEARGHSFEFRLNGED
+PGRNFLPAPGTLTRFRMPSGPGVRVDAGVTEGETVSGAFDSMVGKLIVTGADRRQALQRA
+ARALAEAEIAGMPSVLPFHRAVVADPAFAPELAGSEEPFAVHTRWIETEFAHQIEPTALT
+PAAAPDRPERHTVTVEVNGKRVDVTLPTWGEAMHQLQGAAARAGAGRRRPRGARRAGAAP
+AAPGTDSLTAPMQGTVVKVAAQNGDRVAEGDLIVVMEAMKMEQPLTAHRAGVVSGLEVAA
+GDALTAGAVIAVIADAE*
+>NZ_CP097650.1_523
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDA
+LHVKLADEAVALGGESAADSYLVVGKILDAAERAGADAVHPGYGFLSENADFARAVADAG
+LVWIGPPAAAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEFGLPVAIKA
+AYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVSEEITGIDLVREQFRLARGEALGYTDPQPRGHSIEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGETVSGAFDSMVAKLIVTGADRRQALQ
+RAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPSA
+LTPAEPAPREARHTVTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGKRGAPV
+AAAVSTDALTAPMQGTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVE
+PGQTVTAGTVIATIADAE*
+>NZ_CP097650.1_1781
+MTTTPAARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLP
+GASSADTYLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRA
+LGDKITARSLAQQAGAPLVPGSDGPVPDAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVR
+ELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGHVAVLGTRDCSLQ
+RRNQKLVEEAPAPFLTDEQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTR
+LQVEHPVTEEVFGVDLVREQFRVAAGEPLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPG
+PIDAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVWGEDRAQAVARARDALAELRID
+GVPTVVPFHRAVLEQDAFTSGDRLGVYTTWIESEFAEPLAESPYLSAEVPAGGRTAVTVE
+LDGRAVRLGLPADLYAALLGGGGAGAAAPAGAAGAGKPDDDGAVASPVTGTLASWKVEDG
+AEVVEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAIARLGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000020.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebf066f8a0540f6cf0dbb01fd4f63d6d2a5576c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000020.fa
@@ -0,0 +1,73 @@
+>NZ_CP042169.1_502
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSLITSN
+LPAESRAQAYVALINSEAVRERVAQDTGQDGDGSLSAVLVPESSMIKVTATSTDPETAAQ
+LANSALQATADVAADVDKNSPLEVVPLSDARVPSAPVSPDTRRNVLLGVVAGLGAGLAIA
+VLRRLLDVKVRSRADVKEITGAGVIGAVPENASLTRTGEEAVDLDPRAGEAIRALRTNLK
+FVSVDEPPRVVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHDLFQVAG
+DVGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFFV
+IVDSPPLLPVTDGSLLATAVDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVA
+RSQRGGGYSYGYGYESTYHKSHDKYLQGTGKGGKKSRRAARAKKG*
+>NZ_CP033200.1_232
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSLITSN
+LPAESRAQAYVALINSEAVRERVAQDTGQDGDGSLSAVLVPESSMIKVTATSTDPETAAQ
+LANSALQATADVAADVDKNSPLEVVPLSDARVPSAPVSPDTRRNVLLGVVAGLGAGLAIA
+VLRRLLDVKVRSRADVKEITGAGVIGAVPENASLTRTGEEAVDLDPRAGEAIRALRTNLK
+FVSVDEPPRVVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHELFQVAG
+DVGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFFV
+IVDSPPLLPVTDGSLLATAVDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVA
+RSQRGGGYSYGYGYESTYHKSHDKYLSGVGSSAKKGRRSRRKARTRG*
+>NZ_CP033200.1_243
+MNIIDFLRVLRANRLVILGCAALGLALGLLYSLLQPTLYTATSTAFVTVEGEASISGTET
+AQTRAQSYIPLINSRTVRERIAAEGLDTAGATLSAALVPNSNLITVSAVAPDAQQAAALA
+NGALVATADVANELDPTSNVKVTAMEDALAPAAPSSPDRVRHLLYGLGAGLVLGLIVAFL
+RRLLDVNVRTTTDAQVAGGAGLLGAIPLDPSMKAERTAPMAPLSPRASEAVRQLRTNLRF
+AAVDDPPRTIAFTSSNPGEGKSTVIGNLALTVAAAGQPVILIDADLRRPRQALQFGVDGR
+VGLSEVLNGDVALQDVLIPVGEDGLLLLPAGRTPPNPSEQLGSERMRDLLTALAETHMVL
+VDAPPVLPVTDSTLLATAVDGTVLVIRHGKTRKEHLEVARDMLAGVNARVLGVVLNGTPA
+SGVGSDYYGGGYGADGGSYDAYYQAPRDAAEAAAGTAGDASRR*
+>NZ_CP040019.1_1189
+MDLQQYLQTFRKYWRSILTVLSVCVGAALVFTFLQTPKYSSTSSALIAVDTAATPGELSS
+GALYAERQVSSFVALADSALVLDPVINELGLNVTPQALRSRVSVSAPAGTSIVDVTVTDT
+NAGRAAEVANAITASLKNVTSDVVPTGPDGDEIVTVTVVEPAAASSRPVSPRPVVNIALG
+LIAGVVIGLGQALVRRLLDSRIRTRDDLVEITDAPVLASVVHHKGSDRPKDEAAPARGTA
+WASAESYRKLRTAVGFVALGGERRSSIVVTSSVQGEGKTETSTNLAKVLAETGARVLLVD
+ADLRRPQVGARLGLDDELGLSDVLTGRADLNDVLLSVDDLSVLTAGTVPPNPSELLGSEA
+MAELLALVEAHFEYVILDAPPLLPVTDAAILSHQAGGAIVVARSGVARQNQLAEALSILE
+AADASVYGVVLNDVPVSHIDGYSQYYR*
+>NZ_CP040019.1_2371
+MNIIDFLRVLRANRLVILGCAALGLVAGLVYSLLQPTLYTATSTGFVTVQGEATISGTET
+AQTRAQSYIPLINSRTVREKIAEGGLDTAGASLSAAVVPGSNLITVSAESEDPEQAAALA
+NSALVATAETANGLDPTSNVQVTAMEDALAPTSPTSPDYVRNMLYGLGAGLLLGLVIAVL
+RRILDVNVRTTTDAQVASGAGLLGAIPLDATLKAERDAPRGEPSPRAAEAVRQLRTNLRF
+AAVDDPPRTIAFTSANPGEGKSTVIGSLALAVAASGQPVILIDADLRRPRQALQFGVDGR
+VGLSEVLNGDVALQDVLVPVGDHGLLLLPAGRTPPNPSEQLGSARMRDLLTALAETHMVL
+VDAPPVLPVTDSTLLSTAVDGTVLVVRHGKARKEHVEVARDMLAGVNARVLGVVLNGTPA
+SGVGSDYYGGSYASKGDDYHAYYQASRDAESRPSDEAVPEGPAAQR*
+>NZ_CP083691.1_2249
+MNILDFLRVLRANRLVLLGGVVLGLLGGLVYSLLQPTLYTSTSTGFVTVAGEASISGTET
+ALTRAQSYVPLINSRTVREKVAESGVDVSGSTLSAQVVPNSNLITVTALAPDPQRAADLA
+NTALGATAEVANSLDPTSNVKVTAMEDALPPAGPSSPDHLRNALIGAGIGLLAALAVAFL
+RRVLDVNVRTTTDATEASGAGLLGAIPQDGTMKAERTAPLGVPSPRAAEALRQLRTNLRF
+AAVDDPPRVVMVTSSNPGEGKSTVIAGLAQAVAVSGQPVILVDADLRRPRQASQFGVDGR
+VGLSEVLSGDVLLEDAVQDLGDGLLLLPAGRTPPNPSEQLGSHRMQELLRVLAETHLVLV
+DAPPGAAGDGLHPAGGRRGRDRAGGAPRQDPEGPCGGGPGHAGQGQRPHAGRGAQRRARL
+RCGLGLLRRGLRRGRRQLRRLLPGAPGRRRRRGRDRGRHVATLIAPGGRARSSHRRRRPG
+DAEGPRL*
+>NZ_CP097650.1_502
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSLITSN
+LPAESRAQAYVALINSEAVRERVAQDTGQDGDGSLSAVLVPESSMIKVTATSTDPETAAQ
+LANSALQATADVAADVDKNSPLEVVPLSDARVPSAPVSPDTRRNVLLGAVAGLGAGLAIA
+VLRRLLDVKVRSRADVKEITGAGVIGAVPENASLTRTGEEAVDLDPRAGEAIRALRTNLK
+FVSVDEPPRVVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHDLFQVAG
+DVGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFFV
+IVDSPPLLPVTDGSLLATAVDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVA
+RSQRGGGYSYGYGYESTYHKSHDKYLQGTGTAGKGGKKSRRAARAKKG*
+>NZ_CP097650.1_513
+MNIIDFLRVLRANRLVILGCAALGLAMGLVYSLLQPTLYTATSSAFVTVEGEASISGTET
+AQTRAQSYIPLINSRTVRERIASEGLDTAGATMSAALVPNSNLITVSAVAPDAQQAAALA
+NGALVATADVANELDPTSNVKVTAMEDALAPATPSSPDRVRHLLYGLGAGLVLGLIVALL
+RRLLDVNVRTTTDAQVAGGAGLLGAIPLDPSMKAERTAPMAPLSPRASEAVRQLRTNLRF
+AAVDDPPRTIAFTSSNPGEGKSTVIGNLALTVAAAGQPVILIDADLRRPRQAMQFGVDGR
+VGLSEVLNGDVALQDVLIPVGEDGLLLLPAGRTPPNPSEQLGSERMRDLLTALAETHMVL
+VDAPPVLPVTDSTLLATAVDGTVLVIRHGKTRKEHLEVARDMLAGVNARVLGVVLNGTPA
+SGVGSDYYGGGYGADGGSYDAYYQAPRDAPEAAAGTAGDTSRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000027.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000027.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d073f6494da55c130db3983de1b73fc5dccda4f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000027.fa
@@ -0,0 +1,14 @@
+>NZ_CP042169.1_154
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR*
+>NZ_CP042169.1_1032
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR*
+>NZ_CP033200.1_323
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR*
+>NZ_CP033200.1_334
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR*
+>NZ_CP033200.1_761
+MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR*
+>NZ_CP040019.1_708
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR*
+>NZ_CP097650.1_980
+MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000028.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17bbf1a0d4007e59f71fc4b71cc329a2c3051c74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000028.fa
@@ -0,0 +1,49 @@
+>NZ_CP042169.1_155
+MSTPATRGRADGGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW*
+>NZ_CP042169.1_1031
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW*
+>NZ_CP033200.1_322
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW*
+>NZ_CP033200.1_335
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW*
+>NZ_CP033200.1_760
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLHDRYGIAHATLQVEGAGSDGCHD
+LSW*
+>NZ_CP040019.1_709
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGTKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW*
+>NZ_CP097650.1_979
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000029.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55c2fe02da308bf1d13128026b2649d42bb17b1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000029.fa
@@ -0,0 +1,68 @@
+>NZ_CP042169.1_162
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAALSPNPAFLIGARALLAVGAAAMMPATLALIRLAFNDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVVIALVATAIIAPHNDPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAASALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH*
+>NZ_CP033200.1_347
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAAFSPNPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVAIALVATAIIAPHNHPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAAIALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH*
+>NZ_CP040019.1_162
+MSALRRWSALAVLVLPVLLISIDMSVLGIAVPALSADLDPTSGQLLWIIDLYSFLLAGLL
+IFMGSLGDRIGRRRILLIGAPLFGAASLAAAFASSAEMLIAARALLGVGGATLMPSTLGL
+IRTIFPDRAERRTAIAVWAMAFSGGAALGPVVGGILLERFWWGSVFLMNVPVMAVFLLVA
+PFLLPESRDPSPGPFDPLSSVLSIAGIVGLVYALKTAAKSPDWTALAGLVVGATALAWFI
+ARQRRLAHPMIDVALFRNVAFTSAVSVNVISVFAFMGLMFFLPQFLMLVQGMGPAEAGLW
+MLPLAAAAVVGTLLAPLLARVVAVRTVILTGLALVIAGFAVGTRLDGAAPLVAFVLLSCL
+FGVGVGLAETLTNDVILTAAPPERAGAAAAISETGYEFGGAMGTAVLGTVGMAVYAARVQ
+EAAGLPGLGPADAEAAAQTLAAAHRIGEGLPDGGARLVEVANGAFTAGMDLVAGIGIGVA
+AVTLLLAWRGLRSEARVERPVED*
+>NZ_CP040019.1_182
+MVILNETIMSVALPRLMAEFTVTAATAQWLTTGFMLTMAVVIPFTGWLLNRMSLRAVFIL
+AMGTFTAGTAIAGLAPTFGLLLTGRVVQAVGTAIMMPLLMTTVLNVVPLSRRGRVMGLIS
+IVISVAPASGPAVGGVILEHLSWRWLFFTVLPIAAIALAAGAAWVRNVTEPRPVRLDVLS
+GVLSAVGFASLIFGLSSIGEAAAGNAAMPPWIPVAVGVLALALFAVRQLRLKDDALLDLR
+TLSRPTFTVALAVMLTSMLALFGTIVLLPIYLQEVLGWTTQQSGLALLPGGMVMALLGYV
+VGHLYDRVGAPPLIVPGAVLGAAGLWGYTFLSEDSSAFMVVGLHVLISTGLSMLFSPLMT
+TALSALPRSLYAHGSALVSTLQQVAGAAGTALFITLLTVGTASSVAGGLGEVASLMDGVH
+LAFLSGALVFTVNVVAVWFVKRPAPNPL*
+>NZ_CP040019.1_2173
+MLSGTSTTSRGTGPAPVRAWLVLCAMSMLQFFIAVDVTVVNIALPSIGADLGVAGHSLTW
+VVVGYTITGGGLLMLGGRIGDLLGRRRTLLVGTSVFGAASLLAGLAPSFPVLVAARLLQG
+AGEAVALPAAMATIVLLFPEGPRRSRALSVWAAVASCGLVLGFALSGIITAHLGWRWVFL
+VSVPFILVVIVTALLLVPADRPASGGRVRLDLPGSLLLTACPLLFVYAAVEAGEPATGLW
+VSGVALLCAVLAAAGFVRVESRSPNPLVPLTFFADRARLRANLTTMLLSGALSTSFLLFT
+FYLQDRLGIGPLGAGLTMLPLAVALIVASVLVPRLLGRWGARACVLVGLGAAAGAMGVVA
+LVAVLGSGATWLLPAMLLIAAGMGFGLVGLQYIAVSGTTEEDAGIASGVQRASDQLGGAA
+GVAVYVGLGFAPALHADAGDPFVVAAVLAVVGLVVGAVVISRSPSTAAGQPQAG*
+>NZ_CP040019.1_2289
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAAFSPSPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVVIALVATAVIAPHNDPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAAIALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH*
+>NZ_CP097650.1_1955
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAAFSPNPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVAIALVATAIIAPHNHPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAATALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000032.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..306ddc6bd8eaa99bbe783b27b3b34340ab4e7bcd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000032.fa
@@ -0,0 +1,58 @@
+>NZ_CP042169.1_252
+MPDSSPSTPSVRSGAPSRARRSSAWRQARSLRWRAFWAAAPLSRVYLAFGSAFLLASTAS
+DIGLFGPGHGAIPVLDGIAIASATSAFLAQWWRSTVGFALLLPGAVATVVGGSEVLFAVV
+APVVLGAVAATARSWGFVVTAAVLALTWGVAQPFAVGQSNATWFILLLMSMGLGGGLFIR
+ESLARRERDRRRVFEAEERARLAAEAERRSLARDLHDVVAHNLTIISMQARTARYLGAPE
+AAQGVLDVVGDSAKDALRDLRRMLSILQEDGIVDPSGEPGAAGGADGATSADPVLSVAQL
+AEELRSLGMTVETDVRCDQNAMPISVRSTLHRVLQEATTNVAKHAGEGARVCIELRDAGP
+DVVLEVENTVTERSGPPQWNSSGVGLNSMRDRVATFGGTIEAGPGGWGWRVRAVLPRSV*
+>NZ_CP033200.1_2221
+MPDSSPSTPSVRSGAPSRARRSSAWRQARSLRWRAFWAAAPLSRVYLAFGSAFLLASTAS
+DLGLIGPGLGAIPVLDGIAIASATSAFLAQWWRSTVGFALLLPGAVATAAGGSEVLFAVV
+APVVLGAVAATARSWWFVVTAAVLALTWGVAQPFAVGQSNATWFILLLMSMGLGGGLFIR
+ESLARRERDRRRVFEAEERARLAAEAERRSLARDLHDVVAHNLTIISMQARTARYLGAPE
+AAQGVLDVVGDSAKDALRDLRRMLSILQEDGIVDPSGEPGAAGGADGATSADPVLSVAQL
+AEELRSLGMTVETDVRCDQNAMPISVRSTLHRVLQEATTNVAKHAGEGARVCIELRDAGP
+DVVLEVENTVTERSGPPQWNSSGVGLNSMRDRVATFGGTIEAGPGGWGWRVRAVLPRSV*
+>NZ_CP040019.1_101
+MPESTAVRSRLLSGAPRRARRSSSPDEESLGPAGRWRAFWAAGPLSRVYLVAGSVLLLVS
+AASDLGLIGGGAFATAPLDVAVIVSTTAAFLAQWWRSTVGFALLVPAGAATIAGGTEALV
+TLVTAAMLAAVTVTARSWAFVVAAATLALAWGVVRPVASGRPSEAWFVLALMTAALGVGL
+FIRESVARRERDRRRILEAEERARLAAERERRSLARDLHDVVAHNLTIISMQARTAQYLG
+TPEAAQSVLAVVGDSAKDALVDLRRMLAILQEDGIVDPAGEPGAAGGADGATSADLALTA
+GRMAAELRSLGMSVEQDLRFDPEAVPMSVRSALHRVLQEATTNAAKHAGTGAEVRIMVAE
+QGRDVVLEVENSVAAPQRSMRWNSSGVGLQSMRDRVATFGGTLEAGPGGRGWLVRAAIPR
+APEGA*
+>NZ_CP040019.1_574
+MAGVELAYLSDFISEMPWRHGVGWVALGAAVLALPLAWRRRFPVTVMLTISVLYIALASW
+VGIELYASQVVLFLGFYSVGAWCPDRRRALWSRTAVAAAMAVWLGWVTVDGFTDPEVGER
+GVNAYAAVAAIQFLVNLAYFSGAWIFGDRAWREAIRRQRLEAAHAEIRAQQARIAAQEVS
+LERLRIARELHDVVAHHVTAMGVQAGAARLTLDRDPEAAAGHLRGIESSAREAVAELKTM
+VHTLRDADAAPDSLPRLADLEDLVAQAVRLGTDARLTRVGPEPRLGAPAELALYRVAQEG
+LTNARRHAGPRAAVEVRLRTEPERVELEVSDDGRARPDAEAGSERSPGGAGGAVPAGTGL
+GLVGMAERMASVGGTVRCGPKPGGGWLVRASVPTLPEPGEDAAWDAPDEPAPAPDETVQP
+ETMPDPTTEATR*
+>NZ_CP083691.1_69
+MSRARLGSTLRSLLDPVSPPAGGRVRFWDAAPANRVYLVVGSVFSVASTTSDVMIELGRG
+GGDTRADIAFMVLACLAFLAQWWRTTVAYAVVLLLMAASLVGGDAVSVVLVLPFVLGTVV
+ATAQSGRYLLAAGATALAWVVAVSLVGSGKVDGVAWLTLLLVVVGLGVGASIRAAKLQRV
+QDGRRIAEAERLAREAAERERRILARDLHDIVAHNLTIIAMQANAAQYLGTPEAAQQVVR
+VVGESARDALTDLRRMLSILQEDGVVEPAPTPGTPETDDAATVAQLGPGAERLAEELRLA
+GVDAAVRVELGEVGLNLGVRAALYRVMQESVTNVAKHAGPGQACEISIEARGGEVVLEVV
+NTLPEDGPRSVVGNSSRVGLTSMRDRIEAFGGRLEVGPCGGDRWRVRAAVPRPEA*
+>NZ_CP083691.1_508
+MVGGLLLVWETADLALGAAGRPGGGLLDSADALFSLGTGVTLVLALAGARALMGCYTLLV
+LSALASGFYALPVVTVGLAMGFAALYLSRTPLVVFSCTLLATTVLTAALRPDHLDVLPLM
+LVPALAGTAVGLLLRRESVSLERARRRNLELVEARDRATADIRRSLARDLHDVVAQDLAV
+LAMQTQAIRVAPDRAAQQRMADAVADVARQAHANLRGLLQVLYAGTDVDARRGTGTPDAL
+DTALVTSSAQAARDAAARLRAHGFDVDLQVQEQDGVRAPRHVDATVHRIAHEAVTNVVKH
+APAGGACQVLFTLSPGQVRLRVLSELSPAQHPGRPRDAPQPDGSFGVLNIRERAGLLGGR
+ADVGPREGRWHVDVRIPFGVPA*
+>NZ_CP097650.1_250
+MPDSSPSTPSVRSGAPSRARRSSAWRQARSLRWRAFWAAAPLSRVYLAFGSAFLLASTAS
+DIGLFGPGHGVIPVLDGIAIASVTSAFLAQWWRSTVGFALLLPGAVATVVGGSEVLFAVV
+APVVLGAVAATARSWGFVVTAAVLALTWGVAQPFAVGQSNATWFILLLMSMGLGGGLFIR
+ESLARRERDRRRVFEAEERARLAAEAERRSLARDLHDVVAHNLTIISMQARTARYLGAPE
+AAQGVLDVVGDSAKDALRDLRRMLSILQEDGIVDPSGEPGAAGGADGATSADPVLSVAQL
+AEELRSLGMTVETDVRCDQNAMPISVRSTLHRVLQEATTNVAKHAGEGARVCIELRDAGP
+DVVLEVENTVTERSGPPQWNSSGVGLNSMRDRVATFGGTIEAGPGGWGWRVRAVLPRSV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000035.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c04d4c87cfd0dd143af82908798ffa51b030c4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000035.fa
@@ -0,0 +1,33 @@
+>NZ_CP042169.1_725
+MAARGETTADRRGGRGTDRRPGTAGAVALGGAAGVLCGAGVMNAVTALAGAPNFRGTFGA
+AFGAVDVLVQALPLFVVNVLGSFLLGLLWAASRRRGPDWRPRLVAGLGTGFLGAFTTISS
+AVALVLWPVRLGAAVSGAGGVLAAAVAVLLVLALMAALSTAAAMLGLRAGGAPGSRVVGT
+DRSEEDA*
+>NZ_CP033200.1_464
+MAARGEPTADRRGGRGTDRRPGTAGAVALGGAAGVLCGAGVMNAVTALAGAPNFRGTFGA
+AFGAVDVLVQALPLFVVNVLGSFLLGLLWAASRRRGPDWRPRLVAGLGTGFLGAFTTISS
+AVALVLWPVRLGAAVSGAGGVLTAAASVLLVLALMAALSTAAAVLGLRAGGAPGSRVVGA
+DRSAEDA*
+>NZ_CP040019.1_2138
+MRAPGVRGAVALGGAAGVVAGSTAMELVGVGGLLALAGRDGGVGLGPVAALAFAALPLAV
+VNVLGSFLLGLLLARSRHAGLDRRPALVAGLGTGFLGSFTTIATAAAVFLLTPLEAGWSA
+IAASSGVGGFLSATAGLLLPPLALLALLAALSTAAAVLGLRLGGAPARGADAEARVDGVA
+SDGTAADGAPA*
+>NZ_CP083691.1_669
+MNAALIVVVALGGGAGAAGRFLLDGLINTGREFRLPVGTLTINITGSLLLGIIVGAATHL
+GAVPVAVLGTGVMGGYTTFSTASFETVRLARSGRITAAAINGLGMLVVSVAAATAGILLG
+GTL*
+>NZ_CP083691.1_670
+MTTRTDTPMPDDQLPPDPDVDVSDPATTMRPVHLRWRYVGLVAVGGAGGTALRDVISSVL
+PADGGVSWSIFWINITGALALGVLLEALAHRGPDAGRRRVLRLLLGTGVLGGFTTYSTLA
+ESTAALFLDGHGLAGTGYALLTVLSGAIATACGLVVAGWFRPRTEEA*
+>NZ_CP083691.1_2029
+MADARPAAGGAAARRTLPWVALGGAAGALASLGAGALIAQAMGPGDPSISGPLGTASATL
+ASVAAVNVLGSFLLGLLRGASGRPGARWDPRLVAALGTGFLGAFTTFGTVAATLALPVMM
+TAGLAATGDTWWILLAVVVVGLLIAVAVLAALSTAAAALGLHLGGRGAGSGSAGRPDGAA
+A*
+>NZ_CP097650.1_688
+MAARGETTADRRGGRGTDRRPGTAGAVALGGAAGVLCGAGVMNAVTALAGAPNFRGTFGA
+AFGAVDVLVQALPLFVVNVLGSFLLGLLWAASRCRGPDWRPRLVAGLGTGFLGAFTTISS
+AVALVLWPVRLGAAASGAGGVLAAAVAVLLVLALMAALSTAAAVLGLRAGGAPGSRAVGT
+DRSAEDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000046.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5833a54bfd057d09724b9a815e707d866074f0fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000046.fa
@@ -0,0 +1,78 @@
+>NZ_CP042169.1_1753
+MSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAG
+PEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQ
+PPARTPRNLTRLPASGVVVLEEGGPSPEEAVARAQAWLRKRRYRVERRLEAGGASVGAER
+GYLREIGNILFHVSLIGVLVFMAYGGMTKYGGQKIIVEGEGFANNLVAYDSFTPGTYFSA
+DDLQPFSLTLDSFDAVFDRESETHYGQPLDYTAVMDVREGSGGELQRQILKVNQPLDIDG
+VRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQNYGSQATIKVPDARPDQLGFVGFF
+LPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNE
+NGGIVLSPGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFV
+RRRRVWVRARTDDDGRTRVEYALLARGEEFGLHEEHVALRAAMEKWWPIVAATETADDAA
+AGAAPQSTPTAPETPAGPADARSGD*
+>NZ_CP033200.1_1461
+MSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAG
+PEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQ
+PPARTPRNLTRLPASGVVVLEDGGPGPEEAVARAQAWLRKRRYRVEHRPEAGGASVGAER
+GYLREIGNILFHVSLIGVLVFMAYGGMTKYGGQKIIVEGEGFANNLVAYDSFTPGTYFSA
+DDLQPFSLTLDSFDAVFERQSETTYGQPLDYTAVMDVREGTGGELQRQILKVNQPLDIDG
+VRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQNYGSQATIKVPDARPDQLGFVGFF
+LPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNE
+NGGIVLSPGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLVISLFV
+RRRRVWVRARTDEAGRTRVEYALLARGEEFGLHEEHVALRSAMERWWPVAAPESEEEAVA
+SAAAVGHTGTTPETLAGPRTPRSGD*
+>NZ_CP040019.1_383
+MSRTEDQDPGRRPEVALPALGFWGTLRFAWTQLTSMRTALMLLLLLAVAAVPGSLFPQRP
+AGPGIVQDYIDDNPVLGEWLDRFQMFDVYSSVWFSAIYLLLFISLIGCVAPRAVKHAQAL
+RSAPPRTPRRLSRLPEYGRVVLEPGGPAPVEAVEQAARYLKRRGYRIEVRQEDAGGASVG
+AARGYLREVGNIVFHLSLIGVLVFMATGSLLSYRGQKILVEGEGFANTLVAYDAFTPGSA
+FSEEMLTPFSMTLKRVEYVYDRQSPTHYGQPLD*
+>NZ_CP040019.1_1050
+MGDAPVSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVP
+QRRAGPEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHA
+KALRQPPARTPRNLTRLPASGVVVLEEGGPSPEEAVARAQAWLRKRRYRVEHRPEASGAS
+VGAERGYLREIGNILFHVSLIGVLVFMAYGGMTKYYGQKIIVEGEGFANNLVSYDSFTPG
+TYFSADDLQPFSLTLDSFDVVFDRESEALYGQPLDYTAVMQVQEGGGGEPREEILKVNHP
+LSMDGVRVYLVGNGYAPVLTVRDGEGDIAFQGPVVTRVQDVNFNSLVTLKVPDARPDQLG
+FVGQFMPAAVEDESGVAVSVDPELYNPQLILDSYYGDLGLDGGVPQNVYVLDTETLTELN
+SRKNENGGIVLSQGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLA
+ISLFVRRRRVWVRARTDEAGRTRVEYALLARGEEFGLHEEHVALRAAMEKWWPVAAATAP
+ETTPETPCRPRRRPIRRLTVFNPTAPVNEQLALYSDLFMLIAAFVYAAAFVLFTIDMATS
+SATIRRLEEDLAAQRGPARLAPARETVGAGFGGSSLGGSSSVGSTGAGSSAGGPGVLPGE
+ARAAGLGDEPGLVDEDMDYTGGGRRPIANVAVAVLAVGWALHAFAVIARGLAASRVPWGN
+LYEFMTTGALVITTVYLLFLFRKDLRFVGTFVTGLVVAMMCAATMGFPTPVGHLQPPLQS
+PWLVIHVSIAVLATALFTLTAAMSMLQLIQDRAEKRAAATGERPWAFLRLVPSAQALENW
+SYRINAVGFVMWTFTLIAGAIWAEASWGRYWNWDTKEVWTFVIWVVYAAYLHARATRGWT
+GARAAWLSIVGFLCVVFNYTIVNTYFPGLHSYAGLPG*
+>NZ_CP040019.1_2590
+MSRPSDYDDGTGAGGTLRAESPELGFAGWLRWFWRQLTSMRVALILLLLLAVAAIPGSLV
+PQRGADPNGVVQYQKDHPDLFPILDAFPIQAFDVYGSVWFSAIYLLLFISLIGCVLPRIA
+HHWKAWRGRPPKTPARLQRMAGFSEIRLSNPDATPAEREAFAARAVDEAAAILKKLRYRV
+EVQRASRRGVDEVSVSAERGYLRETGNLLFHVSLLGVLVSVGLGGVFTFNGQKVLIEGET
+MVNQLIDYDTATSGRSFDSSSLEPFSLRLDTLDVTYNTPDDGNVQAIGLVKDYTANMTLI
+SPEGDESEHVIRVNHPLRVHGSPIYLIANGYAPKITIRNAEGTVVYSEAMPFIPQDNLNM
+TSLGVVKVPDGIVDESGEPVQLGLRGFFYPTKADLDTGAYTSNYPDLENPVLTLDVFVGD
+LGINDGIPKSVYALDTSDMEQVTGRAVDLDSIELRPGEQTELPNGFGTIEFESVPRYASF
+DVMQNPAQEWILVFAVLALGGLMWSLFVPRRRMWVKALPSEDGVVLQYAALARGDDPALE
+RAVEELRDRHRELL*
+>NZ_CP083691.1_984
+MGDAPVSSTSAPKDPAPRNRTRDDVTLPALGVGGTLRWAWTQLTSMRTALLLLLLLAVAA
+VPGSLVPQRRAGPEAVDQWIEDNPFWGPILDALQFFDVYTSVWFSAIYLLLFISLVGCVL
+PRALKHAKALRQPPARTPRNLGRLPESGVVVLEAGGPAPEEAVRQAQRWLKRKRYRVELR
+PEAGGASVGAERGYLREIGNILFHFSLIGVLAFMAYGGMTKYTGQKIIVEGEGFANNLVA
+YDSFTPGMYFDAASLQPFQLTLKSFDATFERQSQTHWGAPLDYTAVMEVRHGTGGDPEEQ
+VLKVNHPLEIDGAKVYLVGNGYAPVVTVRDGNGDIAFQGPVVTRVTDQNFNSLAVIKAPD
+ARPDQLGFVGQFMPAAADVGQGVEVSVDPEPLNPKLILNSYSGDLGLDAGVPQNVYVLDT
+STLTELNSRRSENGGITLSVGQTHVLPDGKGSISLDGVRRYVGLDIHYDAGKWGVGVFSV
+LALIGLAVSLFTRRRRVWVRARTGDDGRTRVEYALLARGEEFGLREEHVALREAFEKMWP
+VSAPEADTGETTPATPAPAAAPTPRSGD*
+>NZ_CP097650.1_1674
+MSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAG
+PEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQ
+PPARTPRNLTRLPASGVVVLEEGGPSPEEAVARAQAWLRKRRYRVEHRPEAGGASVGAER
+GYLREIGNILFHVSLIGVLVFMAYGGMTKYGGQKIIVEGEGFANNLVAYDSFTPGTYFSA
+DDLQPFSLTLDSFDAVFDRESETHYGQPLDYTAVMDVREGSGGELQRQILKVNQPLDIDG
+VRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQNYGSQATIKVPDARPDQLGFVGFF
+LPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNE
+NGGIVLSPGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFV
+RRRRVWVRARTDDDGRTRVEYALLARGEEFGLHEEHVALRAAMEKWWPIVAATETADDAA
+AGAAPQSTSTTPETPAGPADARSGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000047.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a52442f066ad003f2062c282ec6d72e27801379
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000047.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1755
+MQTPRPSRRTVLTGLSLLGLAPVLAACSGDDSLTRQAGNADGKNYIAGDGSVLEIAPAER
+GAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVRFL
+GVNVRDTVTTAQAFERTFEIPYPSIEDARGEVLLNMTDYVPPQAVPSTLVLDVEGRVAAR
+VLGAVEESTLRALLTTVVDEAAA*
+>NZ_CP033200.1_1463
+MQTPRPSRRTVLTGLSLLGLAPVLAACSGDDSLTRQAGNADGKNYIAGDGSVLEIAPAER
+GAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVRFL
+GVNVRDTVTTAQAFERTFEIPYPSIEDARGEVLLNMTDYVPPQAVPSTLVLDVEGRVAAR
+VLGAVEESTLRALLTTVVDEAAA*
+>NZ_CP040019.1_384
+MPIPQPHREGHHRPPGLPPRPGRRQVLAGLAGVASLPLLAACSAEDPLAAQAGKADGKNY
+IAGDGSVLEIGPAERGEPVQFSSAMFSGEPIIAQDLAGDPAVLNFWYAACAPCRVEAPDL
+QALHEQFAPEGVRFLGINVRDTIATAQAFERKFGITYPSVEDRGGQVLLAMTDYVPPQAV
+PTTIVLDHQGRVSARILGIAERSTLRTLITTVLDEQA*
+>NZ_CP040019.1_1048
+MHTPPRPSRRTLLTGLALASLAPALAACSGGDDSLARQAGNADGKNYIAGDGSVLEIAPA
+ERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVR
+FLGVNVRDTVTTAQAFERTFEIPYPSIEDTRGDVLLNMADYVPPQAVPSTLVLDVEGRVA
+ARVLGAVEESTLRALLTTVVDEAAA*
+>NZ_CP040019.1_2592
+MNRRRTGAALALPIAALFALAGCSGGDGNLAAEWNEASGKGYVSGDGSSLSIAPDQRTEP
+VEFSGETEDGDIYGSDDTVGSVTVVNFWYAGCAPCRAEAPDLVEAYDEFSPQGVKFVGVN
+TRDQVAQARQFSVRFDIEYPSIMDNAGGRAVQRAFAGQVPLNAVPTTLVLDAEGRVAHRV
+LGQLAGASQLRTLIGETLAEAGGGAAADPASDPAPADEATEQ*
+>NZ_CP083691.1_982
+MPFPPRPSRRAALAGLSAAALAPLLAACSGTDDSLAQQAGNAGGKNYIAGDGSVVEYAAD
+QRGAPVEFSAAGFDGETVSGETLRGEPALLNFWYAACAPCRVEAPHLVKLHGEFEPKGVR
+FLGVNVRDTVTTAQAFERTFGIPYSSVDDTSGSVLLAMSDYVPPQAVPSTLVLDRQGRVA
+ARVLGAVEEGTLRALLDTVVAEA*
+>NZ_CP097650.1_1676
+MHTPPRPSRRTLLTGLALASLAPALAACSGGDDSLARQAGNADGKNYIAGDGSVLEIAPA
+ERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVR
+FLGVNVRDTVTTAQAFERTFEIPYPSIEDARGDVLLNMTDYVPPQAVPSTLVLDVEGRVA
+ARVLGAVEESTLRALLTTVVDEAAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000048.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb3bb3476aa7b34d87a928da4992196719923251
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000048.fa
@@ -0,0 +1,49 @@
+>NZ_CP042169.1_1805
+MATSSLPLSDIVETGRPFTRGDLRAAGVSERLVRGGDVRRVTHGVHRLRSDHLGSWADLG
+YVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRVFAS*
+>NZ_CP033200.1_1512
+MVTSSLPLSDIAEAGRPFTRGDLRAAGVSERLVRGADVRRVTHGVHRLRSDHLGSWADLG
+YVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRIFAS*
+>NZ_CP040019.1_988
+MSMSTSTSTSLPCPQDRRPPVPARPLDVVAAGGPLFTRADLSAAGLPADRLRAADVRRVT
+HGVHRRADDVPGDWGALGYAEPPVAFAPEETAAIVTASRGVASHLSALLLHGIPVPPFLV
+DDGRVHVSRPHSRGASERPEVRSHARSVPEADAVVLHGIRVTSVERTWADLAALVRPGHL
+DPVVAAGDAVVTGIWTPQGRLPPRATILRLRAGLARSGRFKGARTARAALELIRAGADSP
+PETALRLALLHAGLPEPELQLVLHRGRRRSPDADLGWRAWRLVVHYDGDPHLDPAQQAVD
+AWRNGGWARAGWSQIVATVDDARDDFRRVVAEVLAHRARLGGRAYVA*
+>NZ_CP040019.1_1005
+MSPREPAPLPAAFSDLPFGAADLRRAGVSVERTRRADLRRVSQGLHRAREAERGEWADLG
+YPVDPLPWVPEEAAAVVPLTGGVVSHLSALLLHRLTVPPWVRPDGRLHVSRRHGRGVCDR
+SGVATHGRSVPQEDVVALHGIAVTSVERTWLDLASLMPRGPVDPLVIAGDALVNRPWIAG
+DGRRGEPVTSVESLRAALRRAGRFKGVRAARAALDLVRVGADSPPETELRLALVDAGLPE
+PELQVSGDPGDRFAPVADLGYRDWRLALQYDGGHHRSREQQARDARRDGWFHDRGWRSLR
+LTADDRLDGFRRAIAWVRRHRP*
+>NZ_CP083691.1_931
+MALESLADVLGSAPLPIRAEGPPPLGLFTRSDLRAAGLGGHRVHGRDVRRVTHGVHRLAT
+DPAGDWAVLGHRCPPAPFAPEETAAIVEAAGGVASHLTALLLHGVPLPPFLAEDGTVHVS
+RPHARGASGRLEVTSHARSVPAADVTSLHGIRVTSLERTWADLASLVPPGLVDPVVAAGD
+AVVRHPWTPQGRSAPRTTPARLAAALDRAGRFKGVRTARRALEAVRVGSDSPQETALRLA
+LVHAGIPEPELQLVLHPGRERSPDADLGWRMWRLVVHYDGASHLEPAQRAVDARRHEGWE
+RAGWAQIVATVDDARDDFRRVVAEVQAHRRRLGGRVYVC*
+>NZ_CP083691.1_945
+MAPRAPLPLPAHLADRPFTRVDLTTAGWSIERARRGDLVRVVHGVHRSWEAETGDWADLG
+FPVDPVPWPPVDAAAVVRRARGVLSHQSAALVHGLVVPAWVRPDGRLHLSRPHDRGLSGL
+PRVQTHARSVPPVDVTSIHGIPCTSLERTWVDLASLMPRGPVDPLVIAGDALVNHPWAGE
+GQARGAARTTVVSLRAALERAGRFKGVRAARLALDLVRVGADSPPETELRLALLAAGLPE
+PELQARIDPADPWAPAVDLAYRPWRLSLQYDGAHHRTREQQGRDARRDGLVQDAGWRSLR
+LTAEDRHDGFRRAVEWVRRHGSP*
+>NZ_CP097650.1_1725
+MATSSLPLPDIVETGRPFTRGDLRAAGVSERLVRGGDVRRVTHGVHRLRTDHLGSWADLG
+YAEAPAPFAPEETAAVVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRIFAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000055.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000055.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91f5357bea15bd3971ef40f95419a8bba5c04a7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000055.fa
@@ -0,0 +1,42 @@
+>NZ_CP033200.1_1652
+MEHATALENVMLPLRYGPDRVPRGEQRRRAGEALERVGLGMRTGHRARTLSGGEKQRVAV
+ARALINEPPLVLADEPTGALDQARTRDVVDLLRGAVGPERAVVVVTHDPRVAAACDRRWH
+LVDGELAPQD*
+>NZ_CP040019.1_839
+MTLLEVHDVDKTFHSGGEAVPVLRGASLLVPAGEMHAVTGPSGSGKSTLLRILACLDSPD
+SGRVLLGGEPLPEPWSRGGDRYRNQRCGIVLQDFALMEHATALENVMLPLRYGPDRVPRG
+EQRRRAGEALERVGLGTRTGHRARTLSGGEKQRVAVARALINEPPLVLADEPTGALDQER
+TRDVVDLLRGAVGPERAVVVVTHDPRVAAACDRRWHLVDGGLAPQD*
+>NZ_CP040019.1_992
+MSDGSAPPLLELAGVLKSFKGADRPALDGVDLTVRDGDFVAIVGPSGSGKSTLLNVLGLL
+DRPDGGSYRVSGTDTMSMGERERDRLRSRWFGFVFQSSHALGDEPVAVNAALGLRVQRTP
+PEQRDARAGEALALLGLSHRLDTRAKLLSGGERQRLAIARAIATRPRVILADEPTGNLDS
+VNSRIVIDHLRALHAQGATVLLITHDPEIARQADRQVRIEDGRITELAGHRTAASASADM
+AGTGHGWSAPGAARRHRSPRSSAMLDDLVEAVSSLSTRFLRTVLLMAAFAVGIGGLVASV
+GLTQTATDQVGALLTAAALDEVVVTVPQAEGLLDPGDGRLASWADGLAALPHVTAAGHVA
+QVAPADVVITRHDPSDPEPAVAISLVAASSSYAGLAGLTLPSETSRTLLDSPDARLAWAT
+PAAARALELPVTDTGMLSPGYRVWIQGHAVDVAGIVTLSERTPELDASLVVTPAVMTGVA
+QAHPQLVVRTEAGFPYPVSQAAPLVIAPENPGSVTVRTVADLRNLRAGVSDDLGAFVGVL
+SGVLLVLAVISASTAMYLSVQARTAEIALRRAIGSPRGLIARLFLLEGALIGLAGGAVGA
+AVGSGVILAVSQARGWAAVLPPGAVPLALGLGLVAGVVSALYPGWVASRQRPADALRG*
+>NZ_CP083691.1_775
+MSLLEVHDVDKSFTTAASEVPVLRGVSLSVPAGQMHAVTGPSGSGKSTLLRILACLDSPD
+AGEVLLEGVPLPPPWSRGGDRHRNRRCGIVLQDFALMEHATALDNVLLPLRYGPGGGSRA
+EQRRRAALALDRVGLADRAHHRARTLSGGEKQRVAVARALINDPPLVLADEPTGALDQAR
+TRDVVKLLRSAVGPQRAVVVVTHDPEVAAACDQRWHLEDGRLHSQG*
+>NZ_CP083691.1_852
+MTASAPVLTLDRVQVGYRHPDGGTRVLIESLDLTLAPGEVVGLWGRSGTGKSSLIRHLAG
+LSRPLAGRIAYRSPDGSLNGEVADLSAGDLARYRREHLGYVDQSCELIGELSALDNAAVW
+IHGGRIAGSACDAQETVQGLLERLGLGHRLGAPASRLSGGEAQRVALVRALSKRPHLIVA
+DEPTGHLDGVTAREAIALLREHAEAGAAVLVASHDPLVHAAVDRAVRVGED*
+>NZ_CP083691.1_924
+MNTAPLTPPVLAARGLTKAYGSTHALTGVDLEIRPGESVAVMGPSGSGKTTLLHVLSGII
+APDGGRVTLAGADGTVHEVTALTEEQRARLRRERLGFVFQEGLLLPELTAVENVAMPLML
+NGVDRRAAEQTAARWLGSLGLAGMEDRRPGELSGGQRQRVAIARAQAVEPDVVFADEPTG
+ALDSDTSEAVLDSLIASTVARGRTLVVVTHDPSVAAACSRLIRVRDGRIESDQAQAAAGT
+TREQVR*
+>NZ_CP097650.1_710
+MSLLTVHDVHRSYRGPAGDVPVLRGVSLQVPGGGVHAIMGPSGSGKSTLLRLLACLDTPD
+AGSIRVAGRSLPAPWSSDGDAYRNRTCGIVLQDHLLIDRATAVDNAALPLLYARPRTSKR
+ERRTMAAELLTRLGLGDRLHHPVGRLSGGERQRVAIARAVIMGPSLLLADEPTGALDEER
+TDEVMGLFRSMSQPERAIVVVTHDPAVAARCDHTWRLRAGRLE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000056.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a7df788128b8a903373dd2c83a049c887fbcde7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000056.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_23
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESIALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRGGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGATAPAPDRLVEDPPAAAPREPSPAPRVGP
+RPAPRRAAAPAAPAAPSHADQPTVVMGRPVTEPAGPALELDGRMLPLDGDDLILGRSAER
+ADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTE
+LLFFGGTGGRA*
+>NZ_CP033200.1_1997
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESLALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPREPSPAPRVGP
+RPAPRRAAAPAAPAAPAAPAAPAHADQPTVVMGRPVTGPAGPALELDGRMLPLDGDDLIL
+GRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVV
+TVGQTELLFFGGTGGRA*
+>NZ_CP040019.1_356
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFDRARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDTDVRAGD
+LRVVTGLDDGSLPAPAPHDDGASPATAHGPGATATAPDRLVEDLLGGRTP*
+>NZ_CP040019.1_357
+MGRPVTEPSGPALELDGRMLPLDGDDLILGRSAERADLVIPDSSVSREHLRLLTVGSTVT
+LLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTELLFFSGTGGRA*
+>NZ_CP083691.1_339
+MGLLDNLERGLEKAVRSAFSAGGARAVQPVEIASALRHAMDDESFALSEGHTVAPNDFTV
+HFAPADFDRARTWGSTLAGELCDEVIRHAQSQGYTLPGSVRVAFHEDAQVHAGQVEVDAR
+IDDGSSPVPSPPAATSAPAPAAARTADDRGPRPSRAPRHGATAAPAPRRDPSPAPRPAPT
+PARSESARRAPADEQATVVMPRRTSPAPAVPWLEADGVRHPLTHEDMVLGRSSERADVVV
+PDSSVSRQHARLVRVGRSVTLIDLGSRNGVTVNGRRVDGSTVLREGDRITVGQTDLVFHI
+DPADGRPRA*
+>NZ_CP097650.1_23
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPRKPSPAPRVGP
+RPAPRRAAAPTAPAAPAHADQPTVVMGRPVAEPAGPALELDGRMLPLDGDDLILGRSAER
+ADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTE
+LLFFGGTGGRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000058.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7800e2ddbe90d27b539b1c55914e20d861a8bf5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000058.fa
@@ -0,0 +1,44 @@
+>NZ_CP042169.1_46
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGEDA
+TVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFVSAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRARFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAA*
+>NZ_CP033200.1_2015
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGEDA
+TVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPEEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFVSAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRTRFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAA*
+>NZ_CP040019.1_341
+MQQIHDPASRGFASDNYSGVHPEVLAAIAEANGGHQTAYGEDAYTGRLAEVVRGHFGEDA
+QVWPMFNGTGANVVALQSMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLTVPTPDGKL
+TPELIDVQAWGWGDEHRAQPLVVAITQSTELGTLYTPEEIRAITEHAHARGMTVFLDGAR
+LANAAAALDLPLRAFTTDVGVDVLSLGGTKNGALGAEAVVALNPAATTGMTYLRKSQMQL
+ASKMRFVSAQLLALFDGDLYLRTARHANAMAQRLQDAVAAGIADGSLPGVALTQRAQVNA
+VFATLPAGVADRLRRSFRFYDWDEANGEVRWVCSFDTAEEDVDAFVAALRAELAPAD*
+>NZ_CP040019.1_1582
+MSAGAPAAGLRAFASDNYAGVHPDVWAALADVDAHHAPAYGADPHTERLQEAVREAFDAP
+DAVALPVFNGTGANVVALQSMLPPWGAVVAADTSHIHHDEGGAPERMGRTKLFTVPTPDG
+RLTPELVDREAHGWGFVHRAQPAVVEIAQVTELGTVYTPEQVRALADHAHGHGMGLYMDG
+ARLFNAAAALELPLSAFTTHAGVHVVSLGGTKAGALGAEAVVVLRPEAVTLASLVPERDL
+PADAGPRERARLAVEYVRKSSMQLASKMRYVSAQLTALLKGDLGIRLAGHANAMARELAG
+RVAGIDGVEVTRTPEANAVFAVLDPQAADRARVRHPFYDWDAARHEVRWMTSWDTTAADV
+DSFAAALGEALSPGRRR*
+>NZ_CP083691.1_1475
+MSAARPAGLRAFASDNYAGVHPDVWAAMADADADHAVSYGEDPTSAALQEKVREVFGERA
+FAVPVFTGTAANVLALQALTPPWGSVVTAASSHLIHDEGGAPERLGRTPLVPVPTPDGRL
+TGELAAAHVRRDGFVHASQPAVVEIAQATELGTVYSAAQVREVADAAHAAGAALYMDGAR
+LSNAAAALDLPLRAFTTDAGVDVVSYGGTKNGGLGAEAVIVLNPEAVVAARMVGPADVPG
+GDAADARDRARAALGYLRKQDMQLASKHRYLAAQLLALLTDDLGIALAAQANRMARVLAD
+AVAGLDDVELARAPEANAVFARLDPDVAAEVRLRHPFYDWDAAAHEVRWMTSWDTTDADV
+ESFVDALAAALRARRPR*
+>NZ_CP097650.1_41
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGKDA
+TAWPMFNGTGANVVGLQTMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFISAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRARFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000061.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c19f23e872b4c316647845e95fda12ae1914448
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000061.fa
@@ -0,0 +1,29 @@
+>NZ_CP042169.1_65
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAEGEESPTDEPQGRAVDTEEAQ
+PATEEGEATDEPQGR*
+>NZ_CP033200.1_2034
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFNAEGEESPTDEPQGRAVDTEEAQ
+PATEEGEATDEPQGR*
+>NZ_CP040019.1_313
+MPHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDAMV
+LLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPADKRFDHITELEHIEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWQGRADAEAELEASIARFDAAGEHSPTDEPQGRDVETEDPS
+PATEEGEEKDVPQGR*
+>NZ_CP083691.1_253
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+FLPGFDLVPGCIVEARPVGVFNMTDDGGGDAKLLCVPADKRFDHIQELEDVEESLKQEIE
+HFFTRYKDLEPGKWVKADGWEGREAAEKELEASIERFAAEGEHSPSDEPQGRDVDTEEAA
+PAAEQEA*
+>NZ_CP083691.1_668
+MLFDVTIEIPRGSGNKYEVDHTTGRIRLDRAVFTSMVFPQDYGSIDNTLGDDGDPLDALV
+LLPRPTFPGVVITVRPVGMLRMVDENGGDDKILTVPAGDDRFAQLRDITDVPEHTLAEIE
+HFFAHYKEIEHGKHVTTNGWADRAAAEAVIRTAQNAHTRHP*
+>NZ_CP097650.1_59
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAQGEESPTDEPQGRDVDTEEAQ
+PATEEGEPQGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000062.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..283b45dfde98e6ab5105cac38830a1a623774736
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000062.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_73
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RFLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGTPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRTAAAWAGAHAPGEPVSE
+DVLP*
+>NZ_CP033200.1_2042
+MDESIDAAAREANRALLGRLPAGRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RFLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGTPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRAAAAWVGAHAPGEPVSE
+DVLP*
+>NZ_CP040019.1_304
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRSGARAVPPAEEQARILPVIEALLAEDVVVSVDTRHTATARAALALGP
+VIVNDVSGLVHEPEMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RLLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGAPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRTAAAWVGAHAPGEPVSE
+DVLP*
+>NZ_CP040019.1_2293
+MLRSRVTVFGILNLTEDSFFDESRRLDPAGAVTAAIEMLRVGSDVVDVGPAASHPDARPV
+SPADEIRRIAPLLDALSDQMHRVSIDSFQPETQRYALKRGVGYLNDIQGFPDPALYPDIA
+EADCRLVVMHSAQRDGIATRTGHLRPEDALDEIVRFFEARVSALRRSGVAADRLILDPGM
+GFFLSPAPETSLHVLSNLQKLKSALGLPLLVSVSRKSFLGATVGLPVKDLGPASLAAELH
+AIGNGADYVRTHAPGDLRSAITFSETLAKFRSRDARDRGLDHA*
+>NZ_CP083691.1_245
+MLPKPFHELPDRTLVMGILNVTPDSFSDGGAHDRVDAAVAHGLDLLAQGADLIDVGGEST
+RTGATPVDPAEEQRRILPVVEALLAEGAVLSIDTMHTATARACLALGPVIVNDVSGLVHE
+PDMPALVAESGAPCILMHNRGHAQVMDSLAHYEDTLGEVVRELSEVTDRFLAAGASPEQI
+ILDPGLGFAKAGEQNWELLRGLERIESLGRPVLVAASRKRFLGTVLAGEDGTPRPALDRD
+HATAAVSAISAAHGAWGVRVHDVRSSVDAVRVGDAWRGAAPRPAGPGEARA*
+>NZ_CP097650.1_67
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RFLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGTPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRTAAAWAGAHAPGEPVSE
+DVLP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000068.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d9c30dea6727a07e54acda9ae031a419448f234
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000068.fa
@@ -0,0 +1,53 @@
+>NZ_CP042169.1_200
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+AFEDVVEFVVPALQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR*
+>NZ_CP033200.1_2149
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSTVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+TFEDIVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR*
+>NZ_CP040019.1_175
+MAEHPAARPEQDATTSTSAATSTSPASRAGRELLFNAFDMNCVAHQSPGLWRHPEDRARD
+YNTLGYWTHLAQTLEKGLFDGLFIADVLGPYSVYGGTAEAAIRSGAQTPVNDPFLLVSAM
+AAVTGHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQM
+EHDERYEHADEYLDVVYKLLEGSWEDDAVRYDKETGVFADPAKVHDIGHEGRYFKVPGAA
+VTEPSPQRTPVIYQAGASTRGRAFAGKHAEAVFINSPTKELTAATVKKIRQALVDAGRDP
+YDVKIFAMQTIVTGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDV
+KSNAIQSAVEAFQKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDV
+DGYNLAYHITPGTFEDVVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPEGHHGASF
+ALRRRG*
+>NZ_CP083691.1_121
+MSTAENAGAGAPTRPDEHREILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTRLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGTWFKVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEGWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+TFEDIVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFAFRNRRG*
+>NZ_CP083691.1_123
+MSTPTPTLGIALTTQTPADARGHWTRLSQALEETSLDWAVLTDPLGTAPQAGTHRIDAVL
+AACWTATRTHRIGLVPEVTTTHTEPFHVSIGLATLDHVSHGRAGWLATVSAAPEVSALFG
+RRRHPAERTPGLQASRVDLELWEELQDAVAAVRDLWESWEPDAEIRDIATGRFIDRERVH
+HVDVEAERFSVRGPSITPRPPQGRLPVLVEAAGPAGLEAARRTADVVLLPAAEVGRTDAA
+RLPDRRRRGATPAVPVEPTRIVADVTLEGDGARVADAVRHALQAGADGARLVPNPTADPF
+DALALAADVHDRLDDIRPPDTGTVPLRECLGLAPALSPWRHPEDPTARPTDEEATA*
+>NZ_CP097650.1_200
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+AFEDVVEFVVPALQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000073.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000073.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2df4a4c101f602055ac684be67779744d04e612e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000073.fa
@@ -0,0 +1,66 @@
+>NZ_CP042169.1_242
+MTVQDPTAVAAPSPTEVFRVARDLLVECQTDDERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARADVPALIIAEDDGRSTERTFAELSAASNRVANWLSAQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGAEDLAKFAGVGEGLHLVHVPG
+VFAEGPARRAPEVAGHTVLSYDDAADAATELAPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMARYGVTSFCAPPTVWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWG
+TTIRDGFGMTETTLQVANTPGQKVVIGSMGRPLPGMDVTLIDPLTGQEAEEGEICLRLDP
+RPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERAQTGAAPDGYGTEFREEDLDLHR*
+>NZ_CP033200.1_2210
+MTVQDPTAVAAPSPTEVFRAARDLLVECQTDYERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARADVPALIIAEDDGRSTERTFAELSAASSRVANWLSAQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGAEDLAKFAGVGEDLHLVHVPG
+VFAEGPARRAPEVAGHTVLSYDDADDAATELTPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGGVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMERYGVTSFCAPPTVWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWG
+TTIRDGFGMTETTLQIANTPGQKVVIGSMGRPLPGMDVTLLDPLTGQEAEEGEICLRLDP
+RPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERAQTGAAPDGYGTEFREEDLDLQR*
+>NZ_CP040019.1_112
+MTVQDRTPADAASPTEVFRAARDLLVECQTDYERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARQDVPALIIAEDDGRSTERTFAELSAASNRAANWLAEQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSADLEDRVSRADAAWAVAGAEDLAKFAGVGEGLRLVHVPG
+VFAEGEARRAPEVPGHTVLSYDDAAGASAELSPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLQPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMDRYGVTSFCAPPTVWRMLIKADLAQLKTPPTKTISAGEPLNAEVIDQVQKAWG
+ATIRDGFGMTETTLQVANTPGQKVVIGSMGRPLPGMDVVLIDPLTGQEAAEGEICLRLDP
+RPVGLLKSYFGNQEKTDEVFRDGVFHTGDIASRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETAQSILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERSETGTAPSGYGTEFREEDLDLTR*
+>NZ_CP083691.1_80
+MTTTSVTERLRAARDLLVECQEDYDRARAEFEWPRFEHFNFGFDWFDQLAARPDRADVPA
+LIISDAGGGHLSRTYAELSAASNRAANWLRERGITPGDRVILMLDNQVELWELMLACIKL
+RVVMVPTTTQMTSADLADRVERAEARWVVASAENLAKFDGVDSGLHLVHIPGVAAQGDAR
+TAPVVAGHEVLSYDDAASASPELTPDSPTPADETLLLYFTSGTTSKPKLVEHTHTSYPVG
+HLTTVYWIGLQPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDAAALMADMD
+EFGVTSLCAPPTVWRMLIKADLSLLKTPPVKTISAGEPLNAEVIDQVHRAWGTTIRDGFG
+MTETTLQIANTPGQKLVIGSMGRPLPGMDVVLIDPLTGEEAAEGEICLRLDPRPVGLLKS
+YYGNEEKTAEVFRDGVFHSGDIASLDESGVLTYVGRADDVFKSSDYKISPFELESVLVEH
+PAVMEAAIVPSPDEVRLAVPKAFVTLAPSYEPTAETARQILQHTLTQLPPYKRIRRIEFR
+ELPKTISGKIRRVELRKAEAERAETGQAPEGYGIEHREEDLDLKR*
+>NZ_CP083691.1_2418
+MSVTARLRAARDLLVEHQQDYAGARAAFEWPRFETVNFGSDWFDAVAATPERADQDALVI
+VEEDGTVLRRSYARMSADTDRVAGWLQHLGVGRGDTVIVMLDNQVELWEAMLACMKIGAV
+VIPTTTQLVAADLQDRVDRAGARWAIANAGNLVKFADVVGDCTLIHVPGVYASEAEHALP
+EVPGHPVHSYGDAASFAGTWSLETPTSADDPLLLYFTSGTTSLPKLVEHTQASYTVGHLS
+TMYWVGLRPGDVHLNVASPGWGKHAWSSFFAPWLAEATIFVLNFRRFDAATLMRAMDEGG
+VTSFCAPPTVWRMLIKADLTQLQAPPRNAISAGEPLNAAVIDQVQRGWGVTVRDGFGQTE
+STLQIANTPGQRVVIGAMGRPLPGFDIELRDPQTGDRVDGEGEGEICVGLDPRPVGLFQR
+YHGDPEKTAEAFRDGVYHTGDIARRDEHGIYTYVGRADDLFKSSDYKLSPFELESVLMTH
+PAVLEAAVVPAPDELRLSVPKAFVTLAAGHEPGEEAARAILQHVTDRVPAYKRIRRIEFR
+PLPKTVSGKVRRVELRAEEEQRRAGVAGLGVEHREEDLGIRRQRRA*
+>NZ_CP097650.1_242
+MTVQDPTAVAAPSPTEVFRAARDLLVECQTDDERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARADVPALIIAEDDGRSTERTFAELSAASNRVANWLSAQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGAEDLAKFAGVGEDLHLVHVPG
+VFAEGPARRAPEVAGHTVLSYDDADDAATELTPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMERYGVTSFCAPPTVWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWG
+TTIRDGFGMTETTLQIANTPGQKVVIGSMGRPLPGMDVTLLDPLTGQEAEEGEICLRLDP
+RPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERAQTGAAPDGCGTEFREEDLDLQR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000078.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27ed2d1a4fb65458af83a7bc2278a02609f45fa6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000078.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_287
+MLSEKSRPVIEATAAAVAEHMPEITPLFYAHMFEAHPELLDGVFSRANQRNGEQAQALAG
+SIVKFAVHLLENPGTLPEAVLSRIAHKHTALGIVEEQYPIVYENLFWAIGEVLGDAVTPE
+VADAWTEVYWLMADALIKIEKGLYAQQANDRMWTDWKVVAKEPTGNAAVTFRFEPADDTP
+QSRGKAGGYVSVRLKVEDGLRQCRQYSLSEKAESATERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLLLHGDAS
+WEAVALREQVTESLAALAHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA*
+>NZ_CP033200.1_4
+MLSEKSRPVIEATAAAVAEHMPEITPKFYAHMFEAHPELLDGLFSRANQRNGEQAQALAG
+SIVRFAVHLLENPGTLPEAVLARIAHKHTALGITEDQYQIVYENLFWAIADVLGDAVTPE
+VAEAWTEVYWLMADALIKLEKGLYAKQANDKMWLDWKVVSKEPTGNAAVTFRFEPADDTP
+QTPGEAGGFVSVRVKVADGLRQARQYSLSDHAASTTERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLFFHGDAS
+WEAVALREQVTESLAALPHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA*
+>NZ_CP040019.1_51
+MLSEKSRPVIEATAAVVAEHMPEITPKFYAHMFEAHPELLDGVFSRANQRSGEQAQALAG
+SIVTFAVHLLEHPDTLPEAVLARIAHKHTALGIVPEQYQIVYENLFWAIADVLGEAVTPE
+VAEAWTEVYWLMADALIKIEEGLYAQQANTKMWTDWKVVAKEPTGNAAVTFRFAPADETP
+QTPGRPGGYLSVRLKVEDGLRQCRQYSLSDHAESTDERVITVKLDEGGEVSPVLIQNVEV
+GDVIELSNPYGDITLRDDAETPLVLATAGIGITPAAAILDTLASRGSQREVHFFHGDASW
+DSVALREQVAESLQALENGTGRLWLGVPPQEAPAAFTTTEGLMEFDDVELPADASYLLCG
+PLAFMQATRSKLIDAGVPATSIRYEIFGPDLWLAA*
+>NZ_CP083691.1_29
+MLSEKSRPVIEATAAVVSANMPQITPAFYGHMFEAHPELLDGTFSRANQLNGEQAQALAG
+SIVHFAAHLLEHPDSLPEAVLARIAHKHTALGITEDQYQVVYENLFWAIAQVLGDAVTPE
+VAEAWTEVYWLMADALITLEKDLYAVQANDRMWTDWKVVAKEPTGNAAVTFRLEPADDTP
+QTPGRPGGYVSVRVTVADGLRQARQYSLSESASSTGQRVITVKLDEAGEVSPVLIQEVEV
+GDVVELSNPYGDITLQDSDAPLVLMTAGIGITPAAAILDSLAASGSQREVRVLHGDASWD
+SVALRDQVLEDVASLPHAQADLWFGVAPETAPEGVSVHEGKVDTAAAALPEGADYILCGP
+LAFMKSERSALIEAGVPAPRIRYEIFGPDLWIAAT*
+>NZ_CP083691.1_1199
+MPAHGWGARAGRTSFREHPVDVQECLWRGAHASSHDRSALHSRPSRGGSADPAPADRPPP
+PLTPAPGPAGIRDRPAGRIPAWWRDASGSLLWLVLLAVTALWVHGGGVQDLAAVGSGLTS
+LGRLTGLIASALLLAQVFLMARVPLVEQAWGQDRLTRVHRRVGFTSFTLMFAHLALITAG
+YAWDTPAGLWGTLVDFAVDYPGMLLAIAGTAALVMVVVTSFKAARARLRYESWHLIHLYG
+YLGAGLALPHQLWTGQEFLASPVATAFWWTLWAVTAGAVVVFRALLPLWCSARAGLRVQS
+VTAAGPHAVTVTVAGRGAHRLHARGGQFFQWRFLDGPGWTRAHPYSLSAAPDGRTLQFTA
+AVVGDGTGRLWDMRPGTRVLVEGPYGRMHDGVRTGRKALLMGAGIGITPMKALLESLPAD
+AGEITVVHRVSDPDDPTLHADLLAAARTRGARYIRLEGRRRPGADSWLPASAGDVDDVTA
+LRRICPDLAEHDVFVCGAPAWTDLVRQAARRGGVPAERIHDERFSF*
+>NZ_CP097650.1_294
+MLSEKSRPVIEATAAVVAEHMPEITPLFYAHMFEAHPELLDGVFSRANQRNGEQAQALAG
+SIVKFAVHLLENPGTLPEAVLSRIAHKHTALGIVEEQYPIVYENLFWAIGEVLGDAVTPA
+VADAWTEVYWLMADALIKIEKGLYSQQANDRMWTDWRVVAKEPTGNAAVTFRFEPADDTP
+QSRGRAGGYVSVRLKVEDGLRQCRQYSLSEKAESTTERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLFFHGDAS
+WEAVALREQVTESLAALPHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000079.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ffd03e5be24276730f74c195135f8217f33e489
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000079.fa
@@ -0,0 +1,43 @@
+>NZ_CP042169.1_298
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPAGQLMAVP
+DGVGLVEAAALPEVACTVHSTLVGRAGVQAGDRVLVHGATGGIGSFAVQFLTAVGARVLG
+TAGGPEKVALGRGLGAEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVTDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA*
+>NZ_CP033200.1_22
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPTGQLMAVP
+DGVGLVEAAALPEVACTVHSALVGRAGVQAGDRVLVHGATGGIGSFAVQFLAALGARVLG
+TAGGPEKVALGRRLGTEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVVDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA*
+>NZ_CP040019.1_23
+MSETTRTPGTGRGTMRAVRFTGEGGAGSLAVGQEPIPTPGPGEVLVKVAAAGLNRADVMQ
+REGKYPPPPGASDVPGLEVSGVVVALGEEAGLPGEGRFAPGDEVCALLAGGGYAEHVVVP
+AGQLMAVPPGVDLVTAAALPEVACTVWSTMSERGGVRAGDVVLVHGGSGGIGTFAVQYLA
+AIGARVLATAGGPAKCERVRGLGAEDVFDHRSGEPGAFADWVLERTGGRGADVVLDVVGG
+PYLDANVRCLAEEGRIVVIAVQGGPKADGFNLMRLVSKRGWLTGATLRARSVVDKARIVA
+GTERAVAPLVAAGRIDLAVGARFPLDDAAAAHRRFEAEDRVGRVLLVTDPADALWPQEDR
+T*
+>NZ_CP083691.1_19
+MDTAPDMLAVRFAGAGGTDVIRVGREPVPEPGPGEVLVRVAAAGLNRADVVQREGHYPVP
+PGASEVPGLEVSGTVVALGPQAGVAGEGRFAVGDRVCALLAGGGYAEHVAVPAGQLMSVP
+DGLDLVSAAGLPEVACTVHSNLEGRAGVRPGEWALVHGATGGIGAFAVQYLSAVGVRVLA
+TAGGPAKVARALELGADAAFDHRAAAPGAFADWVREITGGHGADVVLDVVGGPYLAPNVK
+ALAMDGRIVVIAAQDGPVPEDFHLMRLAARRGWVTGSLLRPRPPDEKAGIVAAAERAVWP
+LVAAGRIDPGVTARFPLREAAAAHAHFEGAARMGKVLLVTDDADALLPGGAA*
+>NZ_CP083691.1_638
+MHPSLPRTMLAAIIPAPGGRPELRQCPVPEPGPGEVLVRVMASSVNPTDVMTWRRGMFVT
+GQTVPFVGGYDMSGIVVKLGRGVTALDVGDAVTGMPRFPAPAAAFAQYSAVPARHLARIP
+TGTEDLSAGAWGRWAGLPLAGLTAYQALVDTAHLQSGQTVLVHAASGGVGSLACQLAVNL
+GAQVTAVTSDRGRTLVEVLGTRHVVDRATVDWQRFAGCFDVVLDTVGGDTTPRSLAMASP
+DGVVVALHPYAHDDLAQRDPRLRRMLVEPDHHALELLIEQAARGRLTVQVGAGYPLSDLG
+DALLHVETNKTPGKTIIHIQGDNA*
+>NZ_CP097650.1_305
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPAGQLMAVP
+DGVGLVEAAALPEVACTVHSALVGRAGVQAGDRVLVHGATGGIGSFAVQFLAALGARVLG
+TAGGPEKVALGRRLGAEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVVDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000085.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f25fed948d3ce681063155f4ce0fb8b48fc0d5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000085.fa
@@ -0,0 +1,54 @@
+>NZ_CP042169.1_398
+MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERRGTTADTADTAGEQA
+AAPAAPTRLSRLDEVAAEQDARPAAAVKPAGGPAASETAAAGRETDESVAGVAGGAGVTV
+DQQDAPRTDATAETSRPTAAPTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDE
+QTPAADVAAAPASPSPVTETPAPAAPAAEAPQHRSHLTPAPEHVHGTVPAEEVAAEHTPT
+KEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTQQNDADGAERSAAGSLRIDGT
+PGVPGRVAEAGREPARTEDHRADAAQPAAVEPAAERPSLEAAAERPSLEATPATRRAEAP
+ETHAGTTPATPLGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAATAGTAGTA
+APTSSTPTTVAPDTSTSSAPTNEEPAEDDTEGAALPDLRADRDETRGSDAEGESKLAQAG
+AVAASAFETVRDKVAIPLRDNVAVPAKDKAVKVVKDKLAQAQERRWGKR*
+>NZ_CP033200.1_128
+MPQSTLYWIIAAIIVVLLILIIVSVIASRRRREAEAEAAETRLERRGVSADTAGEQAAAP
+AAPTRLSRLDEVAAEKDARPAPAVRPAGGLAAFDTAAADRETDESGAGVAGGAGVTVDQQ
+DAPSTEATAQTHRRDAAAPATRGTLRPAPAVPSTVREADTVGLGAAGVAGGSGVTLDEQT
+PAADVPATPASPSPVTETPAPAAPVAEAPQQRSHLTPAPEHVHGTVPADEVAAEHTPTKE
+FATDGIPVPQGEHLETHTVATTAHGSVTVVATESDQAQQTGVDGTERSAAGSLRIDGTPG
+VPGRVAEADREPARTDDHGADVAQPAAVEPAAERPPLEAAPATRRAEAPETHAGTTPATP
+LGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAGTAAPTSSTPTTVAPDTSTS
+SAPTDEEPAEDDTEGAALPDLRADRDETRASDAEGESKLAQAGAVAASAFETVRDKVAVP
+LRDNVAVPAKDKVVKVVKDKLSQAQERRWGKR*
+>NZ_CP040019.1_2493
+MPTDAEPAADDTEGAALPVQDATRADAVRPGTARTDASAGDSKLAQAGAAAGTVLETVRD
+KVAIPLRDNVAIPAKDKAVKVLKAKLAEAQERRRNKR*
+>NZ_CP040019.1_2494
+MGESTLYWIIGAIIVVLLILIILSVVASRRRRAAEAEAAEAQLERRRVTPTAAGVGASHE
+DALEETHDADARPHTVASTGGDVAPAAAAGAAAGTTRLSQLDDVAPVAAAAADADAESLP
+ADGVAAGSGVTVDQQDASDQSVRPAAPAAPAGADTRGPNASVKSAGAAAAAVGLGAAGVA
+GGRGVTVDQQDAAADVPSTPASPSPVAQTPAAPSSAGATTAQDDRADRTAQDAADAEPVK
+GTVPLSEDAHAVPPAADPPSGGDAVADDAHLEAHTVATTEHGSVVVVTAEQDEDDQATAA
+SRETETETDDSRGDDAGQDRDAERAVAEGVAGGTGVTVDQKAVAEAAATQGAPASAAGAA
+SAAGAAARRRDRGRRLDPACGGARLLQDRRHAGHARPRRLRGAGRGRGGDRPARPPRRRP
+GDARLHHPRDAPGRRAGAGPGRRRRGLPQGRGRDPAAPPRGRRPGAKPRRRPTSTRPRPR
+PPRRTAPAR*
+>NZ_CP083691.1_2358
+MPQSTLYWIIGIIIVVLVIILIVSSLRAKRGREEEAAAAGRHADSAPAPLAATAARGGTV
+GASTVPATGDAPADRTDGRAAGATALPSFDVDEVDRRAAEQREQDVVERRRATGAEAGAA
+GHAAVPGVTGGSGVSVDEAEGVAKDATGQDVTPVADAQRRNGSSAAPAATGAGLGLAAAG
+VAGGTGVTVDDAGTGADLPAPKGSPAGVVEVAETQAEAAQADAAPAEHTVVPGVAGGDAV
+TVDTADVQSSSAPQGAQAAAGRSDLTDAEARTYPVTGLPGVPSAVDPEQVAAARVQDAAE
+LKAAEGQGAEHERGASQPADPESVPGTVPLTGEEAVIEAPVHTHEMPEPVLGTPAYIQDS
+TTGQDPTEDLPEGQVYGTTPLSGEDAIVEPADQLPAEAAETEDRAASDAGTASAETAVVP
+VEETETAVVPVAETRSADAGPSEDSVALTGQGVETADRVEPAAPVAGTPARDEARTHDEH
+RSRLEIVKDAVAETAGTVATTAGTAAEKAAPVVRSAARTVGKAAGSAASTLKDKLAQAQE
+RRWGKR*
+>NZ_CP097650.1_401
+MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERRGTTADTADTAGEQA
+AAPAAPTRLSRLDEVAAEQDARPAAAVKPAGGPAASETAAAGRETDESVAGVAGGAGVTV
+DQQDAPRTDATAETSRPTAAPTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDE
+QTPAADVAAAPASPSPVTETPAPAAPAAEAPQHRSHLTPAPEHVHGTVPAEEVAAEHTPT
+KEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTRQNDADGAERSAAGSLRIDGT
+PGVPGRVAEAGREPARTEDHRADAAQPAAVEPAAERPSLEAAAERPSLEATPATRRAEAP
+ETHAGTTPATPLGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAATAGTAGTA
+APTSSTPTTVAPDTSTSSAPTNEEPAEDDTEGAALPDLRADRDETRGSDAEGESKLAQAG
+AVAASAFETVRDKVAIPLRDNVAVPAKDKAVKVVKDKLAQAQERRWGKR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000086.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000086.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f46d0cda8fd24e8ddf3a0f76fe1b54aa1966a7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000086.fa
@@ -0,0 +1,61 @@
+>NZ_CP042169.1_403
+MPSPTTTTAPGPASPAGPLRPPHTAAESAERVKRRGALYFAEHQLRNMRRYGAVLIVGAL
+GEPVLYLLAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALMTASVEFSYPVMGG
+FQWHRTYYAAQATPLSPAQIALGHLAAVSLRFVFQAAVFLLVMLAFGVVSSPWAWVQVLT
+ATLGGLAVGAPIMAFAASLKEDKGQFATLQRLVVMPLFLFSATFYPLDVLPVWLRWIGWL
+SPQWHAAQLGRMLSYGMAEPAWLTVAHVAFLLALALGGARLAVRIYTRRLGWVRGTPDRD
+AGTAARRDRAPRLGRRAPRLGRRAARTGAARADVAPAAAQADPAAPSSSVVREHAVAVPP
+LPEIPVRRGPLAGAYSGNVRAVMERAFLSLKSNNWVVFFSGFFEPVLYLASLGLGLGALV
+GDVAGPDGTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKTYQTMLSTRLGPLD
+VALGEIAMALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGMAVTSWM
+KTFQHMDWVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAVGVLSWA
+TAGHVLYFVVMAGVGVWLAARRLGALFLR*
+>NZ_CP033200.1_133
+MPSPTTTTTPGPASPAEPLRPPVTAAASAERVKRRGVLLYAEHQLRSMRRYGAVLLVGAL
+GEPVLYLLAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALMTASVEFSYPVMGG
+FQWQRTYYAAQVTPLSPAQIALGHLVAVSLRFVFQAAVFLLVMLAFGVVSSPWAWVQVLT
+ATLGGLAVGAPIMAFAASLREDKGQFATLQRLVVMPLFLFSATFYPLEALPVWLRWIGWL
+SPQWHAAQLGRVLSYGMAEPVWLTVVHVAFLLALALGGAWLAVRIYTRRLGWVRGTPDRD
+AVTVARRDRAPRLGCRAARTGAARADVAPAAAQADPAAPSSSVVREHAVAVPPLPEIPVR
+RGPLAGAYSGNVRAVMERAFLSLKSNNWVVFFSGFFEPVLYLASLGLGLGALVGDVAGPD
+GTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKTYQTMLSTRLGPLDVALGEIA
+MALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGMAVTSWMKTFQHMD
+WVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAVGVLSWATAGHVLY
+FVVMAGIGVWLAARRLGALFLR*
+>NZ_CP040019.1_2486
+MTAAAGAEPAAPSSSVVLEHTAAVPPMPEITLRHGPLAGMYAGNVRAVMERAFLTLKSNN
+WVVFASGFFEPVLYLASMGIGLGALVGDVAGPDGTPIPYGMFIAPALLAVSAMNGAIYDS
+TWNVFFKLRHAKTYQTMLSTKLGPLDVALGEIVMALLRGLIYAVGFLIVMTVGGLVTSWT
+AVLMVPGALLVALGFASLGMAVTSYLKTFQHMDWIQIVLMPMFLFSATFFPLSVYPQAIQ
+WVIQVLPLWHAVELMRALAVGVVTWGTAGHILYFVAMSAVGIWFTSRRLGALFLR*
+>NZ_CP040019.1_2487
+MDASTTTTAPGPAAPRASASPAPLSPPISAAESAERVTRRGALYYAEHQLRNMRRYGSVL
+IVGALGEPIVYLLAMGLGLAQLMGGGAAQEGLGGVSYVAFLAPALLASGALMTAAVEFSY
+PVMGGFQWQKTYYAAQATPLTPAQIAVGHLGAVSLRFLFQGLVFFLVMLAFGVVHSPWGW
+LQILTATLGGLAIGAPIMAFAASLTEDKGQFATVQRLVIMPLFLFSATFYPLEALPVWLR
+WIGWISPQWHAAQLGRVLSYGMAEPVWLTVLHVVVLVAMAAVGTWLAVRIYTRRLGWRRG
+TPDRDALARP*
+>NZ_CP083691.1_2353
+MAAQIPASAPLQPPITAAESAVRVKARGAWFYAEHVLRSMRRYGAVLIVGALGEPILYLL
+AMGLGMAQVMGGGAPQESLGGVSYVTFLAPALLASGALMTAATEFSYPVMGGFQWHRTYY
+AAQATPLSPAQIAVGHLGAVALRFLFQAAVFFGVMLAFGVVHGPWGWVQVLTAALGGLAI
+GAPIMAFSASLKEDHGQFATLQRLVIMPLFLFSATFYPLEALPVWLRWVGWISPQWHAAQ
+LGRVLSYGMAEPRWLTVLHVAVLLALAFGGAWAAVRMYTRRLGWRPGTPDRDAVARPRAQ
+RASRLGRRATRVDRMAGAHAEAAAASSVVREHTAAVPPMPEITVRRGRLGGLYSGNVAAV
+MERALLTLKSNNWVVFASGFFEPVLYLASMGLGLGALVGAVPGPGGAPIPYGMYIAPALL
+AVSAMNGAIYDSTWNVFFKLRYAKTYQTMLATRLGPLDVALGEIAMALLRGLLYAVGFLV
+VMAVAGMATSWTALLMVPGALLVALGFASLGMAVTSWMKTFQQMDWIQLVLMPMFLFSAT
+FFPLTVYPEPIQWLIRVFPLWHAVEMMRALAVGAVTGATAGHALYFGVMSGLGVWLTSRR
+LRALFLR*
+>NZ_CP097650.1_406
+MPSPTTTTTPGPASPGPRSGTSAPSATPAEPLRPPVTAAESAERVRRRGVLLYAEHQLRS
+MRRYGAVLLVGALGEPVLYLLAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALM
+TASVEFSYPVMGGFQWQRTYYAAQATPLSPAQIALGHLVAVSLRFVFQATVFLLVMLAFG
+VVSSPWAWVQVLTATLGGLAVGAPIMAFAASLKEDKGQFATLQRLVVMPLFLFSATFYPL
+EALPVWLRWIGWLSPQWHAAQLGRVLSYGMAEPAWLTVVHVAFLLALALGGAWFAVRIYT
+RRLGWVRGTPDRDAVTAARRDRAPRLGRRAARTGAARADVAPAAAQAEPAAPSSSVVREH
+AVAVPPLPEIPVRRGPLAGAYSGNVRAVMERAFLSLKSNNWVVFFSGFFEPVLYLASLGL
+GLGALVGDVAGPDGTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKTYQTMLST
+RLGPLDVALGEIAMALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGM
+AVTSWMKTFQHMDWVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAV
+GVLSWATAGHVLYFVVMAGVGVWLAARRLGALFLR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000088.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000088.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d58eaa15cade93a2c193a635f9a4edb8f149642
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000088.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_468
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+DAACAAQADWARTPAKERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNG
+FLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCLLITPWNFPLAMATRKVGPAVAAG
+CTMVLKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVSFTG
+STPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAAN
+RFLVHEDVAEEFTQKFVAKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGE
+VLTGGHKIEGDGYFYAPTAIKVEKGNPILQQEIFGPVAPIVTFSSEEEAIEMANDTEYGL
+ASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAEGIEEYTS
+VQYIGIADPWAATKA*
+>NZ_CP033200.1_198
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+DAACAAQADWARTPAKERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNG
+FLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCLLITPWNFPLAMATRKVGPAVAAG
+CTMVLKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVSFTG
+STPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAAN
+RFLVHEDVAEEFTQKFVAKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGE
+VLTGGHKIEGDGYFYAPTAIKVEKGNPILQQEIFGPVAPIVTFSSEEEAIEMANDTEYGL
+ASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAEGIEEYTS
+VQYIGIADPWAATKA*
+>NZ_CP040019.1_2411
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+DAACAAQADWARTPAKERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNG
+FLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCLLITPWNFPLAMATRKVGPAVAAG
+CTMVIKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVSFTG
+STPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAAN
+RFLVHEDVAEEFTQKFVAKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGE
+VLTGGHKIEGDGYFYAPTAIKVEKGNPILQQEIFGPVAPIVTFSSEEEAIEMANDTEYGL
+ASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAEGIEEYTT
+VQYIGIADPWAAVKA*
+>NZ_CP083691.1_2291
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+EAAVAAQADWARTPAQERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVVYGNG
+FLRWFSEEATRHYGRTMIMPDGKLRMQVHHKPVGPSLLITPWNFPLAMATRKVGPAVAAG
+CTMVLKAAKLTPLTTQLFAQVMLEAGLPKGVLNVVSGSSASAISGPILEDPRLRKVSFTG
+STPVGVRLMQDAAKNVLRSSMELGGNAPLIVFEDADMDKAVDGAFAAKLRNMGEACTAAN
+RFLVHESVAEEFTRRFVERLEALKPLRGTDPESTLGPIVDEGARDDIHALIEEAVAAGGE
+ILTGGHKIEGDGYFYAPTALKVGKDNPILKKEIFGPVAPIVTFSTEEEAIQMANDTEYGL
+ASYVFTEDNARMHRVTEQIDFGIVGYNVGVVSNPAAPFGGVKQSGLGREGGAEGIAEYTT
+VQYIGIEDPFAGR*
+>NZ_CP097650.1_467
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+DAACAAQADWARTPAKERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNG
+FLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCLLITPWNFPLAMATRKVGPAVAAG
+CTMVLKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVSFTG
+STPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAAN
+RFLVHEDVAEEFTQKFVAKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGE
+VLTGGHKIEGDGYFYAPTAIKVEKGNPILQQEIFGPVAPIVTFSSEEEAIEMANDTEYGL
+ASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAEGIEEYTS
+VQYIGIADPWAAAKA*
+>NZ_CP097650.1_1504
+MTPTPDPTATQYIDGAWVPSSDGGTRTIHCPADGSEVGVVAEGTREDALAAIAAARRAFD
+SGEWSSTPAAERGDLLIRLADHILEHRDEFARAEALDTGKRLVEAEGDMADIAACFRYFG
+KIADQNPGRLVDAGDPTVLSRVVTEPVGVCGMITPWNFPLLQAAWKIAPALAAGCTFVLK
+PAEQTPHTAILTMRALESLGLPAGVANLVLGPGATVGEPLSSHPDVDLVSFTGGLATGKT
+IAQAAAGTVKKVALELGGKNPNVIFPDAHYEAALDNALNAAFTDSGLVCSAGTRLIVHES
+IAERFVDDLVERAGHIVMGGPFDEHAETGPLISAAHRDKVTDYVRRGVEAGARLRVGGHW
+GGEEHKDGFFYAPTVLDRCDRDNPAVIEEGFGPVITVETFSTEAEAIEIANHTEYGLAGA
+VWSSDAGTCQRVSRALRHGTVWINDYHPYLPQAEWGGFKASGIGRELGPTGLGEYVEHKH
+IYQNTEPAVTGWFADRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000092.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000092.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f75c5729eb5c1bb3d2507e7d8269e52b7e642b66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000092.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_525
+MHPDDAPTPDLTWLDSAGSTQDELLARLDREGHRHGAAVATADQRAGRGRHSRVWSAAPG
+AALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVPTHVKWPNDVLATDGRK
+LCGVLATVALSSDGKGPGVVVGMGVNLDHRGAAPVDTATDLAEWIGADAVPAPRDLAVEL
+RDAVVAAVDRFAAGVAGQAAAVDGRHPAVAAVADRLSTLGRAVRAELPGGGVLEGTAVGL
+GPGGTLRVKRVTPDRGTIETEVSAGDVAHLRGDVHRGA*
+>NZ_CP033200.1_259
+MHPDDAPTPDLTWLDSAGSTQDELLARLDREGHRHGAAVATADQRAGRGRHSRVWSAAPG
+AALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVPTHVKWPNDVLATDGRK
+LCGVLATVALSSDGKGPGVVVGMGVNLDHRGAAPVDTATDLAEWIGADAVPAPRDLAVEL
+RDAVVAAVDRFAAGVAGQTAAVDGHHPAVAAVADRLSTLGRAVRAELPGGGVLEGTAVGL
+GPGGTLRMRHVTPDRGTIETEVSAGDVAHLRGDVHRGA*
+>NZ_CP040019.1_2353
+MGVNLDHRGAAPVATATDLAEQIGAEAVPAPRGLAAALRDAVVGAADRFAAAVAGEAEAV
+DGRHPAVAAVTQRLSTLGREVRAELPGGDVLEGTAVALGPGGALRVSHVTADRGRIETEV
+SAGDVAHLRGDVHRGA*
+>NZ_CP040019.1_2354
+MHAPHDPAAPGLVWLDSAGSTQDEVLARVGREGPRHGLAVATADQRAGRGRHSRVWSAAP
+GAALALSVHLRPAAGGTPLAPVHLSWLSLVASAAVVEHLAGLGAAAHLKWPNDVLAPDGR
+KLCGVLATVAPAADGGGPGWSWAWG*
+>NZ_CP083691.1_2233
+MGYTWGMGTLLWLDAADSTQDELLRRLAAADGAARPGHGDGVGTADQRAGRGRHGRAWQA
+PPGAALALSVHLRPTGPSGPLAPAHLSWLSLVASAAVARRLVGLGVPAHLKWPNDVLDAE
+GRKLCGVLATLAPAPVFPGADAGETPGVVVGMGVNVDLSSGRPVPTAAALTDHLPGAEVP
+APRDLAQALLRDVAAAADRLARDLDGVVEPVDGTHPALAEVAAVLSTPGRRIRAELPGGE
+VLEGVATGLGAGGVLAVRVVTGERETITREISAGDVVHLRGDVRRGG*
+>NZ_CP097650.1_528
+MHPDDAPTPDLTWLDSAGSTQDELLARLDREGHRHGAAVATADQRAGRGRHSRVWSAAPG
+AALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVLTHVKWPNDVLATDGRK
+LCGVLATVALSSDGKGPGVVVGMGVNLDHRGAAPVDTASDLAEWIGADAVPAPRDLAVEL
+RDAVVAAVDRFAAGVAGQTAAVDGRHPAVAAVADRLSTLGRAVRAELPGGGVLEGTAVGL
+GPGGTLRVKHVTPDRGTIETEVSAGDVAHLRGDVHRGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000096.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000096.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cd5a1f5c6c39d162a3de9c5fe6e4802bdd8b1c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000096.fa
@@ -0,0 +1,42 @@
+>NZ_CP042169.1_589
+MTSTDPTPAKAASAPNRQRRAKIIVWVVLAALVLAGVVAFFAARAPSTPEAAPAQAGQAA
+SSGTGQTAASEAAPVVRPDSRVLSQAPNEKAVLVEFLDFECEGCKAAHPVVEELRAEYAD
+TVTFVHRYFPLPGHPNSMTAAVAVEAAAQQGAYEAMYQKMFDTQEQWSHTGQDRSPVFRG
+YAEDLGLDMTAYDKAVADPATRARIEADVADGVALGVQGTPTFFLDGQVLTLNTLEQFRA
+EVDAAASN*
+>NZ_CP033200.1_314
+MSTPTRNPTPSDPSTPGTTSRKAKTIVWVVLAAVVLAGLIVGVVAASGPRDAAPQGSGQT
+ASSGTGQSAPSEATPVMRPDSRVLSKAPNEQAVLVEFLDFECEGCKAAYPVVEELRAEYA
+DTVTFVHRYFPLPGHPNSMTAAVAVEAAGQQGQYEAMYQQMFDTQEQWSHTTEDRSPVFR
+GYAEDLGLDMAAYDAAVADPATRDRIEADVADGTALGVQGTPTFFLDGQMLTLNTLEQFR
+AEVDAAATTD*
+>NZ_CP033200.1_1727
+MTSPDPTASTPSSPTPSRQRRAKIVVWVLLGLVVAAALIGYLVARGTATAQQQDPNQSTA
+QSTGQSTGSAGQLVRENSRVLSQAPNEKAVLVEFLDFECEACAAAYPFVEDLRAEYADTV
+TFVHRYFPLPGHPNSVTAAIAVEAAAQQGAYESMYQKMFETQTEWSHTTEDRSPVFRAYA
+EELGLDMAAYDAAVADPATRDRVELDVADGTALGVAGTPTFYLDGEPLTVNSLEEFTAAV
+EAATQD*
+>NZ_CP040019.1_2299
+MSTPTRNPTPANSSTSGTTSRKAKTIVWVVLAAVVVAGVIAGVVAVGAARNATPDAAATQ
+AGQSAAQGSGPTTAEEAGELVVRPNSRVLSKAPNEQAVLVEFLDFECEGCGAAYPVVEEL
+RAEYADTVTFVTRYFPLPGHRNAMPAAVAVEAAAQQGEYEAMYQRMFETQAQWGEATEDK
+SPVFRGYAEELGLDMAAYDKAVADPATRARVEADVADGIALGVQGTPTFFLDGEMLTLTS
+LEQFRAEVDAAASN*
+>NZ_CP083691.1_1167
+MSWRTIRTEAGSAVLLVVVTAVALLWANSPLSEAYFGLWDVEIGFDVGGFGLHMNLHHWI
+NDGLMMTFFLVVGLEVRQEFAHGTLRDASRARLALIAGVVGVALPAVFYILIVAAAGGEG
+LGGWGAVVGTDTAFLLGALALVGPKLSGQLRVFLLTLTVVDDFLAVSIIGIVYSDEIRLV
+PLLIAGACLVGLWLLGRSRQWSATPYVLIVIVLWFATVESGVHASLAGMVAGLLIPAYPT
+RRQQVVEARQLFRDFWQSPSAASARAVDRGLAQGISVNERMHEVLRMPTALVIVPIFALA
+NAGVDLRGGVLVDSFQSSVTWGVIVGLVLGKLLGIGLATFVAVKLGAGRLPEGVGMGSVF
+GGAALSGIGFTVSLLVIGLAFGSTSDLGRQATVGVLVAMVLATALGWLIFRVAAKRWGEE
+TADLPMVLTPPVDPEVDHIRGPEDAQLTLVEYIDFECAYCAHATGSWDDLRSRFGDDLRY
+VVRQLPHHPHGPLAARASEAASNQGMFWPWLDFVFTRQDALEREDLIRYAEELGLDVAQF
+TADLDSAAVGARVERDLESADASGAHATPTFFVDGRRLLGSYDARTLTSALEASRRGTRT
+QEVRS*
+>NZ_CP097650.1_1953
+MSTPTRNPTPSDPSTPGTTSRKAKTIVWVVLAAVVLAGLIVGVVAASGPRDAAPQGSGQT
+ASSGTGQSAPSEATPVMRPDSRVLSKAPNEQAVLVEFLDFECEGCKAAYPVVEELRAEYA
+DTVTFVHRYFPLPGHPNSMTAAVAVEAAGQQGQYEAMYQQMFDTQEQWSHTTEDRSPVFR
+GYAEDLGLDMAAYDAAVADPATRDRIEADVADGTALGVQGTPTFFLDGQMLTLNTLEQFR
+AEVDAAATTD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000098.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000098.fa
new file mode 100644
index 0000000000000000000000000000000000000000..576ecf2d3137b9b160d206febc090e4b50028249
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000098.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_598
+MVGQTVGYVRVSSAEQNLDRQLEAVGECDRIFQDKISGSSRAKRTGLAELMQYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTGKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKLSGTDVEQARVMIEMGIPKAEVARTFGVSRQTL
+YTSLRRFESG*
+>NZ_CP033200.1_348
+MVGQTVAYVRVSSAEQNLDRQLEAVGECDRIFEDKISGSSRAKRAGLAELIGYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKLSGADVEQARVMIDMGIPKAEVARTFGVSRQTL
+YTSLSRGAGAEG*
+>NZ_CP040019.1_1288
+MVGQTVGYVRVSSAEQNLDRQLEAVGECDRIFRDKISGSSRAKRAGLAELLGYVREGDLV
+KIASMDRLGRDTRDLYAIVDELTGKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKLSDTDVEQAKAMVDMGIPKSEVARTLGVSRQTL
+YTSLGRIASS*
+>NZ_CP083691.1_673
+MVGQTVGYVRVSSVEQNLDRQLEAVGECDRIFEDKISGSSRAKRTGLAELMRYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTGKGCAVQFVSERITVDKSGTSPVDGLMLGILAGFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKMSDLDVEQARVMISIGIPKAEVARTFGVSRQTL
+YASLRRVAP*
+>NZ_CP083691.1_2162
+MVGQAVGYVRVSSAEQNLDRQLEAVGECDRVFEGKISGSSRAKRTGLAELMRYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKLSGTDVEQARVMINMGIPKAEVARTFGVSRQTL
+YTSLARMGL*
+>NZ_CP083691.1_2166
+MHVGYARVSTLEQDLSAQREALERLGVENKDIYFDHGLTGTTRARPGLREALAATRDGDT
+LVVTKLDRLARSLPDARDIADELTTKGVALSLGGSVYDPNDAVGRLLFNVLGMVAEFEAD
+LIRLRTREGMAIARSKGKLKGKKPKLSPSQRKHLLTLHAAGEHTQAELAELFNVSRTTIY
+RELRRTTTDT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000100.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000100.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0e8686b052909917639e31a3014e081190ed4f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000100.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_605
+MPAAYPREFRQDVVAIARKGQIPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK*
+>NZ_CP033200.1_359
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK*
+>NZ_CP040019.1_375
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK*
+>NZ_CP040019.1_396
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK*
+>NZ_CP083691.1_2140
+MPAAYPREFRQDVVAIARNGQMPIAQVAKDLGITASCLRRWLAQDDVEAGIRPGLTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK*
+>NZ_CP097650.1_581
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000105.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000105.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2bdea7eace35bbe6fee8b14bea5cf89f89cf6cf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000105.fa
@@ -0,0 +1,48 @@
+>NZ_CP042169.1_669
+MAPPRRAATREEPALRPAPPPAAVRPDRPARRRLPGVDAARAIALLGMITVHVLDPVTAD
+GAPHPAFLWFAGRASVLFVLLAGVGLALSTGGATPATGVRRAALRRRIARRAGLLFVLGL
+ACGTLGVPVAVILCHYALLFLLALPLLGLRARALGLIAGAWLVLGPVLVFAVVAAAQAAV
+GRQEFFVGGRLWLSPGPADLLRPGLLLADLTVTGYYPVLSWGAFLVLGLALGRLPLDRRR
+VAAGILGGGATAWAAAGVVGAAVLRAPGTVGRVAAAIGTDPVETALTLRTGEPRLALLIP
+DPLWLALPTPHSGSVVAAVLAAGWACAVLGACLLARPLVGHAALRPLVGAGRIPLTLYVG
+HLVVLALVDATGLDPADGALLTALVVLSLAAGLAAELSGRRGPLEAVMARLSRTGGERAV
+GGR*
+>NZ_CP033200.1_415
+MAPPRRAATREEPALRPAPPPAAVRPDRPARRRLPGVDAARAIALLGMITVHIVDPVTAD
+GAPHPAFLWFAGRASVLFVLLAGVGLALSTGGATPATGVRRAALRRRIARRAGLLFVLGL
+ACGTLGVPVAVILCHYALLFLLALPLLGLRARALGLIAGAWLVLGPVLVFAVVAAAQAAV
+GRQEFFVGGRLWLSPGPADLLRPGLLLADLTVTGYYPVLSWGAFLVLGLALGRLPLDRRR
+VAAGILGGGATAWAAAGVVGAAVLRAPGTVGRVAAAIGTDPVETALTLRTGEPRLALLIP
+DPLWLALPTPHSGSVVAAVLAAGWACAVLGACLLARPLVGHAALRPLVGAGRIPLTLYVG
+HLVVLALVDATGLDPADGALLTALVVLSLAAGLAAELSGRRGPLEAVMARLSRTGGERAV
+GGR*
+>NZ_CP040019.1_2218
+MHGACERSPPCTPPRPPAATTPTPSVRRPRLRGVDAARGVALLGMVAVHVVDPTTAAGDP
+HPVFLGFAGRASVLFVLLAGVGLALSTGGTRPAEGARRAALRRRITRRAGLLFVVGLACG
+ALGTPVAVILGHYALLFLLAVPLLGLRAPALGAIAGAWLVLGPVAVFAASTAGQALLGRD
+EFLLDARLWLSPMPEDLLTPGVLLADLVVTGYYPVLSWGAFLVLGLALGRLPLDRARVAA
+ALLAAGALAWGAAAAAGAAVLRAPGVLERIAAGTGADPAQLTATLRTGEHRLAYLPPDPL
+WLALPTPHGGSPVAALLAAGWACAVLGLCLLVGAALDRALAGRTPADRGGGGRRGRASCG
+RRRDPSRGRGGSR*
+>NZ_CP040019.1_2219
+MRAASRPLTGAGRIPLTLYVGHLLVLAAASRLEIDASDAQLLTVLVALCLAAGLAADLTG
+RRGPLESAVARLSRAGEADAPSHLRR*
+>NZ_CP083691.1_2391
+MTPKHRQDPLAEPPEGDFTEARPAPGRRPSRTPWTDISRRRADAAPDTAAPPPPPPPPGK
+VGHRDAPPVSWRTQALRSARRLHGLDLARFLALAGMMAVHVWADAIDDRGLGGFIGTVVA
+GNAAAVFAFLAGITLIFLSGGSRGARGRDLQRARVAIAVRAVMLLVIGLGLNLIDFPAYD
+ILPYYAMLFLLAIPLLGLGPAALALCAAAALLTGPVLRMVLVSTGTPVPGFDPTLISLFA
+RPGPTLIQLFVTGTYPAITWMAYVCAGMAAARLNLFDRQRQAFVAVGGLAATGVAAGLSW
+AALHVWDGRERIAEVTGIRPDLVELRASRGLSAEMLSTTPWWLAARGPHLDTPLSTLHAV
+GVAAAVVGFVLMLTSGLMRPDGSLPAWTEPLRAAGSMSLTVYVSHLLLLTVPGWEERRGW
+FFVGQLVLLVSFATLWRRVSAQGPLETVVSRVPKAVARALVPGRPAGAGPDYEPLEAADP
+R*
+>NZ_CP097650.1_638
+MAPPRRAATREEPALRPAPPPAAVRPDRPARRRLPGVDAARGIALLGMITVHVLDPATAD
+GAPHPAFLSFAGRASVLFVLLAGVGLALSTGGATPATGARRATLRRRIARRAGLLFVLGL
+ACGTLGVPVAVILCHYALLFLLALPLLGLRARTLGVIAGAWLVLGPVLVFAVVAAAQAAV
+GRQEFFVGGRLWLSPGPADLLRPGLLLADLTVTGYYPVLSWGAFLVLGLALGRLPLDRPR
+VAAGILGGGAAAWAAAGVVGAAVLRAPGTVGRVAAAIGTDPVETALTLRTGEPRLALLIP
+DPLWLALPTPHSGSVVAAVLAAGWACAVLGACLLARPLVGHAALRPLVGAGRIPLTLYVG
+HLVVLALVDATGLDPADGALLAALVVLSLAAGLAAELSGRRGPLEAVMARLSRAGGERAV
+AGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000106.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000106.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6015d18c0ec2e71f0a14a139f1aba67269859fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000106.fa
@@ -0,0 +1,115 @@
+>NZ_CP042169.1_708
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGPRSVTYAERVGSA
+PARGPELAVVTEHGPDAGRLVPLGEGGLSTGRGGARLLLDDPSAPSRPMRLRLAPTGLHV
+HDGPRDTGRLWDGRSPLPVGRTALGLVRGPGAALPRPVTPEPPAVDLGSPPARQSVVIPL
+VAALGPLVLGVALVLMMGNPVFLLFGVLSVTVALVMLAMQRRTRLRHARLLAARADALVR
+RRAQAALSPGAVARAVRSGATDRFGLTSGADEAVAVSWGSGVGALSLSRDDPDEAWVEAV
+TSRRTVMTTSPPESRVVVLGPPRDVAGACRWAVFQLLRHAVAADGAFVVEAGGVRRTWWS
+GGSGPRLLVSAPEDAALDPAWRAWRAAIGGDAGTTPTARADLPWTRYDFTGPSPAPGDAV
+VDLRGRTVVVPAEQQRFEDVTADGLADGTLVAWLTELADDVVDLGLLPADDGDGTLTPPG
+QVGARDAVDGLTVTLARSGDETGVVEMDLAADGPHLLIAGTTGSGKSDLLLSLLLGAAAH
+HPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHVGTASLRALSAIRAELHRREALFAE
+AGVSDYPGFRRRHPDAALPRLVVAIDELRVLVDDHPDAAAVLQRLAATGRSLGFHLILAT
+QRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVS
+FRASQWTVDGGTPVWRRLGEAAAAPAVAPWEAVVSVLVENYAAGDWPTPPPVVTPALPER
+WVPDRARRAEATALALLDDAAHGRHRPWRWPTGAEGRTAWIVEAAGGRAETLAAVVEVAL
+RSGRPVAVLDGTGEAAAAARSGTPVLTPDAEGAGEAALARLRELAAAGGTAVITGWNAWS
+GLRVGDTYRTVEEDVHDWLGRPTAAGLRLAVFGGRELATGRLLLHLPHRFFVPAGTNAEH
+RLIWPRLTEVEPLPGRAVHISPAVPEPGMPCQLASPAPA*
+>NZ_CP033200.1_448
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGRRSVTYAEGVGSA
+PARGPELAVVTEHGPDAGRIVPLGEGGLSVGRGGARLLLDDPSAPSRPMRLRLAPTGLHV
+HDGPRATGRLWDGRSPLPVGRTALGLVRGPGSALPRPITPEPPVVDLGSPPARQSVVIPL
+VAALGPLVLGVALVLMMGNPMFLLFGVLSVTVALVMLAMQRRTRLRHARLLAARADAVVR
+RRARVALSPGAVARAVRSGATDRFGLTAGADEAVAVSWGSGVGALSLSRDDPDEAWVEAV
+TSRRTVMTTSPPESRVVVLGPPRDVAGACRWAVFQLLRHAVAADGAFVVEAGGVRRIWWS
+GGSGPQLLVMAPEDAALDPAWRAWRAAIGDDAGTTPTARTDLPWTRYDFTGPPPAPGDAV
+VDLRGRTVVVPAEQQRFEDMAADGLADGTLVAWLTELADDVVDLGLLPTDDGDGTLTPPG
+QVGARDAVDGLTVALARSRDEAGVVEMDLAADGPHLLIAGTTGSGKSDLLLSLLLGAAAH
+HPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHVGAASLRALSAIRAELHRREALFAE
+AGVSDYPGFRRRHPDAALPRLVVAIDELRVLVDDHPDAAAVLQRLAATGRSLGFHLILAT
+QRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVS
+FRASQWTVDGGTPVWRRLGEAAAAPAVAPWEAVVSVLVENYAAGDWPTPPPVVTPALPER
+WVPDRARRAEATALALLDDAAHGRHRPWRWPTGAEGRTAWIVEAAGGRAETLAAVVEVAM
+RSGRPVAVLDGTGEAATAARSGTPVLTPDSEGAGEAVLARLRELAAAGGTAVITGWNAWS
+GLRVGDTYRTVEEDVHDWLGRPAAAGLRLAVFGGRELATGRLLLHLPHRFFVPAGTNAEH
+RLVWPRLTEVEPLPGRAVHISPAVPEPGMPCQLASPAPA*
+>NZ_CP040019.1_2178
+MGWTVRILGGRTPETWRVSPLPRDPTLRDRAVRERAPGRSLRAVASGPGSVTYAPWGGAE
+PAPGPELSVVTERGPDGGRLAPLTGGGVSVGRGRARLLLDDPAAPSRPTRLRLAAAGLHV
+EGAVEGAPRLWDGRRPHRIGRTTLGLVRGPQPPLPPPSLPAPPCVDLGSPPAGQSLAIPL
+LTAAAPLVIGVALVLVMRNPIFLLFGLLSVAVALTMLGLQRRARMRHAALLAERAAAVTA
+HRASAALSPGDVARAVRARTPDRFGLTGAAEGPATLSWGLGMGALGLSRDDPDQAWVAAV
+TARREALTVPSPAARTVVLGPPREAAGVCRWVVFQLLRHAVAAGACLVVESGGSRRCWWA
+GGTGGALLVTAPADAALEAAWTAWTAGIGGAPGERTGAQPARIDFTGADCAPGETVVDLR
+GGMLTDPGQEQRITGLEADGIAPATLPGWAAELADDVVDLGLLPADAGAGALFPPADVGT
+RDAVDALRVSLEAGSDGGPGALALDLAADGPHLLLAGTTGSGKSDLLLSLLLGVAAHHPP
+AEAAFLLLDFKGGASFGPLAALPHTMSLETNHVGAASLRALNAIRAELHRREALFAEAGV
+SDYPAFRRRHPEAALPRLVVAVDELRVLVDDHPDAAAVLQRLAATGRSLGFHLVLATQRA
+TGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAATRLDPRRPGSAILSTAGREPVPFRA
+SRWAVDGGAPVWRRLGEAAETPAAAPWKAVVAQLVERYAAGRWPTPPPVVTPALPERWVP
+DRTRRAGATALALLDDAAHGRHRPWRWAPGGGGRAAWIVEPAGGRAEALAAVLEVGVRGG
+APVVVLDGTGEAAAIAAPEGVRLLRPDEEGAGERAAACLRELAAAGGTAVLTGWTTWAGL
+RLGESYRTLEEDAQGWLGGREAAGLRVAAFGGRELATSRLLLHLPHRFFVPAGTSAEHRL
+VWPRLVEVEPLPGRAVHVSPDVPEPGLPCQLASPGAHRSGAADAASTL*
+>NZ_CP083691.1_329
+MTRRLVHRPGRTVPPARLLPEDVITGPQPVDPAMDQGSGPNLLMIVPMVAAAASMLTMMA
+FRQSPFAAVGALAMVVTLTAMLILYGSQAGKARRRRTTLRETYTRYLDRQRRRLIAEDEQ
+ARAIAASAAPPPGALLDVVRRPDRLWERRRTDEDFLQTRVGLGARPVRALRVAVQDNATQ
+VQDEFMLKQAESLATRFRTTDDMPVSLPLDSLGNLAVVGPREFGLTAARSLVLGACVQQA
+PEDLVVALLVPPERRADWPWFDRLPHARVADAASPTGNRLLVAADADDLMRMLRADLARR
+AGIAAETLRASTRDGRAATELSRLVIVVDSHGEPAAGLPLEGSHLPLVSRGITLITLVSD
+RLDEPSDVRLRLSATGGTDVTGAAEFQVDDARQDEGRPTVSHGRLDTFDAATALGVATDL
+QPLRLSADSLEHAEDDLSSTQTFLQMLGLSPELTLEELRRRWRPRGQDEFLRVPIGEDDR
+GDAVHLDLKEAAQLGMGPHGLCVGATGSGKSELLRALVFALLASHAPERMSLLLVDFKGG
+ATFAPFHGAPHVAGIITNLSDDLSLVERVYASLSGEILRRQEVLKAAGNLANITDYQVHR
+ERELAQGRSVEALPHLIVIIDEFGELLTARPDFIDLFLSIGRIGRSIGVHLLLSSQRIES
+GRLRGLETYLSYRLGLRTLSESESRTVLDTADAFHLPPLPGFGYLKVDTSVYTRFRSGYV
+SSPLEEEAAARAEQERVLTADDDVPPALPVPDYGLQLVLPTEGAEPQLSSGAGAAQVMEE
+PEDHRPTIMETLMDRLREVPSPVEPLWLPPLPEALTLDQAAGDVAVTDHGLRLPAGGDLE
+VPIGLIDDPEHQWQGLWMLDFASGSGHLIVQGGPRSGKSTLLQTIVTSLALTHSPQQVGV
+YCVDLLGSSLLPLQGLPHVGGVAIRTNREMVTRTLREVSAMLTLREKLFEAEGIDSMTTL
+RRRHADGSLPDLGSADVFLVLDGYGQVNEEFADLTPVLNGLISRGAAYGIHIITTVARQG
+EIRSTQQTFFTHRVELRLSTPSDSAIDRKAAEEVREDTPGRGLASTRLHGQVALPRVDGA
+ADPGTAAEGLAETVQRIAESARGEAMAVRVLPPTTERPPLEQLEDPGRLPVGLLEDDLSV
+RSLDIDGRERHVVALGDAQTGRSSMLRQFARHFMDTHADTEMMFVVFDPRGELKGVIPDA
+YMAGYAGNATVAVPLARALVSELEKRQSTDPKDAGPMRQARIVVLVDDYDVLTVAGDSPL
+APLLPYLPMARELKLHVFLTRRMKGASRGLYEKFLASLVSQDAVTLMFSGDRSEGVLFDG
+LRPKRLPPGRAVLIGASRRHETVQTFTGPPAPGRG*
+>NZ_CP083691.1_2050
+MTWRVRVLGLPVEQDWAVSELPLDVDGQDRVVAEHFAPLRVERARGGGTTLTYVAHPSGT
+PPVPAAGSGPELAVGTSAGPDAGRLVPLTAAGLTVGRGRSRMLLDDPQCPSRPVRLALGP
+SGVSVDDGRTRRTWDGLDGLPIGDSILRLVRGRQRPLPPALTPPPAQIDLGAAPAEQSLL
+VSLAMAVGPVLIGLVLAVTTRSPLFLLFGIVSLLGVGVLLGVQRRTRRRHADLLRERALD
+VVRRRVAAVSGPADVSAACRAKAEDRFGLVSARPGDGPALLWGRARGSVAFTRGDVADHW
+RSAACVDQPVLGVAAADRGTVLCGTGRPAQAAARWTLFQLLRHAVATGSSLVVRSPDGAR
+VWWPAVPGAPTIALELEDTAPLAGAWEVWTASLGAEMSETRRHGCADEVLVRCTGTPPAD
+LDADVVDLDARQATLPGQGLELTDLTPLGISADTLQWWLAELADDVAHLGLGGPPASAPP
+LRRPHDVGAHRAVRNLAVPLTSSSAGDAAPMVLDLAADGPHALIAGTTGSGKSDLLLSVL
+VGLAARHAPAEVSFVLLDFKGGASFGPLRRLPHTMSVETNHVGAASLRALQAIGAELRRR
+EALFAEARVADYPAFRAAHPDTALPRLVVAVDELRVLVDEHPDANAVLQRLAATGRSLGF
+HLLLATQRPGGAVSADVRSNLGTTIALRTATEQESWDLVGSAAASRIDPAAPGTALLARG
+TGAPVPFRASPWSAGPVRPRWTPWGVPVASAASGTDWPSVVEDLVQACRDRDLPIPEPVV
+SPPLPGSFAPDRSRRRSADVLALVDDAARARHVPWRWPLGAQGNGAWIVEPAGGRALVLA
+AVLEAAGRTSPAVLILDGSGECAAALPTVADALPDLADVTLLTPEAQPADVGEQVCGAVA
+DLAAVGGTLVITGWQSWAGVRVGETYRTLDEELHRLLGTQAARGLRVAAVGGRELVTARI
+APHLPHRFYVPAGTTPDHRLVWPPKLVEVEQLPGRAVHVHPGGPTVGVPAQLAFPAHSAA
+GAGTDSDDQQ*
+>NZ_CP097650.1_671
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGPRSVTYAERVGSA
+PARGPELAVVTEHGPDAGRLVPLGEGGLSTGRGGARLLLDDPSAPSRPMRLRLAPTGLHV
+HDGPRDTGRLWDGRSPLPVGRTALGLVRGPGAALPRPVTPEPPAVDLGSPPARQSVVIPL
+VAALGPLVLGVALVLMMGNPVFLLFGVLSVTVALVMLAMQRRTRLRHARLLAARADAVVR
+RRAQAALSPGAVARAVRSGATDRFGLTSGADEAVAVSWGSGVGALSLSRDDPDEAWVEAV
+TSRRTVMTTSPPESRVVVLGPPRDVAGACRWAVFQLLRHAVAADGAFVVEAGGVRRTWWS
+GGSGPRLLVSAPEDAALDPAWRAWRAAIGGDAGTTPTARADLPWTRHDFTGPSPAPGDAV
+VDLRGRTVVVPAEQQRFEDVTADGLADGTLVAWLTELADDVVDLGLLPTDDGDGTLTPPG
+QVGARDAVDGLTVTLARSGDETGVVEMDLAADGPHLLIAGTTGSGKSDLLLSLLLGAAAH
+HPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHVGTASLRALSAIRAELHRREALFAE
+AGVSDYPGFRRRHPDAALPRLVVAIDELRVLVDDHPDAAAVLQRLAATGRSLGFHLILAT
+QRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVS
+FRASQWTVDGGTPVWRRLGEAAAAPAVAPWEAVVSVLVEKYAAGDWPTPPPVVTPALPER
+WVPDRARRAEATALALLDDAAHGRHRPWRWPTGAEGRTAWIVEAAGGRAETLAAVVEVAL
+RSGRPVAVLDGTGEAAAAARSGTPVLTPDVEGAGEAALARLRELAAAGGTAVITGWNAWS
+GLRVGDTYRTVEEDVHDWLGRPTAAGLRLAVFGGRELATGRLLLHLPHRFFVPAGTNAEH
+RLIWPRLTEVEPLPGRAVHISPAVPEPGMPCQLASPAPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000108.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000108.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a0cca31124e990e249a325903dd12d49501782b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000108.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_738
+MNASFPAGAAAATPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMGGRVVASGSPRDVLTVENL
+DIAYGRGALHGPSTAVEDAADFLDDPAGGRRH*
+>NZ_CP033200.1_477
+MNASFPAGAAATPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMGGRVVASGPPRDVLTVENL
+DIAYGRGALHGPSTAVEDAADFLDDPAGGRRH*
+>NZ_CP040019.1_2125
+MSRSAAVVPEAAPAPLAVAEHLELRHGDHLAVEASSFTLPAGCVVAVIGPNGSGKSTLLQ
+ALAGVLDPAAGRLEVRGESPSRHGRLTSFVMQSLQFPQGVPLTVRDVVTMGRYTTAGWFR
+RLGATDRAAVAAAMERVRVTDLADRHLDQLSGGQRQRVYVAQGLAQEHDVLMLDEPVTGL
+DIVSARTIDEIIHEQPERGVSVVYTTHDLDEAAAADHVVLMDGRVVASGPPAQVLTAANL
+DAVYGRGALHAPLLVHLDDPADCSPDRG*
+>NZ_CP083691.1_512
+MNPAAPAPAIRLADVSAAYDRRRPVFTGADLVIDGPGLVRVHGRNGGGKSTLIELVSGYL
+RPSDGQVRIGGLPAHDPRAHERRRVCRTEPALYPLMDVHDHVVFASRWAGADPAEGLARA
+ERYGLGPWMHAPAQTLSTGNRRRLWIVQCTVGAFDTVVLDEPFNGLDDESSAVLAAELAA
+WARTRCVVLICHLPPPGLAFDRVVRWPPGQAAADPAPPADPGVRP*
+>NZ_CP083691.1_2016
+MTRTVPTAPTPGAGVLAEARGLELRRAAHVAVAPSDLTLPAGVLVAVIGPNGSGKSTLLH
+ALAGTLEPAAGSLTVRGESPSRHARRTAFVMQTIPVPQGVPLTVRDVVRMGRYPRVGWFG
+RFGAADREAVDAAMERMSVTDLARRHLDELSGGQRQRVYVAQALAQEHDVLMLDEPLTGL
+DLVSARTIDRLLHEEPARGVSVVHTTHDLDEAAAADFVVLMSGRVVAAGTPRQVLTEANL
+EAAYGHGVLHGPRLPFLDDPVDGVR*
+>NZ_CP097650.1_701
+MNASFPAGAAAAPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVGAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMSGRVVASGPPRDVLTVENL
+DIAYGRGALHGPSTAVEDAAEFLDDPAGGIRH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000109.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000109.fa
new file mode 100644
index 0000000000000000000000000000000000000000..436d774675d541d6fc8013d5dff5413f1acbf062
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000109.fa
@@ -0,0 +1,51 @@
+>NZ_CP042169.1_745
+MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVKR
+ISELLAERSKDIAAVITTEMGKSLGAAVGEVRYGAQIFGYYADEAEELLADQPIKQFSGQ
+EAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFTE
+AGLPEGVYQNVFATHDQISTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARAAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRSSEMKPG
+DPTSRDADVYGPLSSESAADGLAEQIAEAKQAGATVHVGGERTSGPEGEGFYVSPAVITD
+VDQENPAYTQELFGMASVVYKVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVADQLEV
+GMANVNLASAAGANLPFGGVKRSGFGRELGPLALDEFANKRLYAVQGPLEG*
+>NZ_CP033200.1_484
+MQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGSDPYIVLSAPDARAAARDALATRMGNW
+GQACNSNKRMIVMEDLYDDFVDELVQRSSAMKPGDPTSRDADVYGPLSSESAADGLTEQI
+AAAKEAGATVHVGGERVSGPEGEGFYVSPAVITDVDQENPAYTQELFGMAAVVYKVSSAE
+EAVALANDSQYGLGGAVFSTDLDEAKRVADQLEVGMANVNLASAAGANLPFGGVKRSGFG
+RELGPMAVDEFANKRLYAVQGPLEG*
+>NZ_CP040019.1_790
+MARYITRNPATGETLEEFAELPASEVESVIERADTAYRAWRERPVAERAAVLARAADLYE
+ERAEQLAQDVTTEMGKPISAARGEMKTVAGIFRYYAEQGPAMLEHERIEVAGGGTAYVRR
+DPVGVLLGVMPWNFPHYQIARFAAPNLLLGNTMILKHAGICARSALNVEQLLLDAGLPEG
+AFVNAFIGHEAVAQIVADERVQGVSLTGSDKAGQIIGEQAGRNVKKAVLELGGSDPFIVA
+GDADVARAAKDAVSGRCVNSGQTCTSSKRFIVVEEHYEQFLSAFVEGMRAVPHGDPTDES
+TVVGPLSSPEAVQEVHELVQDAVAHGATLHVGGEPGEGPGAYYPPTVLTDVDESARAFRE
+EIFGPVAVVHRVKDLDAAIELANDSPYGLSSSVYTTSAEVAEEVSARLETGMVWVNSTSK
+SSAELPFGGVKRSGIGRELGTLGIEEFANHKLVRSPEGLIGA*
+>NZ_CP040019.1_2118
+MTTTSASQGYRTINPATGELLKSFDTATDQQIADALDASQAAYEQWSQKSVAERAAVVKR
+ISELLAERSKDIATLITTEMGKSLGAAVGEVRFGAQIFAYYADNAEELLADQPIKDFSGQ
+EAFVERLPLGPLLGIMPWNFPVYQVARFVAPNLILGNTILLKHSEINPQTAALLEDLFRE
+AGLPEGVYQNLYATHEQVSTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARQAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRASAMKAA
+DPTSRDEDVYGPLSSESAADGLAEQIKAAKDAGATVHVGGERVSGPAGEGFYVSPAVITD
+VDQDNPAYTQELFGMAAVVYKVSSPEEAVALANDSQYGLGGAVFSTDLDEARRVADQLEV
+GMANVNLPSAAGANLPFGGVKRSGFGRELGPFAVDEFANKRLYAVKGPLQG*
+>NZ_CP083691.1_2010
+MTTTTSASQGYRTINPATGELIKQYDNATDQQVQDALAASQAAYEQWAATTVAERAGVVK
+RISELLAERSKDIAALITTEMGKSLGGAIGEVRFSAQIFAYYADNAEELLADQPIKDFSG
+QEAFLEKLPLGPLLGVMPWNFPVYQVARFAAPNLVLGNTILLKHSEINPQTAQLLQDLFE
+EAGLPAGVYQNLYATHDQISTIIADPRVQGVSLTGSERAGASIAEQAGRHLKKCVLELGG
+SDPYIVLSAPDARQAAREALQTRMGNWGQACNSNKRMIVMEDLYDEFVDELVKQSTALKP
+GDPTSRDEDVYGPLSSESAADGLAAQIRDAKEAGATVVGGERLSGPSGEGFYVSPAVITD
+VDQENPAYSQELFGMASVVYRVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVAEQLEV
+GMANVNLPSAQGANLPFGGVKRSGFGRELGPFAVDEFANKRLYAVKGDLQG*
+>NZ_CP097650.1_708
+MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVKR
+ISELLAERSKDIAAVITTEMGKSLGAAVGEVRYGAQIFGYYADEAEELLADQPIKQFSGQ
+EAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFTE
+AGLPEGVYQNVFATHDQISTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARAAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRSSAMKPG
+DPTSRDADVYGPLSSESAADGLTEQIAAAKEAGATVHVGGERVSGPQGEGFYVSPAVITD
+VDQENPAYTQELFGMAAVVYKVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVADQLEV
+GMANVNLASAAGANLPFGGVKRSGFGRELGPMAVDEFANKRLYAVQGPLEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000115.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000115.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e052e35a0d093830a6437f29869bcfa9915b9bd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000115.fa
@@ -0,0 +1,41 @@
+>NZ_CP042169.1_991
+MTTPSNISRRSFAGLSLAAVGAFALTACNSQAEEKSDDGAQTVRIGVVSENESHRALVKL
+AKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYNQASGKDLTMIGTTEII
+PLPLYSKKYTDVSEFKKGDTVAIPNDTVNQARAINVLVAAGLLKLSNETIRPEVRDIDEA
+ASTVTVQPVAAQQTVNALESVQGAVINNTFSADAGIDTNTALFKDDPEDDSAKPYVNGFA
+VRREDRDNETYKKIAALYHEQPVLDESAKLSSGTSVPVQLDTAQIDETLKQYQDAIAKQG
+A*
+>NZ_CP033200.1_716
+MTTPSNISRRSFAGLSLAAVGAFALTACNSQAEEKSDDGAQTVRIGVVSENESHRALVKL
+AKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYNQASGKDLTMIGTTEII
+PLPLYSKKYTDVSEFKKGDTVAIPNDTVNQARAINVLVAAGLLKLSNETIRPEVRDIDEA
+ASTVTVQPVAAQQTVNALESVQGAVINNTFSADAGIDTNTALFKDDPEDDSAKPYVNGFA
+VRREDRDNETYKKIAALYHEQPVLDESAKLSSGTSVPVQLDTAQIDETLKQYQDAIAKQG
+A*
+>NZ_CP040019.1_176
+MTSRSPLSSRSPLSPRPSRRALLAGLAGVGSAALLTGCGLRTGTAAGGGGASRTITLCAT
+EDAPYQEPVRIAERLLAERGWELKTTFVTDIIQPNIAVDRGEFDANFFQHIAYLKQFNAD
+NGTSVVPAFNVYTSPAGLFSTRYSSLEELPDGARISVPVDPSNNGRALRLLAQAGRITVR
+EGVSVIRLSQHDITANPHGYEFVEVDQQSLALTIEDADAGFLFARQSAKIGLPISESLLF
+ETAEDAVPFRVVVATREGFRDTEAGRALREAFQSEEVRRWYADYLDGALGTEAWGDDPQE
+AIAALEI*
+>NZ_CP040019.1_1821
+MALSPLSRRTALGAGTAALALVLSACGAGGSDTAASSAPTPDPANPVVVKVGANPVPHAQ
+ILEYVDENLAKEAGIDLEIQEFDDYQMPNTALDEGKIDANYYMHEPFFNKQVEERGLKME
+HGKGVHIEPYAAFSKKFDSVDQVPEGATVAITNDPGNQPRALKMLEQAGLLKDVKDDSAA
+LTLTPEQNPKGLTFEENQPEILVQILDDPAVDLAIINGNYFIQAGMTLEDAVVVEEISGE
+NPYANFVAWREGEKTPGVEKLDELLHSPKVKQYIEQTWPGGDVTPAF*
+>NZ_CP083691.1_1710
+MPTRAGDVAPSSKENPMTTPSNISRRSFAGLSLAAVGALALTACNSQAEKKGDDGAQTVR
+IGVVSENETHRALVKLAKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYN
+QASGKDLTLIGTTEIIPLPLYSKKYKDVSEFQKGDTVAIPNDTVNQARAINVLVAAGLLK
+LSNETIRPEPKDIDEAASTVKVQTVAAQQTVNALESVQGSVINNTFSADAGIDTNTALFK
+DDPKADSAKPFVNGFAVRRADRENETYKKIAALYHEQAVLDESAKLSSGTSVPVQLDAAQ
+IDETLKQYQDAIAKQGA*
+>NZ_CP097650.1_934
+MTTPSNISRRSFAGLSLAAVGAFALTACNSQAEEKSDDGAQTVRIGVVSENESHRALVKL
+AKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYNQASGKDLTMIGTTEII
+PLPLYSKKYTDVSEFKKGDTVAIPNDTVNQARAINVLVAAGLLKLSNETIRPEVRDIDEA
+ASTVTVQPVAAQQTVNALESVQGAVINNTFSADAGIDTNTALFKDDPEDDSAKPYVNGFA
+VRREDRDNETYKKIAALYHEQPVLDESAKLSSGTSVPVQLDTAQIDETLKQYQDAIAKQG
+A*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000116.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d4ec03c0a8fa0fe346a8db2178bd97c68d30d8b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000116.fa
@@ -0,0 +1,46 @@
+>NZ_CP042169.1_992
+MAGSHTSDRDAVTPGRPSAGAPGEPVIVFDHVSRVYAAKKGAGVKAVDDVSLAVNRGEVF
+GVIGFSGAGKSTLIRMINGLEKPTSGTVTVLGQQVSHLSEAKLRPLRTRIGMVFQQFNLL
+TSRTVAGNIEFALDTAGWPRSKRRARVAELLEFVGLADKAKHYPEQLSGGQKQRVGIARA
+LAAEPEILLADEATSALDPSTTHEVLSVLRRVNEELGVTIVAITHEMEVIRSIADRVAVM
+DSGRVVESGKVYDLFSRPAHSADAASFVATALKDRPNAEEVARIRARTEGRLIMVSLKDS
+AAVSAVLGTASTRGVGFEIVHGGMSATKDSAYGLLTVALTGEAAAVDAFVADLAGAGDVQ
+EVHQ*
+>NZ_CP033200.1_717
+MAGSHTSDRDAVTPGRPSAGAPGEPVIVFDHVSRVYAAKKGAGVKAVDDVSLAVNRGEVF
+GVIGFSGAGKSTLIRMINGLEKPTSGTVTVLGQQVSHLSEAKLRPLRTRIGMVFQQFNLL
+TSRTVAGNIEFALDTAGWPRSKRRARVAELLEFVGLADKAKHYPEQLSGGQKQRVGIARA
+LAAEPEILLADEATSALDPSTTHEVLSVLRRVNEELGVTIVAITHEMEVIRSIADRVAVM
+DSGRVVESGKVYDLFSRPAHSADAASFVATALKDRPNAEEVARIRARTEGRLIMVSLKDS
+AAVSAVLGTASTRGVGFEIVHGGMSATKDSAYGLLTVALTGEAAAVDAFVADLAGAGDVQ
+EVHQ*
+>NZ_CP040019.1_178
+MISIQNVSTAFGEHRAVDDVSLEIPTGSIQGIIGFSGAGKSTLLRNVNLLLRPSAGRVVV
+DGTDLTALSPSGLREARRGIGMVFQHFNLVHNLTAAQNVALALKFAGVDRRARQARAHEA
+LEIVGLADHAGRYPAELSGGQAQRVAIARALSTRPSVLLCDEPTSAVDPRTTATVLQHLV
+DINRDLGITTVIVTHEMNVIRAVADDVAVMEDGRAVERFALADLERADFAPRTGIGRYLL
+EDEIALERPPLRGAAGAPDGDRAGSGTTPGTSPGTTSIPGDVREAVVAGV*
+>NZ_CP040019.1_1823
+MSSSPTVSTSAHPVGTPMIEVRGLEKTFRQGAKEIRALRGVDLAVAPGRIHGIIGQSGAG
+KSTLVRCLTLLEPPTSGTVSVAGKDLTRESRSGLLDSRRRIGMVFQHANLFSSRTARDNV
+AYPLEVAGGSDAAARRARADELLALVGLKGFEGSYPAQLSGGQKQRVGIARALASDPDVL
+LCDEPTSALDPASTEGVLTLIQDLSQRLGLTVLVITHEMHVVKRLCHEVSLLQDGRIVQS
+GDLGDVAADLDSPLSSALLPLPAPHAAPDQRLIEVLGRGAAASLPITQLVRDAGAGEVEV
+LAGTVEDLAGERFSHQLLGLAGTWAAGDAAVARLQEAGLTARTLSARQASQDQHTADEIG
+GAR*
+>NZ_CP083691.1_1709
+MAGSHSSDRDAVTPGRHSEGAPGEPVIVFDHVSRVYAAKKGRGVTAVDDVSLSVNRGEVF
+GVIGFSGAGKSTLIRMINGLEKPTSGTVTVLGQQVSHLSEAKLRPLRTRIGMVFQQFNLL
+TSRTVAGNIEFALDTAGWPRSTRRARVAELLEFVGLADKAKHYPEQLSGGQKQRVGIARA
+LAAEPEILLADEATSALDPSTTHEVLSVLRRVNEELGVTIVAITHEMEVIRSIADRVAVM
+DTGRVVETGKVYDLFSRPAHSADAASFVATALKDRPNADEVARIRARTEGRLIMVSLKDS
+AAVSAVLGTASTRGVGFEIVHGGMSATKDSAYGLLTVALTGEAAAVDAFVADLAGAGDVQ
+EVHQ*
+>NZ_CP097650.1_935
+MAGSHTSDRDAVTPGRPSAGAPGEPVIVFDHVSRVYAAKKGAGVKAVDDVSLAVNRGEVF
+GVIGFSGAGKSTLIRMINGLEKPTSGTVTVLGQQVSHLSEAKLRPLRTRIGMVFQQFNLL
+TSRTVAGNIEFALDTAGWPRSKRRARVAELLEFVGLADKAKHYPEQLSGGQKQRVGIARA
+LAAEPEILLADEATSALDPSTTHEVLSVLRRVNEELGVTIVAITHEMEVIRSIADRVAVM
+DSGRVVESGKVYDLFSRPAHSADAASFVATALKDRPNAEEVARIRARTEGRLIMVSLKDS
+AAVSAVLGTASTRGVGFEIVHGGMSATKDSAYGLLTVALTGEAAAVDAFVADLAGAGDVQ
+EVHQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000117.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000117.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee3d590802dbc95677e3886d5c2e21abeb971109
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000117.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_993
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR*
+>NZ_CP033200.1_718
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR*
+>NZ_CP040019.1_177
+MSEALSRILQVWPEIVVALGQTLTMLAVTIPLAVLLGTPLGIWLFTHAPGGLSPSPRLHR
+VVDAAVSMLRSFPFLILLIAIIPVTRLIVGTTIGTAAVIVPLTVNAIPYFARFVEQNLAQ
+LGPGPVEAARAMGATRGQIVRDVLLVDARPALVGSLTIMSVSFISYSAMAGLVGGGGIGD
+FAIRYGYYRYETPLMVVAILLMIGLVALLQFAGTRLSQRLDHRRPRTARRPRRRALAPAG
+*
+>NZ_CP040019.1_1822
+MTWLETLTTNPAITDALPEALVETLLMVAISGVATVLIGGLLGIVLHVTRPGGLNPMPAL
+YTVLSTVIVNITRSVPYAILMVALIPLTKWLVGTAIGPIAATVSLTIGTAPFFARLVESA
+LREIPSGTVDAAQVMGSTRGQVIRKVLLPEAMPGLIAATTTTLVTLVGYSAMAGLIGGGG
+LGRLAYNYGYQRFQTEVMVVTIVVIVILVQLIQWIGDLLIRRVDHR*
+>NZ_CP083691.1_1708
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWAFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFVVNLIRPIPFVILIAALQPLTIAVLGSGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRTVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR*
+>NZ_CP097650.1_936
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000120.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9411c34a664d3c023b9085d628f2d355d12845e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000120.fa
@@ -0,0 +1,90 @@
+>NZ_CP042169.1_1064
+MTSPLTRLHDTLGLRTSPAIFFGSAAAVVLFTAAMGLFPGPVQAAFGVVSSWLRYDVGWI
+YTLSLTLLVAFLFILAVTRYGRVKLGDDDAVPEYSGLTWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPMAGTEPFSDRAASEAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKTIDIIAVVSTVFGLGVSVGLGALQINAGMNYVLGTPVAGWVQA
+LILAVVTAVGTASVLVGMDKGVKRLSYANILLAIALLVYVLMWAVSSMDVIRGTVQAIGE
+YASMLPVLSTYNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFARISRGRTIRSFIMAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAPAPGQGGDLTQTIVTDGNVQAALFQHLQGTPLYT
+VAAVVALVVITLFFITSIDSGALVMDAMANGHEDAAPRRQSVFWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAALLLQALREDAGAARPMRTRQWKQVLPVEEYRRR
+ATEDGVDVSDFVIRPEFEVGTEPENDTHTPKTWHQQRIDAAKALVTVGLTGGIAAGRTEV
+GAELERLGAVVVEFDDLMGEILVPGNPVLEELRSVFGEDIVRADGTLDARTLNRLTTESS
+TARTRMYEIVSPAVRDEANRRAREIGEDSVLVVDLALLAETGSGQDFDQVLAVSAPAEVR
+VARLMESHDMTRERAWAFIDEEAADEERAEIADTVIENDGSLEDLQEAVRAYWEAKIQPQ
+LEAARGERV*
+>NZ_CP033200.1_793
+MTSPLTRLHDTLGLRTSPAIFFGSAAAVVLFTAAMGLFPGPVQAAFGVVSSWLRYDVGWI
+YTLSLTLLVAFLFILAVTRYGRVKLGDDDAVPEYSGLTWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPMAGTEPFSDRAASEAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKTIDIIAVVSTVFGLGVSVGLGALQINAGMNYVLGTPVAGWVQA
+LILAVVTAVGTASVLVGMDKGVKRLSYANILLAIALLVYVLMWAVSSMDVIRGTVQAIGE
+YASMLPVLSTYNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFARISRGRTIRSFIMAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAPAPGQGGDLTQTIVTDGNVQAALFQHLQGTPLYT
+VAAVVALVVITLFFITSIDSGALVMDAMANGHEDAAPRRQSVFWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAALLLQALREDAGAARPMRTRQWKQVLPVEEYRRR
+ATEDGVDVSDFVIRPEFEVGTEPENDTHTPKTWHQQRIDAAKALVTVGLTGGIAAGRTEV
+GAELERLGAVVVEFDDLMGEILVPGNPVLEELRSVFGEDIVRADGTLDARTLNRLTTESS
+TARTRMYEIVSPAVRDEANRRAREIGEDSVLVVDLALLAETGSGQDFDQVLAVSAPAEVR
+VARLMESHDMTRERAWAFIDEEAADEERAEIADTVIENDGSLEDLQEAVRAYWEAKIQPQ
+LEAARGERV*
+>NZ_CP040019.1_1760
+MTSPLTRLHDALGLRTTPAIFFGSAAVVVLFTLAMGLFPGPVQAGFGVVSSWLRYDAGWI
+YTLSLTVLVAFLLLLAVTRYGRVKLGDDDAVPEYSGLAWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPLAGTEPFSDQAASQAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKAIDIVSVVSTVFGLGVSVGLGALQINAGMNYVFGTPVAGWVQA
+LILAVITAVGTASVLAGMDKGVKRLSYANILMAIALLVYVLMWAVSSMDVIRGTVQAVGE
+YLTMLPMLSTFNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFAKISRGRTIRSFIAAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAAAPGTGGDLTETIVTEGNVQAALFQHLQGTPLYT
+VAAVLALVVITLFFITSIDSGALVMDAMANGHEDPAPRRQSVIWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAGLLLQALREDAGTARPLRTRQWKPVLPAEEYHRR
+AHEEGVDVSDYVIRPEFEVGTEPEHDTHTPNTWHQQRTVAAKALVTVGLTGGIAAGRTVV
+GEELERLGAVVVEFDDLMGEILVPGSPVLEELREVFGDDVVRADGTLDARTLNRLTAEST
+TARTRMYEIVSPAVRDEANRRARAIGEDSVLVVDLALLAETGSAGDFDQVLAVSAPAEQR
+VARLMDSHDLPREQAWAFIDEEALDAERAEIADTVIENDGTLEDLHEAVRAYWEAKIQPQ
+IEAARGVSP*
+>NZ_CP040019.1_1761
+MNSLLTRLHDRLGLRTSPAVFFSAAAVIILFTVAMGVLPGPVQAVFGAAAHWLRYDVGWF
+YTLAATLLLAVCLILAVSRYGRVKLGDDDASPEYSGLAWFGMMFASGIGAVLMFWGIAEP
+MTHYALPPLEGTEPYSDQAAVQALNIANLHFGLHMWAILVVPGLCFGYFTYKRNLPPRVS
+SAFQLLLGDRIHGPIGKTIDVIAIVSTVFGMGVSTGMGALQINAGVNYVVGVPVAGWVQA
+LILAVALMLWVLMWAASSMDVVRGVIESFGRTLGALPLLTTFNDTLGGGTWSGDWTLFYW
+AWTVSWAPSVGMFVARISRGRTIREFVFASLGLPTAFVIVWMGVYGYSAIFADRAAAPEA
+GTGGPLAQTIAVEGNVQVALFQSLQEMPLYLPIAVLALIVIVIFFVTSIDSGALVMDAMA
+NGHEDLAPRRQRVFWGVSVGAVCTAIIVTAGDDGLNALREVIIVIGFPVMVLTVLQALLL
+LQALREDAGAARPLRTRQWKRVLPPEEYHRRAREDATVREEYAIRPEFEVGTEPEYETHT
+PNTWHAQQPAARRATVSVGLTGGVASGKSAVAAEFERLGAVVVDYDDLMREILVPGHPAV
+DELRDVFTAEVVADDGTVDWLALDALTAESPSARTRLHEVVAPVVRAETDRRATDAGESS
+VLVVDLALLVDAADVRDFDQVLEVLAPAEVRVARLMDERGLDREQAWAEVDADEQRRPAL
+GGTHTVLANEGDRAELERSVRDWWDEVVEPARERGRRPGPRLRRLTRTVPPPPPAAGGGG
+RGWRPGAGSPYRRDRVPDGTRPSARPLDRPPRSVGDPVPGDS*
+>NZ_CP083691.1_1650
+MNSLHTRVHDALGLRTSPAIFFTSAAVIVLFTAAMGLFPGPVQEVFGVVAGWLRYDIGWF
+YTLSATLLALFAVLLACSRYGRIKLGDDDATPEYTGVAWFGMMFAAGVGAVIMFWGIAEP
+MNHYANPPMPGTEPFSDQAALQAMDIANFHFTIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKAIDVISVVSTVFGLAVSTGLGALQINAGMNYVLGTPVAGWVQA
+LILAVITAAGVCSVLAGMDSGVKRLSYINIVVAVALMLFVLMFSISTNDVLRGTVQSVGS
+FVGHLPVLSTFNDVFGSGRWSGDWTVFYWAWTVTWAPFVGMFVAKISRGRTIREFVTAGL
+GLPSIFTMIWMGIYGYSAFQADRATAAGPGQGGDLTRTIVEEGNVQAALFQHLQGMPLYL
+PVAIVALVVITLFFVTSIDSGALVMDAMANGHEDPAPRRQGAFWAISIGAVCAAIILTAG
+ENGLDALQEVIIVIGFPVMLLTLVQAAMLLQALREDAGAARPIRTRQWKQVLPAEEYHRR
+AQEDGVDIQEYVIRPEFEPGTEPEFDTHTPNTWHQQRTVAQRALLTLGLTGGMASGRTAV
+GEELERLGAVVVEFDDLLDELLVPGAPVLDEVREVFGDDVVRADGTLDARAMNALIDASE
+AARSRFYEIVSPLVRAEADARAKAIGDDAVLVVDLALLAETGSARDFDQVLAVSAPAEVR
+VQRLVDERHVTRERAWALLDEGAQDDERAAIADTVIENGGTREELRAAVEAYWAEKVAPA
+VEAARIAGGVG*
+>NZ_CP097650.1_1012
+MTSPLTRLHDTLGLRTSPAIFFGSAAAVVLFTAAMGLFPGPVQAAFGVVSSWLRYDVGWI
+YTLSLTLLVAFLFILAVTRYGRVKLGDDDAVPEYSGLTWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPMAGTEPFSDRAASEAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKTIDIIAVVSTVFGLGVSVGLGALQINAGMNYVLGTPVAGWVQA
+LILAVVTAVGTASVLVGMDKGVKRLSYANILLAIALLVYVLMWAVSSMDVIRGTVQAIGE
+YASMLPVLSTYNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFARISRGRTIRSFIMAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAPAPGQGGDLTQTIVTDGNVQAALFQHLQGTPLYT
+VAAVVALVVITLFFITSIDSGALVMDAMANGHEDAAPRRQSVFWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAALLLQALREDAGAARPMRTRQWKQVLPVEEYRRR
+ATEDGVDVSDFVIRPEFEVGTEPENDTHTPKTWHQQRIDAAKALVTVGLTGGIAAGRTEV
+GAELERLGAVVVEFDDLMGEILVPGNPVLEELRSVFGEDIVRADGTLDARTLNRLTTESS
+TARTRMYEIVSPAVRDEANRRAREIGEDSVLVVDLALLAETGSGQDFDQVLAVSAPAEVR
+VARLMESHDMTRERAWAFIDEEAADEERAEIADTVIENDGSLEDLQEAVRAYWEAKIQPQ
+LEAARGERV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000121.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000121.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40d250c63c151c98c66cc1185dd1e6a64efb6914
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000121.fa
@@ -0,0 +1,106 @@
+>NZ_CP042169.1_1075
+MPKNSSTTVSSAVEAHPGGLASGSGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFKDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGRKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVAAGTPEEVAHVAESHTGRFLAELLA*
+>NZ_CP033200.1_360
+MVESSSFVPPKLSVQPDVRVLGARENNLQDVDLTVPRDATVVFTGVSGSGKSSLAFGTLY
+AESQRRYLESVAPYARRLIDQAGVPDVDSITGMPPAVALQQQRGSGNARSTVGSITTLSS
+LVRMLYSRAGDYPEGQPMLYAEDFSANTVQGACSECHGIGRVYEVNEQQMVPDPSLTIRE
+RAIASWPTAWHGHQLRDVLVALGYDVDVPWRDLPKKDRDWILYTDETPFVPVHSRLTLSE
+SKAAIEAGVEPSYSGTFVGARRYILDTFANTKSASMKRRVAQFLTAAICPTCNGKRLKPE
+ALSVTFEGFDIAEFSQLPLRELATILSGVVAREEDHEAASSDVRPTASRTPEKRAAAVQL
+ASGVLQRLRPLVDLGLGYLSLSRTTPTLSGGELQRLRLATQLSSDLFGVVYVLDEPSAGL
+HPQDVAALLEILDGLKGRGNSLFIVEHSVAVMRHADWLVDIGPGAGEHGGRVLYSGPPDG
+LAGVTESVTRGYLFGGRGLPLRTPREARSWLRLENVTRNNLHDLTVDIPLGVFTAVTGVS
+GSGKSSLVSQALPSLLGDRLGLAARADDEPVSDESLLADAPEHLEGRVAGPVTGVQRLVV
+IDQRPIGRTPRSNVATYTGLFDHVRRRFADTPEARSRGYKPGRFSFNVAGGRCPTCEGEG
+SVMVELLFLPSVYTECPDCHGTRYKASTLEVTWRGRTIADVLSMSVEEANLFFVGDEEIT
+RSLAALSDVGLEYLRLGQPATELSGGEAQRVKLATELQRAQRGDTLYVLDEPTSGLHCAD
+TDRLVAHLQTLVDAGNTVVAAELDMRVVAVADHVIDLGPGAGDAGGTVVAAGTPAHVADQ
+GVGASAGYLAAALQAATNVTPS*
+>NZ_CP033200.1_804
+MPKNSSTTVSSAVEAHPGGLASGSGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFQDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGKKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVATGTPEEVARAAESHTGRFLAELLA*
+>NZ_CP040019.1_1749
+MPKNSSTTVSSAVETHAGGLASGPGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEVYDYLRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFADLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEVVAEKGKKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLAKEMGFSLDTPWRELEPAQREAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVVPYVLRKHGETESDGARERYESFMREIPCPVCHGARLNPTVLNVLVGGL
+SIAEATRLPLREARDFLAGLELSARERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLEDLKANTASITGDYLAGRRAITAPQTRRA
+PQEGRTLTVRGARENNLKDVSVDIPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRAVDGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACSGDGTLKIEMNFLPDVYVPCEVCDGARYNRETLEVTYKGKNIAE
+VLDMPIEEAAQFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRSVYVLDEPTTGLHFDDIRKLLQVLQSLVDKGNTVITIEHNLDVVKCADHVIDLGPE
+GGSGGGTIVATGTPEEVARVEASHTGRFLAELLA*
+>NZ_CP083691.1_1640
+MPKNSSSAAAPARPDAAARGGLASGPARGSAQHERIVVKGAREHNLKNVDVSIPRDSMVV
+FTGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQK
+STNRNPRSTVGTITEIYDYMRLLWARVGVAHCPVCGEVVSKQTPQQIVDQLEQLPERTRF
+QVLAPVVRGRKGEFVDLFSSLSTQGYARALVDGELIQLSDPPALKKQNKHTIAVVVDRLA
+VKEGIRQRLTDSVETALKLADGLVAVEFVDVDVVAQAGKKNQGDLAGEDAEGNPRFRTFS
+EKLSCPHGHPQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVPNDELSLNEGAI
+LPWSLGKSTSDYWLRVLGGLAKEMKFSLDTPFKDLTAQQRDAVLNGKDFKVEVSFRNRFG
+RERRYTTGFEGVLPYVMRKHGETESDNARERYESFMRQIPCPACHGARLNPTVLNVRVGG
+LSIADATRLPLRESLAFLDGLQLTERELAIADQVVREIRARLEFLLDVGLDYLNLERNAG
+TLSGGEAQRIRLATQIGAGLVGVLYVLDEPSIGLHQRDNRRLIDTLIRLRDLGNTLIVVE
+HDEDTIAEADWIVDIGPRAGEHGGEVVHSGSLDELKANTRSVTGDYLAGRRRIEVPAARR
+PVDPKRRLTVKGATENNLKDVTVDIPLGVFTAVTGVSGSGKSTLINEILYKVLADKLNGA
+KMVPGRHRSVAGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDQIRKLFAETPEAKVRGY
+QQGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIA
+EVLDMPIEEAAEFFGAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQK
+RSTGRTVYVLDEPTTGLHFEDIRKLLQVLQTLVDKGNTVLTIEHNLDVVKCADHVIDLGP
+EGGSGGGTVVATGTPEEVAAVPESHTGRFLAELLG*
+>NZ_CP097650.1_1024
+MPKNSSTTVSSAVEAHPGGLASGPGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFQDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGRKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVAAGTPEEVAHVAESHTGRFLAELLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000127.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000127.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b54a3843258f31cbd1b7856c5c733b94a065062
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000127.fa
@@ -0,0 +1,43 @@
+>NZ_CP042169.1_1291
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA*
+>NZ_CP033200.1_1022
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFTAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA*
+>NZ_CP040019.1_1531
+MTEHTAPTPLPLSLLDLATVRDGASVAEAVAESVEQAQAAERAGFRRVWYAEHHNMPAIA
+SSATSVLIAHVAAHTESIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGRTRIPGIEAYPGKGTDVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTREEADR
+EWEAARRARIRMMLGRGRTLSDDEVEMLLHSPAGQQVLTMLECTAVGTGEETATWLRDFA
+AKVQADELIITTAAQDAGVRRRTLELLGEHVVRA*
+>NZ_CP083691.1_122
+MSIPLSVFDPVLLPAETDPREAIDDARTLAAAADALGYRRLWHGEHHLNPGVLGSNPALT
+LALVGPVTQHIRLGSAASLVGPRTPLVLAEDFGLLAAAFPGRIDLGLGRAAAPGGPPPGT
+RAETPTGDGGPAQDPQREPAGAGASSGQDPAAGPSEVDGVVIPAAPDLSAALGSPLRAAS
+RALLPTPSTPALDYGAQVDLLLGLLDGTAQHDGAALGQVVARPAVDVEPWVLGSGPGVSA
+EVAARRGLRFGANYHVSPAGTVAAVRRYRELFRPSPEVPCPVVSVSAEVLIADTAAEARR
+RASGYAAWVLSIRSGAGAVPYPSPAHPEPSRTPQEEALVADRLQTRFVGTAEQVAERLDA
+LARLTGADELLISASAHRVEHRVETLTRLAEIWRTA*
+>NZ_CP083691.1_1425
+MTADVRPVVPPETAPAGVPLSLLDLATVRGDQRIGEALGQSVELAQTAEAQGFTRVWYAE
+HHNMPGIASSATAVLLAHVAAHTERIRVGSGGVMLPNHSPLVVAEQFGTLAELHPGRVDL
+GLGRAPGTDQRTLQALRRSPEAADRFPQDVLELQGYLRGESRMPGIDAYPGRGTDVPLWI
+LGSSAFGANLAAQLGLGYAFASHFAPQMLEHAARLYREHFTPTDALDAPHFIAAANVVVA
+DTDEEAQRLWEATRRSRVRMFLGRGRHLTEDELDMLMDSPAGEQVLGMLRHTAVGTPDVV
+RAWLDDFAARVEADELIVTAAAVDHPARVRTLELLGEHVIRR*
+>NZ_CP097650.1_1246
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000129.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000129.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5291a4af681b4ddd5181c7e5f5df5346067c5a8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000129.fa
@@ -0,0 +1,81 @@
+>NZ_CP042169.1_1326
+MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV
+GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP
+REALRFLRPLVDGLAAAHGAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV
+PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIEAVAAGLDPDAPDRRPAAQPAE
+GPGADPAPAGPAADGLEDAAPDGNLETRALDAGDHHATRVLPALAESDLDEDMTDVIDTR
+VATHGGDPRPAARPAEPIGPLGLDPAPADRHPGRGSRRRLRRAARRPALDLGQGTGRAAA
+IGAAVTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTAR
+HDELRTEGTVVASSPAAGEPAGRGAPVELTVSAGPAPVPVPDLTGVVIRQAHGVARDARF
+TVEVAERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDMTGQDPETAH
+TTLADEGWDARVHRLPLPLSARGESRVLHQSPAAGTALPEGTAVHVWVG*
+>NZ_CP042169.1_1898
+MSLPDARWHVVSPSPFEHEQQGLDILREVLPDESPFQVWTNFEFPDEDGQWHEVDALVLA
+RTKFILVELKYYSGVLRGTGLRWERPGHSPQRSPLALAKKKAERFRSLLERTIESKMPGA
+GRQRIVPYVDYAVFLHHDRFRNEMAPQDSGRLFGLPHNETASNLPSIEHLVLAPATDRFP
+LIGEPREQVLVALMEHLNLADARQPEVGSWLLEERLGEPTPDGQDWLASHRFQERHFARI
+RFQQPREGAPSSDLARVREAARREFDLTRALHHEGLLTASDRVDNELGVGLVFPYDESLA
+PLPLWLESRAATLSQQNRLDLLRQLAETLEYVHSNGIVHRALSPEALWVKTPKQGEPRIL
+VADWQLAGVADRDKVDHAASLTQLSTQFGTTVRSTEELAPTSGALFRAPEDARRVSSLGR
+YKLDVFSVGALAAYLLTGAPAANTVAELHEHLATHQGLDVSVALPSVPEPVRQAILHATD
+PRPTARTATLNDFLAGLTEAQATAPQPASPALDPLEAAPGQALDSRFTLVRRLGKGSTAV
+GLLVDDAQTGSRQVLKVALDDEAATRLDDEAQVLRLLPLHKRLVRLLDGPFDVGGRRALL
+LTSAGTRTLSEVLRERQRLSLDHLERFGSELLEAAQALDAAGLRHRDVKPANIGVVRTPK
+HGEHLVLFDFSLARARSTDVRAGTPPYLDPFLEQGGRTGYDSAAELYAVAVVLYEMASGQ
+KPFYGDPEANPAAVRDDLTVPDGIFDPSLQAPLSALFERALARDAQARFHTVAELAAAWE
+ALFRNDADPVTAQDAETLAARATLETPLSEAGLSARGLSALEAIKVTAGPGGVAVEPHDV
+RTVRDLVLVDPIKLNSLAGSTTETRAEVRARAKQWRAAFKKELMRQATQVPQGTLPTPLD
+AAELLLRHAGAAHAEGVRAQLRLVLGLDGEVPALSTHAVLADARGVTPGLVPQLFGRAQQ
+AWTDVAETRSLLDSLDGALRAAVAERGGVSTPDELTSALEQTLSPATPAEVRDAEPRRIV
+QGLLWLLLDRERAAARGEADVPALVQRRREGRVVAVAEMPVLLDVAETLGAAAEAAVDGA
+GDPESALVPADLVQTRVAAVLDAVDGLPEALRSWRRAAALAAHVSATTCLSAAGEWHHRL
+LAPATAAHHALQGASGTVQLSRERAAERVGARFPALSPLPRDAALDRVLAEAELGLVFDE
+DLGPQGAYRSRQTLAPTTGFATRAETRLVEHQRPLSELGVEGQRLLDSQRNRSYLALGVP
+AQRLARLESALVRRFHAEPLDLTDLFIRLLKDQAAAHPKMTWDHVTAADAEPDGSRPAQG
+LNVLVRNLLPELEQHLSRTIGDPGRAASPVLLTGAAVLARYGHLGVLARWADLAEYRARP
+VWLVVPQVAGNVGPRLDGVSVPKNTPGQYVPLTPEWIDGLAALMAAQPLTEESRT*
+>NZ_CP033200.1_1056
+MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV
+GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP
+REALRFLRPLVDGLAAAHRAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV
+PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIDAVAAGLDPDEPDRHPAEGPGA
+EPAVAAPAADGPEDAAPDGNLQTRALDAGDHHATRVLPALAESDLDADMTDVIDTRAATR
+GADRRPAAHPAEPIGPLGLDPAPADRHPGRESPRRLRRAARRPALDLGQGTGRAAAIGAA
+VTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTARHNEL
+RTEGTVVASSPAAGEPAGRGTPVELTVSAGPAPVPVPDLTGVVIRRAHGVARDARFTVEV
+AERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDVTGQDPETARTTLA
+DDGWDARVHRLPLPLAGRGESRVLHQSPAAGTALPEGTAVHVWVG*
+>NZ_CP040019.1_1498
+MSSTRRDPLVGGIVDGRYEVLARLARGGMSTVYLALDTRLDREVALKVMHPHLAEDPVLV
+GRFEQEAKTAARLSHPHVVAVLDQGHTEDASGEVLAYLVMEHVPGHTLRTVIREQAPLTP
+REALRHLRPLVDGLAAAHRAGLVHRDAKPENVLVRTDGRITVADFGLSRAATAHTSAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAAGIILFELLTGRQPFTAGTALQVAYRHVHERVPV
+PSSLQPGLPEALDDLVLWCTEPDPADRPADAGEVLDRLDAVAAELGPAELDRPPVLVPDA
+VEGRPGPEHDETTTLDALDRLDPKDPLDDADGDETTSLDAGDHHATRVLPSLPADALPTE
+ALAADDVVRRSPARRRRRP*
+>NZ_CP083691.1_1391
+MSSTRRDPLIGDLVDGRYEVLDRVARGGMSTVYRALDHRLDREVALKVMHPHLAEDPALV
+GRFEREAKTAARISHPHVVAVLDQGHTADEAGDVLAYLVMEHVPGRTLRAVIREEAPVAP
+RRAVALLEPVVEGLAAAHRAGLVHRDVKPENVLVRTDGRITVADFGLSRAATGHTSAGQT
+VFGTPAYLAPELISGTGGDARADVYGVGIMLFELLTGTQPFTAATPLQVAYRHVHERVPV
+PSSVRPGLPEALDDIVLWCTEPRPADRPEDAAALLPELRRVAALLPQTAPADEAPAADDA
+PTVALAVSPTVPTVPVPDAADATARLEPRRPDPRRAEPVPTPATATAASPSSDLSSAVPE
+APRPAPVAPRPASARQRRRTARTPEVVLGAGMGRTVAVGAAVTLLLAGMALLLGWILGSG
+GISGPAGVVVPPLWGLEQQEAAARLAEAGLTSAVVSRHDERFSDGVVLDVSPAAGSTVDA
+GGPVRLTVSDGPAPVPAPDLAGLTVTDAHAVAEDGRVGVVVADRVADRAVPAGAVVSQSP
+EAGAEMTPGDEVAVVLSTGPATHPLPDLGGLTVGEARTRLADLGFVPDVRTLPLPGPSGD
+AARVLRQGTPAGTVLPEGASVQLWTL*
+>NZ_CP097650.1_1280
+MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV
+GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP
+REALRFLRPLVDGLAAAHRAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV
+PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIDAVAAGLDPDEPDRRPAEGPGT
+DPAAAAPAADGLEGAAPDGDLPTRALDAGDHHATRVLPALAESALDDDVTDVIDTRAATH
+GGDPRPAARPAEPVGPLAVDPAPADRHPGRGSRRRLRRAARRPALDLGQGTGRAAAIGAA
+VTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTARHDEL
+RTEGTVVDSSPAAGEPAGRGAPVELTVSAGPAPVPVPDLTGVVIRQAHGVARDARFTVEV
+AERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDMTGQDPETAHTTLA
+DEGWDARVHRLPLPLSARGESRVLHQSPAAGTALPEGTAVHVWVG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000130.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000130.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8d724d6fa13ec9189238e079b47143b5ee10e29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000130.fa
@@ -0,0 +1,144 @@
+>NZ_CP042169.1_1393
+MSLSSAAPTPPSVPLDPAGAPHRPQLPGSERTPPARTLVELFDATAREHPDATALDDGVE
+PLTYAELRERVDETARHLWAAGVRAGDRVGVRIASGTAALYVSILGVLAAGAAYVPVDAD
+DPEERARLVFGEAKVAGVLTDERVYAPHPEHTADPAAEARAPGLEDDAWIIFTSGSTGTP
+KGVAVSHRSAAAFVDAEARIFLADDPLAPGDRVLAGLSVAFDASCEEMWLAWRHGACLVP
+APRSLVRSGMDLGPWLAERRITAVSTVPTLAAMWPTEAMDNVRLLIFGGEACPPELAARL
+AEDGREVWNTYGPTEATVVACAAPLTGLGPVRIGLPLDGWDLAVVDPQTTLPVAEGETGE
+LIIGGVGLARYLDPAKDAEKYAPMPSLGWERAYRSGDLVVFEPEGLLFVGRADDQVKLGG
+RRIELGEVDAALQALPGVHGGAAAVQTTPAGHQILVGYLVPADPEAELDLHMAREHLAAE
+LPAALVPRLAVVDSLPTKTSGKVDRHALPWPLPGAEVDEDAPPPDEDTADGWVLRQWADV
+LGAPPKDADTDFFEAGGGSLAAAQLVARLRLRHPAVTVQDVYRNPTAGALVAAVVGDDGP
+RGIEVHDRHVDRTRHRTQWVQTLVGLPVFVLPALRLGVWTGLALNLLTLSGLAPGLPTVP
+WWVLIVAGLLVVTVPGRMLLTAATARLLLRGVSPGSYPRGGRVHLRLWLAQQISDLVDPY
+SLAGATWVPAYARLLGNRIGKDVDMHTVPPVTGMLTVEEGAAIEPEVDLSGYWVDGDVVR
+LGEVRIGADAVVGARSTLLPGAQVGAGAHVEAGSTVAGRVRGGQRHAGSPAVKVGKVKSR
+GPAEAPRETPGWRLMATVLSTLISLLPLVSAAAAAAVAAWSLTWWPPAPEAGPLAAVGTT
+AARLLAASPLVAGVWFLTQMLLVLVTVRLLALGITEGHHPVRSRVGWQVWATERVLDAAR
+DQLFPIYASRFTPTWLRLLGAEVGRGVEASTVVLLPCMTRVGDGAFLADDTMVSSYSLDG
+GWMHVAPAKVGKRSFVGNSGMVPGGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPVRLRR
+NEVTADAALTYDPPARLKAARTAWELLRAIPVWLHVALSLAVGATLAALIAVGTWALAFV
+LGGVVLLAAGAVAASLTVLAKRVFVGRIRAGEHPLWSSFIWRNEVADTFTEFLAAPWFSR
+AAAGTPALVWFLRAMGARIGHGAWVESYWLPEADLVELGDGATVNRGCVVQTHLFHDRVM
+SLDAVVLEDGATLGPHSVVLPAARLGRGTTVGAGSLVMRGEELPAGTWWLGNPVSPWRRP
+DGDPAAAATPSREEA*
+>NZ_CP033200.1_1135
+MSLSSAAPTPPSVPLDPAGAPHRPQLPGSERTPPARTLVELFDATAREHPDATALDDGVE
+PLTYAELRERVDETARHLWAAGVRAGDRVGVRIASGTAALYVSILGVLAAGAAYVPVDAD
+DPEERARLVFGEAKVAGVLTDERVYAPHPEHTADPAAEARAPGLEDDAWIIFTSGSTGTP
+KGVAVSHRSAAAFVDAEARIFLADDPLAPGDRVLAGLSVAFDASCEEMWLAWRHGACLVP
+APRSLVRSGMDLGPWLAERRITAVSTVPTLAAMWPTEAMDNVRLLIFGGEACPPELAARL
+AEDGREVWNTYGPTEATVVACAAPLTGLGPVRIGLPLDGWDLAVVDPQTTLPVAEGETGE
+LIIGGVGLARYLDPAKDAEKYAPMPSLGWERAYRSGDLVVFEPEGLLFVGRADDQVKLGG
+RRIELGEVDAALQALPGVHGGAAAVQTTPAGHQILVGYLVPADPEAELDLHMAREHLAAE
+LPAALVPRLAVVDSLPTKTSGKVDRHALPWPLPGAEVDEDAPQPNEDTADGWVLRQWADV
+LGAPPKDADTDFFEAGGGSLAAAQLVARLRLRHPAVTVQDVYRNPTAGALVAAVVGDDGP
+RGIEVHDRHVDRTRHRTQWVQTLVGLPVFVLPALRLGVWTGLALNLLTLSGLAPGLPTVP
+WWVLIVAGLLVVTVPGRMLLTAATARLLLRGVSPGSYPRGGRVHLRLWLAQQISDLVDPY
+SLAGATWVPAYARLLGNRIGKDVDMHTVPPVTGMLTVEEGAAIEPEVDLSGYWVDGDVVR
+LGEVRIGADAVVGARSTLLPGAQVGAGAHVEAGSTVAGRVRGGQRHAGSPAVKVGKVKSR
+GPAEAPRETPGWRLMATVLSTLISLLPLVSAAAAAAVAAWSLTWWPPAPEAGPLAAVGTT
+AARLLAASPLVAGVWFLTQMLLVLVTVRLLALGITEGHHPVRSRVGWQVWATERVLDAAR
+DQLFPIYASRFTPTWLRLLGAEVGRGVEASTVVLLPCMTRVGDGAFLADDTMVSSYSLDG
+GWMHVAPAKVGKRSFVGNSGMVPGGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPVRLRR
+NEVTADAALTYDPPARLKAARTAWELLRAIPVWLHVALSLAVGATLAALIAVGTWALAFV
+LGGVVLLAAGAVAASLTVLAKRVFVGRIRAGEHPLWSSFIWRNEVADTFTEFLAAPWFSR
+AAAGTPALVWFLRAMGARIGHGAWVESYWLPEADLVELGDGATVNRGCVVQTHLFHDRVM
+SLDAVVLEDGATLGPHSVVLPAARLGRGTTVGAGSLVMRGEELPAGTWWLGNPVSPWRRP
+DGDPAAAATPSREEA*
+>NZ_CP040019.1_1435
+MSHPSVAPVPPPDPVDPADDAAAVHPPQLPGALRTPPARTLVELFDATAREHPDAPALDD
+GVEPLTYAELQARVDETARHLWAAGVRTGDRVGVRIASGTAALYVSILGVLAAGAAYVPV
+DADDPEERARLVFGEARVAGVLTDERVYAPAAVHAPRPDAEDRAPGLEDDAWIIFTSGST
+GTPKGVAVSHRSAAAFVDAEARIFLSEDPLAPGDRVLAGLSVAFDASCEEMWLAWRHGAC
+LVPAPRSLVRSGMDLGPWLAERRITAVSTVPTLAAMWPTEALDNVRLLIFGGEACPPELA
+ARLAEDGREVWNTYGPTEATVVACAAPLTGVGPVRIGLPLDGWDLAVVDPATGVPVAEGA
+TGELIIGGVGLARYLDPVKDAEKYAPMPTLGWERAYRSGDLVVFEPEGLLFVGRADDQVK
+LGGRRIELGEVDAALQALPGVHGGAAAVQTTPAGHQILVGYLVSADPEADLDLHLARERL
+AEELPAALVPRLALMDALPTKTSGKVDRHALPWPLPGAEPDDEAPQPDEASPHGWVLRQW
+ADVLGAPPSGPDADFFEAGGGSLAAAQLVARLRLRHPAVTVQDVYRSPTASALAAAVVGE
+DGGAGGIEVHDRHVASTRHRTQWAQTLVGLPVFVLPALRLGVWTGLALNLLALTGLAPGL
+PTVPWWVLAVAGLLVVTVPGRMLVTALAARLLLRGVEPGSHPRGGRVHLRLWLAQQITDV
+VDPYSLAGAMWVPAYARLLGNRIGADVDLHSVPPVTGLLTVGEGASIEPEVDLSGYWVDG
+DVVRIGEVRIGAGAVVGARSTLLPGARVGAGAHVEAGSTVAGRLRGGQRHAGSPAAKVGK
+VRADGPNVAPPRATGWRAVSTVLSTLVALLGLVAAGAAAAVGAWSLTWWPPADPTGPAAA
+VGVTALRLLAASPLIAAVWFGAQMLLVLGAVRLLSVGITEGHHPVRSRVGWQIWATERIL
+DAARDHLFPLYASRFTPVWLRLLGAEVGRGVEASTVVLLPGMTRVGDGAFLADDTMVSSY
+SLEGGWMHVAPAKVGKRAFVGNSGMVPAGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPV
+RLRRTEVAADASVTYAPTARLKAARTGWELLRAIPVWLHVALTIATGAALAALTAVGTWA
+LAAVLGGAVLLAAGAAAASLTVLAKKAFVGRVRPGEHPLWSSFIWRNEVADTFTEFLAAP
+WFARAAAGTPALVWFLRAMGARIGRGAWVESYWLPEADLVTLGDGATVNRGCVVQTHLFH
+DRVMSLDEVVLADGATLGPNSVVLPAARLGRGTTVGAGSLVMRGEELPAGTWWLGNPVSP
+WRRPDGVPDPSPAPSREAA*
+>NZ_CP083691.1_1342
+MTAPHPSTPRSAPHDAGTPHAPQLPGTDRTPPPRTLIDILDATAREHPEAPALDDSTAQL
+GYAELLDRVLESARFLQAHGIGAGDRVGVRIPSGTAALYVSILAVMAVGAAYVPVDADDP
+EERARLVFGEARVAGVLTGERALDDRAAAERAEAPEARAPRLEDDAWIIFTSGSTGTPKG
+VAVSHRSAAAFVDAEARIFLTADPLGPGDRVLAGLSVAFDASCEEMWLAWRHGACLVPAP
+RALVRSGMDLGPWLAERRITAVSTVPTLAAMWPTAALANVRLLIFGGEACPPDLAARLAV
+PGREVWNTYGPTEATVVACAAPLAGEGPVRIGLPLDGWDLAVVDPASGVPVAEGETGELI
+IGGVGLARYLDPAKDAEKYAPMETLGWDRAYRSGDLVLYDPAGLLFLGRADDQVKVGGRR
+IELGEVDAALQNLPGVQGGAAAVRTTPAGNQLLVGYLKPTGPLEGFDLDAAHARLAEELP
+AAIVPRLALVDSLPTKTSGKVDRNALPWPLPGTAATDDADTPDESTPDGWVLAQWAAVLG
+AAPADGSTDFFSAGGGSLAAAQLVARLRERHPGVTVQDVYRHPTADELVSAVLGEGAEGI
+EVHERNVDTTRRRTQWAQTLVGLPAFILPALRLGTWTGVAVNLLAATGLVPGLPTVPWWI
+LALVGLFVVTAPGRMLVAGLTARALLHGVGPGAHPRGGRVHLRLWLAQQVTDLVDPYSLA
+GAGWIPAYGRLLGNRIARDADLHALPPVTGLLTVGEGASIEPEVDLSGYWVDGDVLRVGT
+VEVGAGAVVGSRSTLLPGAKVGAGAHVEAGSTVAGRLRGHQRHGGSPAVKLGKVKRGSAP
+AETAPDAAGWRVLSTLSSTAVALLPLAAVAAAAAVGAWSLTWWPPAAADASPLQAVGTAA
+ARLLAASPLIAAVWFGVQMLLVLVAVRVLAIGITPGHHPVRSRVGWQIWATERLLDAARD
+QLFPIYASRFTPTWLRWLGARVGKDVEASTVVLLPTMTQVGDGAFLADDTMVSSYTLEDG
+WMHVAPAKVGKRSFVGNSGMVPGGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPVRLRRT
+EVEADASLTYAPPARLKAARTGWELLRAIPVWLHVALTIAVGAALAALAAVGTWWLAALL
+GGAVLLAAGAVAAVVTVLAKRAFVGRVRAGEHPLWSSFIWRNEVADTFTEFLAAPWFSRA
+AAGTPAMVWFLRGMGARIGRGAWVESYWLPEADLVTLGDGATVNRGCVVQTHLFHDRVMA
+LDEVVLADGATLGPNSVVLPAARLGEGTTVGAGSLVMRGEELPGGTWWLGNPVAPWRRPG
+KTPTAHQRAAAATGALPVIPDPTSAGGIR*
+>NZ_CP083691.1_2390
+MTTQQFHPARAPAAATSAVESEDRALYPVEPPPAPRTLVDILKATAAAHPDAVALEGHGP
+GGSAALNYMQLLARAEQVAARLREAGIGPGDRVGLRVPSGTTDLYVALVAILLSGAAYVP
+VDWDDPASRAETVFGEAAVACVIGEGMAITPVDGVAPLRRTGAPGLEDDAWIIFTSGTTG
+LPKGVAITHRNAAALVDAEARMYLQDDPLGPGDRVMAGLAVSFDASCEEMWLAWRHGAAL
+IAAPREVVRSGPDLGAWIAQKRLTAISTVPTLAALWPDDSLVGIRLLIFGGEACPPELVA
+RLATQDRELWNTYGPTEATVIASGAILRPGQEVRIGLPVPGWKLAVVDPEGRPVRWGEAG
+ELVIGGVGLGRYLDPEKDAEKYAPLAALGWDRCYRTGDMVVAEPEGLVFAGRIDDQVKIS
+GKRIELGEVDAHLTAMPGVRAGAAAVQLTDSGTAVLVGYLMPEKGVELDLPRIRELMGER
+LPGGVVPTLAVVDELPMKSSGKVDRTALPWPLPFDAGEAPPLPEDLRWLAERWTAVLGPA
+PLTPESDFFALGGSSVAVAHLVTALREHHPQLEFPQVYANPTLAGMADLLAGMADSGPRV
+ERRQPAAMPRFTGPAQIAWVTALTGVAGLRYVAGATVAIWALGQFFGAGWVVTPPVLPTL
+IAWAVLFSVPGRLYGTALVVRVLNAGLRPGRYRRGGLTHLRVWAADRAIATARLEYLLGG
+PAASHVHRVFGTRVGSGAHLDHMPSATGLVRIGHGVSVGAEADLHGHWVEAGTFVLGEIV
+VGDHARIGARSIVLPGVRVGSWAEIQAGSRVASSVPAHEYWGGSPLRRLGEAGVTWPSED
+PRAARGVRAWPVALAAAGQMFTLAVLALLPMVALLPWVVLVLSPLRGATDFRDVLPVMAL
+WVPVVVVLAVPTWFLLVSAFVRLLAPLVKPGFYPVHSLQAWAAWSIQNVMRRTLIGTYPV
+YASSATPWLMRLMGARIGRNVEISTVEAIPHLTVVEDGAFLADHSMAAVPRVGRGWVHIG
+STVIGRGSFVGNSAIVGPDRDLPDDALVAVLGVSPHRPAPGTSWLGRSPTAIPRVKVAAD
+AAATFAPPRRLKAARWAVELCRFVPAFIVGWLDIAVVYFLATVYMGASGQGSDPLRGVVV
+ATVASLPAAVAAALIASAMPVLFKWALVGEFVPQDRPLFSSFVWRNELMDAFVEVLAVPS
+LIRIGLGSPVLTMWARWMGVEIGRNAWVESWWLPETDLVSIADNATVNRGTVLQTHLFHD
+RVMTMQPVRLDEGATLGPNSFMLPGSSLGPCATVRPGSLVLREDAVPGHSDWSGNPIRAV
+QDAPAAAATGDTATRARARADHLDADERPQTGPIPVVATSTPAREEPTS*
+>NZ_CP097650.1_1342
+MSLSSAAPTPPSVPLDPAGAPHRPQLPGSERTPPARTLVELFDATAREHPDATALDDGVE
+PLTYAELRERVDETARHLWAAGVRAGDRVGVRIASGTAALYVSILGVLAAGAAYVPVDAD
+DPEERARLVFGEAKVAGVLTDERVYAPHPEHTADPAAEARAPGLEDDAWIIFTSGSTGTP
+KGVAVSHRSAAAFVDAEARIFLADDPLAPGDRVLAGLSVAFDASCEEMWLAWRHGACLVP
+APRSLVRSGMDLGPWLAERRITAVSTVPTLAAMWPTEAMDNVRLLIFGGEACPPELAARL
+AEDGREVWNTYGPTEATVVACAAPLTGLGPVRIGLPLDGWDLAVVDPQTTLPVAEGETGE
+LIIGGVGLARYLDPAKDAEKYAPMPSLGWERAYRSGDLVVFEPEGLLFVGRADDQVKLGG
+RRIELGEVDAALQALPGVHGGAAAVQTTPAGHQILVGYLVPADPEAELDLHMAREHLAAE
+LPAALVPRLAVVDSLPTKTSGKVDRHALPWPLPGAEVDEDAPQPNEDTADGWVLRQWADV
+LGAPPKDADTDFFEAGGGSLAAAQLVARLRLRHPAVTVQDVYRNPTAGALVAAVVGDDGP
+RGIEVHDRHVDRTRHRTQWVQTLVGLPVFVLPALRLGVWTGLALNLLTLSGLAPGLPTVP
+WWVLIVAGLLVVTVPGRMLLTAATARLLLRGVSPGSYPRGGRVHLRLWLAQQISDLVDPY
+SLAGATWVPAYARLLGNRIGKDVDMHTVPPVTGMLTVEEGAAIEPEVDLSGYWVDGDVVR
+LGEVRIGADAVVGARSTLLPGAQVGAGAHVEAGSTVAGRVRGGQRHAGSPAVKVGKVKSR
+GPAEAPRETPGWRLMATVLSTLISLLPLVSAAAAAAVAAWSLTWWPPAPEAGPLAAVGTT
+AARLLAASPLVAGVWFLTQMLLVLVTVRLLALGITEGHHPVRSRVGWQVWATERVLDAAR
+DQLFPIYASRFTPTWLRLLGAEVGRGVEASTVVLLPCMTRVGDGAFLADDTMVSSYSLDG
+GWMHVAPAKVGKRSFVGNSGMVPGGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPVRLRR
+NEVTADAALTYDPPARLKAARTAWELLRAIPVWLHVALSLAVGATLAALIAVGTWALAFV
+LGGVVLLAAGAVAASLTVLAKRVFVGRIRAGEHPLWSSFIWRNEVADTFTEFLAAPWFSR
+AAAGTPALVWFLRAMGARIGHGAWVESYWLPEADLVELGDGATVNRGCVVQTHLFHDRVM
+SLDAVVLEDGATLGPHSVVLPAARLGRGTTVGAGSLVMRGEELPAGTWWLGNPVSPWRRP
+DGDPAAAATPSREEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000134.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000134.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4cccb7ca581437e75bfd558fb846ff5079ea86b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000134.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1520
+MTEIAAGPGFALPRGVEPGRAVVVGAGPNGLTAAALLAREGWEVDVFERAPVPGGACASA
+PVLGEGTVVDLGAAGHPFGVASPVFRELGLTDHGLAWLHPAMPMGHPLPDGPAALLHRDL
+EATAAGLGVDARAWRAVHGALVAHVDEILAGALGPVLRPPPHPVAMARFGLRAPWPADLL
+GRAMFRTEAARALFTGSAAHAILPSSRPLTAAFGALFGALGMSSGWPVARGGSGAIVDAL
+VAVLRAHGGRLHLGHEVTDLRALPAADAVVLDLTPRQVLRVAGTGLPPRYAAALRRWRPG
+PSVSKVDFLLDGPIPWRDARLAGAGTVHLGGTAAEIRRAEDDVAAGRMPTRPFVMLCQQQ
+AADPSRATGPARGHTVVWSYAHVPHGHPGDVRPLIEAEVERHAPGFRDRIGAAVAMRPAD
+LEAWNPNLVGGDIAGGSLAGARALLRPTASPRPHRAGRTGLYLASASTPPGAGVHGMGGA
+WAVRTLLADRRR*
+>NZ_CP033200.1_1241
+MTDTAAGPGFALPRGVEPGRAVVVGAGPNGLTAAALLAREGWEVDVFERAPVPGGACASA
+PVLGEGTVVDLGAAGHPFGVASPVFRELGLTDHGLAWLHPAMPMGHPLPDGPAALLHRDL
+EATAAGLGVDARAWRAVHGALVAHVDEILAGALGPVLRPPPHPVAMARFGLRAPWPADLL
+GRAMFRTEAARALFTGSAAHAILPSSRPLTAAFGALFGALGMSSGWPVARGGSGAIVDAL
+VAVLRAHGGRLHLGHEVTDLRALPAADAVVLDLTPRQVLRVAGTGLPPRYAAALRRWRPG
+PSVSKVDFLLDGPIPWRDARLAGAGTVHLGGTAAEIRRAEDDVAAGRMPTRPFVMLCQQQ
+AADPSRATGPARGHTVVWSYAHVPHGHPGDVRPLIEAEVERHAPGFRDRIGAAVAMRPAD
+LEAWNPNLVGGDIAGGSLAGARALLRPTASPRPHRAGRTGLYLASASTPPGAGVHGMGGA
+WAVRTLLADRRR*
+>NZ_CP040019.1_1333
+MGGGETGIGSGARPRPHRTHQHRRVHDRLAHPVAGPAAGPRFALPRGVEPGRAVVVGAGP
+NGLTAAALLAREGWEVDVYERAPVPGGASASAPVLGEGTVVDLGAAGHPFGAASPVFRDL
+DLAAHGLQWLHPAVPMGHPLPDGPAAILHRDLDATAEGLGPDGRAWRAVHGALVEHIEEL
+VADVLGPLVRPWPHPVAMARFGLRAPWPAAHFGRAVFRTEQARALYTGSAVHAIMPPGRP
+LTSAFGALFGALGMSSGWPVARGGSGVITDALVSVLRAHGGRLHLDQEVTDLRALPDVDA
+VVLDMTPRQVARLRGTDLSPSYAAALQRWCPGPAVSKVDFLLDGPVPWRDGRLAGAGTVH
+LGGTAADIQRAEADVAAGRMPARPFVMLCQQQSADPSRAAGPAAGRTVLWSYAHVPHGHP
+GDVRPLIEAEVERHAPGFRDRILGAVDMRPADLEAWNPNLVGGDIAGGSMAGLRLLLRPT
+ASPRPHRAGRPGLYLASASTPPGAGVHGMAGAWAVRTLLADRARATSR*
+>NZ_CP040019.1_2529
+MNAAPTQDTAEDHARFPLPRDAEPGRAVVVGAGPNGLTAAALLARAGWEVDVHERHPSPG
+GACASAPLLGEGTVVDLGAAGHPFGVASPVFADLDLIGHGLRWAHPEVVMAHPLPDGEPG
+LLYRDLERTAAGLDADAARWWAVHAPLVEGAEQLVDNVLGPIVRPWPHPLTMTRFGLRAP
+WPASWLTGGLFRTEQARALFVGSAVHAVMAPSRPFTAAFGALFAALGMSSGWPVAEGGSQ
+AIVDALVRVLRTHGGRLHLGSPVEDLRAFADVDAVLLDLTPTQVARLRGTDLPKHSLSRM
+RRWRHGSAAFKVDMLLDGPIPWADPRVGQAGTVHLGGTAAQVQRAEADVAAGRMPDEPFV
+MLCQQQSADPSRAVGPAAGRHVVWSYAHVPHRHSGDATHAVLARIERFAPGLRDRIVRIV
+ATSPAELEAWNPNLVGGDIAGGAMDGLQLLARPRISAAPHRLRAAAPSAWRTSSGRTAPG
+LYLASASTSPGAGVHGMAGAWAVRTLLSDRRCAR*
+>NZ_CP083691.1_1225
+MPRDAAPIDAPAARDRGFALPQGAEPGRAVVVGAGPNGLTAAALLAREGWEVDVYERHHA
+PGGASASAPLLGRGTVVDLGAAGHPFGVVSPVFRELDLTGHGLRWVHPEFPMGHPLPDGP
+AAVLHRDLDATAEGLGVDGRAWRALHAPLVRDADRLAADVLGPLLRPWPHPVSMARLGLR
+APWPAGWVNRAVFRTEQARALYTGAAAHAILPPGRPLTSAFGALFGALGMSSGWPVAAGG
+SQSIVDALLAVLRAHGGRLHLDHEVTDLRELPAADAVVLDLTPRQVAALAGTDLPPAYAR
+SLRRWRHGSAVSKVDFLLDGPVPWTDVRLAGAGTVHLGGNAAQLQHAEAEAVAGRMPEHP
+FVMLCQQQAADPSRAVGPSAGRTVVWSYAHVPFGWDGDVRPLVEEQVERFAPGFRDRIVH
+AVATRPADLEAWNPNLVGGDIAGGSMGGLQLLLRPTASPRPHRAGRPGLYLASAATPPGG
+GVHGMAGAWAVRTLLRDRARAAF*
+>NZ_CP097650.1_1447
+MTEIAAGPGFALPRGVEPGRAVVVGAGPNGLTAAALLAREGWEVDVFERAPVPGGACASA
+PVLGEGTVVDLGAAGHPFGVASPVFRELGLTDHGLAWLHPAVPMGHPLPDGPAALLHRDL
+EATAAGLGVDARAWRAVHGALVAHVDEILAGALGPVLRPPPHPVAMARFGLRAPWPADLL
+GRAMFRTEAARALFTGSAAHAILPSSRPLTAAFGALFGALGMSSGWPVARGGSGAIVDAL
+VAVLRALGGRLHLGHEVTDLRALPAADAVVLDLTPRQVLRVAGTGLPPRYAAALRRWRPG
+PSVSKVDFLLDGPIPWRDARLAGAGTVHLGGTAAEIRRAEDDVAAGRMPARPFVMLCQQQ
+AADPSRATGPAQGHTVVWSYAHVPHGHPGDVRPLIEAEVERHAPGFRDRIEAAVAMRPAD
+LEAWNPNLVGGDIAGGSLAGARALLRPTASIRPHRAGRAGLYLASASTPPGAGVHGMGGA
+WAVRTLLADRRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000135.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000135.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c62a2388c98e69f3e5086ca16dd4a1a6ed1c300
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000135.fa
@@ -0,0 +1,49 @@
+>NZ_CP042169.1_1532
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVACAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFALPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVSALR*
+>NZ_CP033200.1_1253
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAVALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVAALR*
+>NZ_CP040019.1_1320
+MSAALYLDHAATAPVRRVALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGSDLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFAEAEAERAAAADAWSGLRDRFAARALDGVQELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHSTEPSPALLALGLSEDEARTALR
+CTFGPDADEAMLAAAADAIVDAVRTVSALR*
+>NZ_CP083691.1_1212
+MSTILDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQIVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVTALR*
+>NZ_CP083691.1_1733
+MALDVAAVRQDFPILRSTLADGRPLVYLDSGATSQRPRQVIEAEVEFLTISNAAVKRGAH
+QLAEAATDRYESARETVAAFVGATDPRELVFTRNATEALNLVAYALGNGDDATPEHLRVR
+AGDEILVTEMEHHANLVPWQELARRTGATLRHIPLGEDFALDLVDLGSLVTERTKVVAFT
+HQSNVTGTVNPVATLGEAARAVGALTVLDACQSVPHMPVDVAALGVDFLAFSGHKMLGPT
+GIGALWGRYELLAELPPFLLGGSMIEVVHLDRSTYAEPPARFEAGTPPISQAVGLAAACD
+YLSALGMDAVAEHEHALTARALEHLAGMDRVRVIGAPAGPERSGAVSFAVEGIHPHDVGQ
+VLDSLGVQVRVGHHCAWPLHRRYGVPGTTRASFSVYSTLDEVDAFADGLAQTLAFFQGFG
+R*
+>NZ_CP097650.1_1459
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVAALR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000143.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000143.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a3c2defbf2b9d97750654ea46604e376092f110
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000143.fa
@@ -0,0 +1,37 @@
+>NZ_CP042169.1_1638
+MPDVTPPPPSRSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQATRLPAPDIITT
+AQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQNAHMGSANDWGD
+TGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIECEGLYMLNPPPQS
+LYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILREDVRLSLASGEYH
+VSEGFGADNLFDDAHVTPEYVEEERG*
+>NZ_CP033200.1_1353
+MPDVTPPPLPHSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQATRLPAPDIITT
+AQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQNAHMSPANDWGD
+TGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIECEGLYMLNPPPQS
+LYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILREDVRLSLASGEYH
+VSEGFGADNLFDDAHVTPEYVEEERG*
+>NZ_CP040019.1_1169
+MPEQSPTPSSRPWARRTVLGGTGLAIAAGVAGCSRPEAGEEAEETEAAPKRLPAPDILTT
+AQWGALQPNYHLQTLDERPSYLVIHHTTTPNVTDGSREAAESIAKSIQNAHMSTLNDWGD
+TGQHFTVSRGGFALEGRHGSRYTLEQGQTFMLGVHALGFNAYALGIECEGLYTLNPPPQS
+LYAGLVPLAAYICQQYELPPSRIIGHRDVTATSCCGDAFYGKLPVLREDVRLSLATGEYH
+VSEGFGADNLFDDAHVTPDYLQEQGY*
+>NZ_CP083691.1_31
+MKHALPRHVQHAPVPPAAASPGRRAVLVGGLAAAGAAGAAAAGAVPAAAFAGPVVHSTAQ
+WGARSPRSAAEVVRARPTRLVIHHMASPNTAETSLAHAYGLARACQQDHMGRGFDDSGQH
+FTVSRGGHCLEGRAGSLAALRAGDRHVKGAHVSGQNTGKIGIECEGSYVTGLPTPAQYRA
+LVQLAAHICRQYGIRPADIVGHGDLMATQCPGGAFHARLGVLRADVARTLATGRLSVSDP
+SGRAASIPADPRRAATTTPSAAAPASRRVLGPGSRGADVKRVQALLTTAGHRVPRTGLYA
+ARTTAAVRAFQRRSGLAQDGFTGPLTWAALEAAGRR*
+>NZ_CP083691.1_1098
+MPDHQILSSSWPRRAVLGGAGLAIAGTVAGCGTGGDAAQSTSADGSAASTGPRLPEPEIL
+STIDWGARIPENWQQTLYEKPSYLVIHHTTTPNVTDGSRDAAIALAQRVQNQHINQQWGD
+SGQQFTMSRGGFAMEGRHGSLYALQGGETFILGVHALGFNAYAVGIECEGFYMVSPPPQS
+LYAGLVKLSAFICQQYELPPSRIIGHRDVVKTSCCGDAFYAKLPILREDVKRSLETGEYQ
+ITEGFGADNLLDDAKINVENYEDFQKRS*
+>NZ_CP097650.1_1567
+MPDVTPPPLPHSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQATRLPAPDIITT
+AQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQNAHMSPANDWGD
+TGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIECEGLYMLNPPPQS
+LYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILREDVRLSLASGEYH
+VSEGFGADNLFDDAHVTPEYVEEERG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000144.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000144.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f08f388ddad14a71f4c12db75fa9339599337ee8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000144.fa
@@ -0,0 +1,44 @@
+>NZ_CP042169.1_1726
+MSTAPALPPLPGAPGGPALPSVEELLADAVAVAVPMRVRFRGTDLRHALLLRGPAGWGEF
+SPFPEYGPHESAAWLAAAIEAGWQGWPAPVRETIPVNATVPAVDADDVEAVLARYGDGIT
+AVKVKVAEHGPEGGLVPGGREADLARVRRVRALLPHAQVRVDANAGWTPAEAVDVLTELA
+DVGLEYAEQPVPGITDLAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK
+VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH
+DVVAPAWRPRAGALPAPGERAPAPDPELLDRIRADGTRQAWWADRVRAAHAVLAAQG*
+>NZ_CP033200.1_1444
+MSTAPALPPLPGAPGGPALPSVEELLADAVAVALPMRVRFRGTDLRHALLLRGPAGWAEF
+SPFPEYGPHECAAWLAAAIEAGWQGWPGPVRQTVPVNATVPAVAADDVEAVLARYGDGIT
+AVKVKVAEHGPEGGLVPGGREADLARVRRVRALLPHAQVRVDANAGWTPAEAVDVLTALA
+DVGLEYAEQPVPGITALAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK
+VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH
+DVVAPAWRPRAGALPAPGERAPAPDPELLDRIRADGTRQAWWADRLRAAHAVLAAQG*
+>NZ_CP040019.1_1080
+MRVRFRGTDARQALLLRGPAGWAEFSPFPEYGPAESSAWLAAAIEAGWQGWPAPVRDVVP
+VNATVPAVEAEAVESVLARYGEGITAVKVKVAEHRPGGGLVPGSHSADLARVRRVRELLP
+DAHVRIDANAGWTPAEAIAMLTDLADVGLEYAEQPVPGIKKLARVRRELRARGVSTPIAA
+DEAVRKAEDPLAVAAAGAADLIVVKVQPLGGVRRAAAVVAAAGLPAVVSSALDTSVGIAG
+GAALATHLPALPHACGLGTAALFDDDVVTPAWTPRQGVLEAPGERAPEPDPALLARVRAD
+ERTHAWWRDRVAAAHAVLAAGGR*
+>NZ_CP083691.1_1003
+MTVPAAHDDADPRPGSALPPLPGAPGGPALPDVDELLEHAVAVTLPMTVRFRGTTERRAL
+LLRGPAGWAEFSPFPEYGPAEASRWLAAAVEAGWQGWPAPVRSEVPVNATVPAVDAADVE
+SVLARYGDGITAVKVKVAEHRPGGGLVDPTHAADVARVRRVRELLPEAAVRIDANAGWDE
+DRAFAVLGALQDVGLEYAEQPVPGIAGLAALRSRLRAAGIATPIAADEAVRKETDPLAVA
+QAGAADLIVVKVQPLGGVRRAAAIVAAAGLDAVVSSALDTSVGIAGGAALAAHLPSLPFA
+CGLGTASLFAHDVVSPAWRPADGSLPAPGERAPEPDPALLAAARADAAEHAWWAERLRAA
+HAVLAARGR*
+>NZ_CP083691.1_1771
+MSPAPGQAPVSVAAVRRHRHRAPLLHPFVTAARRTEAVEYVVVEVELSDGTVGQGSAAET
+VAVTGEDAASIETAVDGVFGPALTGATGGLDGLLARLPAPARGATSARSAVDVAVHDAVA
+RAAGVPLTALLAPAGTAVKQTLENDMTVSLEDPATMAARAAEAVAAGTRILKIKLGRDVA
+EDRRRLHAVLEAAPQARLRLDANQGWSVEDAIAIISGMEDEGLPVDLVEQPVAAADVAGL
+ARVRAAVTTPIMADEALWSSEDARRLIEAGAADLFNVKLAKTGGLADAVAIADLAAEHGI
+GCMVGSMMEPRISIAAAVQLSLAHPAVTMVDLDAPLWFASDAPAGGYTQEGADLRLLPGE
+GLALERLDPGTDPV*
+>NZ_CP097650.1_1655
+MSTAPALPPLPGAPGGPALPSIEELLADAVAVALPMRVRFRGTDLRHALLLRGPAGWAEF
+SPFPEYGPHESAAWLAAAIEAGWQGWPAPVRQAVPVNATVPAVDAADVEAVLARYGDGIT
+AVKVKVAEHGPEGELVPGSREADLARVRRVRALLPHAQVRVDANAGWTPTEAVDVLTALA
+DVGLEYAEQPVPGITDLAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK
+VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH
+DVVAPAWRPRAGALPAPGERASAPDPELLDRVRADGARQAWWADRVRAAHAVLAAQG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000145.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000145.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a70cd7cd25a77a4f40d620cfab86678f0e51b5be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000145.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1737
+MDAPASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGLHREV
+DAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPAADSQ
+LVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRIVDAVDRDA
+ARPAVVVRVQAAEDETARGGRA*
+>NZ_CP042169.1_1995
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRIAE
+TQEGAAEQASPRVRLVVDPPR*
+>NZ_CP033200.1_1713
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGG
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRIAE
+TQEAAAEQRSPRVRLVVDPPR*
+>NZ_CP040019.1_1068
+MDAPASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGLHREV
+DAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPAADSQ
+LVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRIVDAVDRDA
+ARPAVVVRVQAAEDETARGGRA*
+>NZ_CP083691.1_712
+MNTARPLTREDLSSAARLRLSALELYAERGEHAASIRDVGRHAGVAPGLVRHHFGSKDGL
+TRAVDDDIIDLVRATLEAVPLEGTPLEISAARDAAFQELLQERPLIGGYLAQALTASRAS
+GESVLDRLVDLSAEQTRQLIDRGLDPRRGLRTSVFTTVVRQVAVFLVAPVAERAWNRLGH
+TLEGASDVAPMPPVRVVVGPAPEEDRR*
+>NZ_CP097650.1_1930
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQVVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLLVDPSADRIWRRIAE
+TQEDAAEQASPRVRLVVDPPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000151.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000151.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb77b1a40010610550669e855867fedc9b6995e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000151.fa
@@ -0,0 +1,57 @@
+>NZ_CP042169.1_1867
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQAWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVVVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVVKLWDGRRVVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMDALRARLAQLLESTDLWDGREHALQVTDATGGVVRIRAVVSARNSGDLWDLRCLV
+REDLVAFLRHEHPEGIVVQRMVVRHPAHDDAAPASEGSDAGARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPHTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHADGPLDDAVTRRRQDDED*
+>NZ_CP033200.1_1574
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQQGAARLSLPAAVAAGLLASRIWLGVMAEEQTWYRP
+ASFLMLIAVAAAGAWAAWRLVGVIEKGILGRYQETSVEHRRERRIRTQTILIRRILNAVI
+VVVAVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVVKLWDGRRMVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMDALRARLAQLLESTDLWDGREHALQVTDATGGVVRIRAVVSARNSGDLWDLRCLV
+REDLVAFLRHEHPEGIVVQRMVVRHPAHDDAAPASEGSDAGARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPHTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHADGPLDDAVTRRRQDDED*
+>NZ_CP040019.1_770
+MDLPQITPLAVAVGLAVAVVGWLLGRLLGAGVAWLFARRGRSPSSARVFGKLVAAGITVL
+SLGAAVTVVFPSVKPVDLLGGIGVISIAAGIAFQTVLGNMFAGMVILARDRFRVGDQIQV
+GEHAGNVVEMGLSSTAVKTFDGRLVLIPNQMLHSQAVTVQTGFSAVRSSLRVDVETGNDL
+ARTREIAVRAMSELPQVLRDPAPQALLASVGVTTVGMDLRFWSGARQMETKEAMDAVIHA
+VLTAFEKNGVATGDDVRVVDAGPELRRILEGPGAPRGQGGPDYPGGLAGPGEPDRAARPG
+SD*
+>NZ_CP040019.1_922
+MLLAALSGPASPPVLGSLARLFAGENVPAGVEGNVQDGAAATTAALGVEWGTLLTVLVAF
+AVGATLVYAALQVTRVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQTWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVAIAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVLKLWDGRRMVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMPALRERLTQLLDSTDLWDGRESSMQVTDAIGGTVRIRAVVSARNSGDLWDLRCLV
+REDLVTFLRSEHPEAIVVQRVVERHPAHDDAVPASEGSDAGARGGDPTGEPGPDGSGVAA
+REPRPRTAALPRVEGGEPRPDTVTTPLTRVDDHAGLYTGSITAVQRNRELHGPGEDAFAE
+RRAQQAKQAAEAATADEAGRRSGAGSHADGLLDDAVTRRRQDDED*
+>NZ_CP083691.1_856
+MPVPALLPVLAQTASSDAALSDAVLSAADQVVPGSVEQDVQQGASAASAALGVEWATVAA
+VLGAFLAGGLVVLGVFLVARLALFRRDRLKADAARLTVPVSLFAGFLTARVGLEVMAHGQ
+PWFEAAAFVLLLAVAASAAWAAWRVVDVVESGILARYHQPGVNDRRERKIRTQTMLLRRV
+LNAVIVVVALAVVLLAIPQVRSLGAGLLASAGLISVIAGLAVQSTLTNVIAGFQLAFTDS
+IRVGDVVDMQGVFGTVEEITLSNVVVKLWDGRRMVYPSKHFTSEPFENWTRTGAAVAGVV
+EMDVDWRVPMDPLRARLTELLESTDLWDGRENAMQVIDAVGGMVRIRAVVSAKNSGELWD
+LRCLVREDLVGFLRAEYPEGIYTQRLVERRPSDPAPEAHDDPAPDAHDDAAPAAAPAAPA
+PSDRGSSTRAEPTPQTRPMPTVTGSVPLARAGENASLYTGSIRAVERNQEMDGPGEEAYA
+ERRARAAEREDRAARDAGRGGAHAARS*
+>NZ_CP097650.1_1787
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQAWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVVVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVLKLWDGRRMVYPSSHFTTRPFENWTRVGAEVSGVVELDVD
+WRVPMDALRARLTQLLESTDLWDGREHALQVTDATGGIVRIRAVVSARNSGDLWDLRCLV
+REDLVSFLRHEHPEGIVVQRMVVRHPAHGDASPASEGSDAEARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPDTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHTDGLLDDAVTRRRQDDED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000159.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000159.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3df972cc325ca2cce7142a6216f466a76c25080
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000159.fa
@@ -0,0 +1,23 @@
+>NZ_CP042169.1_2014
+MSTTTSITAAGLETMNGPEGCCTLSAGPVDSVEAERIASLLKALSDPTRLRLLSHVAAQG
+CNSVCACDLTEPLGISQPTVSHHMKKLVDAGLLTREQKGRWAHYSVVPSAFAELRSFLDI
+A*
+>NZ_CP033200.1_1074
+MDVKVYVPEFAVEFDTCQYVPMSMSGLSARDAALGYCTPLAREPITPAQAEGVSRMLKAL
+ADPVRLRLMSMILSHEGAEACAMCDLTEGFDLSQSTLSHHLKVLHDAGLVDRDKRGVWVY
+YKARTEAMDALRTLFSGDLAAPQLA*
+>NZ_CP040019.1_544
+MTACSVPVSTAAAPVLADDCCSLADGPLGAEDAAELAVLLKALADPMRLRLLSHVAARGC
+ADVCACDLTEELGIAQPTVSHHMKRLVDAGLLTREQRGRWAHYTVVPEAFARLRRVLVLG
+*
+>NZ_CP040019.1_727
+MVATTTIPAPEDTDRPEGDDALGSVACCSLSAGPIDAAQAQRAAGMFKALADPMRLRLLS
+HVAAQGCAAVCSCDLTEELGISQPTVSHHMKKLVEAGLLTREQRGRWAHYTVVPAAFAEL
+GRMLELG*
+>NZ_CP083691.1_470
+MTTTAPSPSDTCCAPAGPALLPAEHAARLAAVFKALADPTRVRVLAHVAASPEGTVCACH
+LPEPLGISQPTLSHHLKTLTAAGLVTREQRGRWAHYTAVPAALDAARAFLADPAGA*
+>NZ_CP097650.1_1943
+MSTTTAITAAGLETMNGPEECCTLSAGPVDSVEAERIASLLKALSDPTRLRLLSHVAAQG
+CNSVCACDLTEPLGISQPTVSHHMKKLVDAGLLTREQKGRWAHYSVVPSAFAELRSFLDI
+A*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000163.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000163.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d21abc52013df65ed38f562c78624039cad1856
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000163.fa
@@ -0,0 +1,90 @@
+>NZ_CP042169.1_2066
+MTHPASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APAGVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAGHAHTSEHGEEHAADHDGVDHHDH
+MAHGPSEDVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHSA
+AFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHSLYFETAAV
+ITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAESLAPGDVVLI
+RPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDALTGATLNTSGRLVARATRVGSD
+TTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLGIAVLTFAVWMIVTGDLPSALRAG
+VAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLDKTGTVTEG
+RMALADVLVLDPAFVAETGASRSAFVDETAPDQAADVLLTLAAAVERGSEHPIARAIVAG
+AEERGLTVPGVADFASTAGGGVSGLVALPHDDGAPGSGAHGAAGPDPVRVAVGRGSVLET
+ALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKETSADAIARLKELGLR
+PLLVTGDNAAVATQVAAAVGIPAEDVVAGVRPEDKVDVVRRLQSEGHVVAMVGDGVNDAP
+ALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAFAYNV
+LGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR*
+>NZ_CP033200.1_1786
+MTHPASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APAGVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAGHAHTSEHGEEHGEEHGEEHAADH
+DGVDHHDHMAHGPSEDVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALW
+AAWPFHSAAFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHS
+LYFETAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAQSL
+APGDVVLIRPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDALTGATLNTSGRLVA
+RATRVGSDTTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLGIAVLTFAVWMLVTGD
+LPSALRAGVAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLD
+KTGTVTEGRMALADVLVLDPAFVAETGASRSAFVAETAPDQAADVLLTLAAAVERGSEHP
+IARAIVAGAEERGLTVPDVADFASTAGGGVSGLVALPHDDGALGSGAHDAAGPAPVRVAV
+GRGSVLETALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKETSADAIA
+RLKELGLRPLLVTGDNAAVATQVAAAVGIPAEDVVAGVRPEDKVDVVTRLQSEGAVVAMV
+GDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNL
+FWAFLYNVLGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR*
+>NZ_CP040019.1_642
+MAASPSPSDRAAEALGRTALQDAEGTRRVDLDVTGMTCASCVGRVERKLGKIEGVEASVN
+LPLERATVTVPASVSDQDLLDAVAKAGYTAAVRPDAQARPARRGRHDDGGTRPGADHAGH
+PDHRDHETPGEDHAGHEGHDDHMAHGPRADVLRPRLIVAAILTVPIVLISMVPALQFPHW
+GWVALALSAPVALWCGWPFHSAAFRAARHGSSTMDSLVSVGVLVAWTYSAVELVLEPGMT
+AHVGGTMAEMMRHSLYFETAAVITTFLLLGRWLEARAKREAGRALRSLLDLGAAQATVLP
+NWDAQTPHPSTSAAATPVAAVSGDFSEVEAASTSDKSPQTHHDGGADALTERVIPAEELE
+PGDVVVIRPGEKVPTDAVVLEGTSAVDASLLTGESVPVEVGPGDEITGATVNTSGRLIAR
+ATRTGADTTLAQMGRLVSDAQTGKARVARLADRISAVFVPIVLVLAVLTFVVWMLVTGGD
+VAPALRAGVAVLVIACPCALGLATPVGLLAGTGRASQLGILIGGPEVLEDTRTVDTIVLD
+KTGTVTEGRMALSDVHAFADDAALTEDRILALAAAVEAGSEHPIARAIVAGARERGLTVP
+RVADFASTAGGGVTGTVALPEAGSVRVAVGRGDLVGEPSPAQQAEFDAAEQAGATAVWVA
+VDGRVAGVLSVKDTVKPSSAAAIARLKELGLRPLLVTGDNAAVAAQVAAAVGIPAEDVVA
+GVRPEDKVDVVTRLQSEGRVVAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMG
+DDLDQVVQALDLSRRTLGIIRMNLFWAFAYNVLGIPVAALGLLNPMIAGGAMAASSVLVV
+LNSLRLTRYAR*
+>NZ_CP083691.1_559
+MTHPASSAPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APADVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAHTSEHGEGHGEEHAADHDGVDHHD
+HMAHGPGEDVLKPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHS
+AAFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHSLYFEAAA
+VITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAESLAPGDVVL
+IRPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDAVTGATLNTSGRLVARATRVGA
+DTTLAQMGRLVADAQTGKARVARLADRISAVFVPVVLGLAVLTFAVWMLVTGDLPSALRA
+GVAVLVIACPCALGLATPVGLLAGTGRASQLGILIRGPEVLEDSRTVDTIVLDKTGTVTE
+GRMALADVLVLDPAFVTDTGASRSASVAETDAPRSAFVAETAPDRATDLLLTLAAAVERG
+SEHPIARAIVTGAEERGLTVPDVADFASTAGGGVSGLVALPHDDGALASGAHGAAGPAPV
+RVAVGRGSVLETALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKDTSA
+DAIARLKELGLRPLLVTGDNAAVATQVADAVGIPAEDVVAGVRPEDKVDVVRRLQSEGRV
+VAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGII
+RMNLFWAFLYNVLGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR*
+>NZ_CP083691.1_701
+MSTSAPPTGGPDIELEIGGMTCASCANRIEKKLNKLDGVAATVNYATEKAKVTVPAGYDP
+SLLVAEVEKTGYTAALPKPKDTTANTSETEAGEEEDSELTSLRHRLIGAIVLTVPVIAMA
+MIPALQFTYWQWASLALAAPVIIWGAWPFHKAAWTNLKHGAATMDTLISMGTSVALLWSL
+YALFLGTAGTPGMTHPFEFTIAPSDGAANIYLEVGAGVTMFILAGRYFEKRSKRQAGAAL
+RALLELGAKEVAVLRDGVEVKIPTSELAVGDEFIVRPGEKIATDGLVTSGSSAVDASMLT
+GESVPVEVREGDSVTGATVNAGGRLVVRATRVGSDTQLAQMAKLVEDAQTGKAEVQRLAD
+RISGIFVPIVIVVAFITLGAWLGGGFPVAAAFTAAVAVLVIACPCALGLATPTALLVGTG
+RGAQMGVLIKGPEVLESTRKVDTVVLDKTGTVTSGKMTLTDVITEPGVDRAELLRFAGAL
+EDSSEHPIAQAIAKGATQEVGQLPTPEDFANVEGKGVQGIVEGTPVVVGRESLLADWSQK
+LSPEVAQAKAQAEGEGKTVVAIGWDGAARGILVVADTVKPTSAEAIRGLKEIGLTPVLLT
+GDNEAVARQIASEVGIDEVIAEVLPKDKVDVVTRLQEEGKIVAMVGDGVNDAPALAQADL
+GLAMGTGTDVAIEASDITLVRGDLRAAVDAIRLSRKTLSTIKTNLFWAFAYNTAAIPVAA
+LGMLNPMLAGAAMAFSSVFVVGNSLRLRGFTSVASK*
+>NZ_CP097650.1_2005
+MTHPASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APAGVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAGHAHTSEHGEEHGEEHAADHDGVD
+HHDHMAHGPSEDVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWP
+FHSAAFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHSLYFE
+TAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAESLAPGD
+VVLIRPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDALTGATLNTSGRLVARATR
+VGSDTTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLGIAVLTFAVWMIVTGDLPSA
+LRAGVAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLDKTGT
+VTEGRMALADVLVLDPAFVAETGASRSAFVDETAPDQAADVLLTLAAAVERGSEHPIARA
+IVAGAEERGLTVPGVADFASTAGGGVSGLVALPHDDGAPGSGAHGAAGPDPVRVAVGRGS
+VLETALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKDTSADAIARLRQ
+MGLRPLLVTGDNAAVAAQVAEAVGIPAEDVVAGVRPEDKVDVVTRLQSEGAVVAMVGDGV
+NDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAF
+LYNVLGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000164.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f5d7fd5bc092629089fb901d841587dacd8a35c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000164.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_2106
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVRTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPEA
+LIAEAERVILELADQVVAEARRAGLVGPDVTGADYLFGLLMVTRSPECALLGHGPDQRGW
+LLDTYLRGLRP*
+>NZ_CP033200.1_1831
+MILELADQVVAEARRAGLVGPDVTGADYLFGLLMVTRSPECALLGHGPDQRGWLLDTYLR
+GLRP*
+>NZ_CP033200.1_1832
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPRP
+SSPRPSV*
+>NZ_CP040019.1_579
+MRADARANRQDLLAAAGRLLEEQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARVSGILHAFLDGGGSADRRWRRLAEELAAVNLTSLVTAGDDLEAADRPQEALIVEAE
+QVIISLTDRAVTEARRAGLVALGVTGTRYLTGLLAVTRPPAGELLARHADQRDWLLGVYL
+RGLRP*
+>NZ_CP083691.1_502
+MQEEDTPPAEAMGRAEDAVMGLADRAVDLAREAGLVGDDVTGRAYMNGLIAVTRPPLPAL
+ESCRDDLEDWLLTVFLRGLRPAA*
+>NZ_CP097650.1_2052
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPEA
+LIAEAERVILELADQVVAEARRAGLMGPDVTGADYLLWVMRFLARGPG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000171.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d15cf8937a3c699d0897361aa21dc51ec5bde07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000171.fa
@@ -0,0 +1,47 @@
+>NZ_CP042169.1_2249
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPHELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS*
+>NZ_CP033200.1_1954
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPHELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS*
+>NZ_CP040019.1_416
+MKTSRRGGLGRGLGALIQSTAEPVDEAPQEADATAEDATAPTAAPAEKKAATSTARRLSK
+ETSEAKTPAPRAASASKSSGGAAKEAPADKKAGSAGRAPAAAKKATPTKKASSSAGEAKA
+NSAAAPAAARKTPDRAAQRPVDVFFSPDPEDAPAARRGTKARPAMPTVKAPTKREAASSS
+GEEAAAGASTAAEGTVSTDIAVLREIPVGDIHPNPRQPREVFDEEHMAELVTSIREVGIL
+QPIVVREVDGPTPYELIMGERRWRATQKAGLDAIPAIVRQTPDQDLLRDALLENLHRSQL
+NALEEAAAYQQLMEDFACTQEELAERIGRSRPQISNTLRLLKLPPLVQRRVAAGTLSAGH
+ARALLGLTDPSDMERLAQRIQAEGLSVRATEEAVAQLQGGLRPGRTPRRTADDARHERLD
+HYATALTSRLDTSVKITLGARKGRIAIDFTTVEDLNRIMDVIQGEKGGRGAAS*
+>NZ_CP040019.1_1911
+MVASVKTQGLLQPLVVAPNPTLEGDYTIIAGHRRLDALKRAGRDDAPVIVRTDLDTEEKQ
+VAAMLQENLHRQDLTAVEEADAFAQLSLFEGWDVKRIARETGVAQTRVRSRIKLTYLSEA
+TLASLHDGQVTLERAQALAEFAGSPEEELLEEHLTATATNWDFYLARAKQTRDRRKALSA
+EQKAHEEAGFEVVPMPESLYTPEREWDRQDFESPTAALEAGAVVAFDPDYDAPVYLVKHA
+EQELEKDAAAAERKAEAAERAARNEALERELATAQETVRLWLVDTVFPKAAAGDERILRV
+AARHLAATACEETHFRRAGLAAIFCPDLGAYAPELRTAVAEVLAGKSAQELAVIIAVATR
+WTSTARVHAWRDATREDSSPAVWLAMRQELGRELAAPEQVAFDAAKAGEL*
+>NZ_CP083691.1_368
+MSTRRGGLGRGLGALIQNTAEIEQPPTREDSSPSAASSNKTTAAPAKRSTRTARTAESSQ
+NGLPASDGATQQDHSSDRAEKTASSGTGSQKTSRSTGSKGAKTPEPTATRSAQEEVPRPA
+DIFFGGGEGTSDEPPESGRHRPTRSARPSMPTVKAPSKPAPKSETEQAAPVRKDEPEGTV
+SADIAVLRELPVGDIHPNPRQPREVFDEDHMAELVASITEVGVLQPIVVREVEGAATPYE
+LIMGERRWRATQRAGLATIPAIVRQTPDQDLLRDALLENLHRSQLNPLEEAAAYQQLMED
+FSCTQEELSQRIGRSRPQISNTLRLLKLPPLVQRRVAAGALTAGHARALLGLTDPAEMER
+LAQRIVSEGLSVRATEDAVAQLQGAVRPAPKSTRSREESTRHERLDYFATALTSRLDTQV
+KITLGARKGKIAIDFASVEDLNRIMDLIQGGGDSTPVKG*
+>NZ_CP097650.1_2192
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPYELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000172.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000172.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ee12484fd44d65963262ddedc7a417f539de823
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000172.fa
@@ -0,0 +1,65 @@
+>NZ_CP033200.1_1973
+MKRSPKGRLELTWMGKDSALIPVEDGKYDYSFVDPNDPRALEVKSIEVLEQVGEVEGPTG
+ANENLLIIGDSGDALRSLGTIPEYAEKYGGKVKLVYIDPPFNTEQAFDHYADQLEHSIWL
+TMMRDRIRDFKPLLHPDASIWVHLDDSEVHRMRALMDEEFGAENFIATVVWQKKYSRDNR
+PAIGTVHDYILVYAPAGAQRWKTLRNRIPRISAAQYRNPNNDPNGPWRPVPMDVQGGHAT
+ASQFYDVITPSGKIVRPANGRAWSVTAPVMQAMRDRGEVYFGLDGSGKPNTIRYLKDDEG
+LVPWTWWPHEEVGNNDDAKKEIIALFGEDQVFDTPKPERLLERVIRIATNADDLVLDCFA
+GSGTSAAVAHKLGRRWLTVELSQEVADTFTVPRLRKVQRGTDSIGISVREAEGFADADMD
+GRVKPDDAKALLRAIKEVQKVGLKSLSPEAGAALVQELRERLKPVSARQSVCQDGGFTVA
+KMGPSMYEVDDEHGMVFLSPEATNGAWSKAIAGQLKFTLTPDDPVFCGVRKRQRLAVIDG
+VADETVVRTVVEHLGEKERAVIVAKGVLPEAGDLLQRLSPGSRIKKAPEDMFPKGTVN*
+>NZ_CP040019.1_1475
+MTDEIYETPSTTPNFQTELAAQLADLIPEAIADGKVDVEKLKELLDGDAADSNERFGLFW
+PGKKRALRAAQEPTTATLKPDFEDSKDWDTTQNVFIEGDNLEVLKILQKHYHAKIKLIYI
+DPPYNTGKDFVYPDNYKEGLDTYLEWTRQVNEEGKKVTTNAETEGRYHSNWLNMMYPRLK
+LARNLLTDDGVIFISIDDNEIDNLLRLAKEVFGEPNVSTTFIRQKKKKPSFLHANVGSMT
+EYLVCITRNKAFTFPFSVDTTTAGKKYPINNAGNSLGKLTFPAGAVRFSQKFAEYEPQDM
+SEGNIVTRLLDHVVVSEGVNRNAFTLEGEWRYSQVTLDEFITAGDLITISKAPFRPNHVK
+AGGEIKKMHNLLTPSTYGVGTNEDGTAELEDLMEGSYFDNPKPTSLVRVLAQAVTYDDPS
+AIVLDFFAGSGTTADAVFRLNAQDGGNRRVISVQLPEPLDERSEAWAAGYRTISQLAKER
+IRRAGVRVLDREALLLEGRGVPLDTGFRAYKLSDTNFSKWRLSSDVEEDALQQHLLSLRD
+SATDDANADELLTEILLKQGYSLTEAVSPAEVAGLDVRFVRDRDGDVAVLAYLNEHVKPT
+LEQLRALVDEEPTRIIVLEDAFQGDDELKTNLAQLAKSKGIELWTA*
+>NZ_CP083691.1_275
+MEMSMDKLRGTSPDLTQDNVARLAELFPTVVTEARDEDGQVTRAVDFDLLRQELSDHVVE
+GPQERYHLDWPGKRAAAFAANAPTTATLRPDREESVDFDTTKNVFIEGDNLEVLKVLQES
+YLGKVKMIYIDPPYNTGNDFVYADDFAESTADYLQRSGEIDDDGARLRANPETNGRFHSD
+WLSMMYPRLKLARNLLTEDGAILASIGEREVSNLRAILNELFGETNFVGELVWEKKKKGA
+FLSSHVTNVKEYILVFCRDRSSFGGLIGEVTHAAETYPVIKSTNSRGIRTIPAGIASNYS
+ERDHEVGAGTRLTSGNMEMILLSDLIIRDGRLAHDVEVESNWIYSQTLIDQFSLSGDLYI
+TRDLYIRRHVREPRTKMLKDLLMMRGESTSGSTFTLEPSLHSDGWGTNEDAFGELHSILG
+EQNLMDFPKPSKLIAKLIRSVTWADSDAIILDFFAGSGTTGQAVTQLNAADGGRRQYLLV
+QLNEAAEESSALRRAGFSSISALSRERLRRSAAAVRETSGTERLDLGFRAFRLDASPFVE
+RNHSADSITPDMLAELENPVLADRSPEDLLTHVLLAWGLDLSATIETVSLAGEEVYDVED
+GALLAALGSTVSDELAHAMAERHPDRALFLDSGFVSDAARINVEQIFREVSPGTDVKVL*
+>NZ_CP083691.1_334
+MSSLSDLLGQVRATNPDLAANLEREIKNRTRRQRQFGLVFEEHRPEAVELPSREVRKGDK
+VRILPPRGETKKGDQTLWRVQRINRADDIAHLVEVDGEQGAEAALADLVVVAEFRDHMYP
+GLVETGRVERGGDKPFHTVINAENFHALEMLTYTHRHQVHCIYIDPPYNTGAKDWKYNND
+YVASDDDYRHSKWLSFMERRLQVARELLNPEDSVLIVTIDEKEYLRLGMLLEQTFPQARM
+QMVSTVINPKGSHRAGGFARSDEYVFFLFVGASQPAPMPLSSEWKVVQDSRALGLRWADL
+LRTADGSTRAARPNMFYPVFIRLAGDGPVFVSVGEPFYDADLTAVEAPEDAVAIWPIKAD
+GSQGRWQIGADTLRDLITKGYVRIGRWRGSKTTLTYLKAGEQAKVEDGRFPVRGRRADGS
+VLVDASEYSASFVPTSQWRISSHNAEQGGTNLLKSIMGDKRFPFPKSLYAVEDALRFLIK
+KNPDAVVLDFFSGSGTTAHAVMRLNKQDGGRRQCISVTNNEVSAEEQKGLRKQGLRPGDP
+EWEQWGICDYVTKPRVTAAITGRTPTGDPIKGDYKFTDEFPMSDGFEENAAFFTLTYESP
+LMVRQDLAFKRIAPLLWMRAGSRGRVITEVHARGWDVAEAYGVLTKVDRATPFAEAVAEA
+GVGTVYVVTDDERRYQAVCALLPEDVTPVRLYESYLTNFEINTGGRAGA*
+>NZ_CP083691.1_678
+MSRLTDLLAQARKTDPQLAADLEAEFRQLTQRSQFGLVFERHQPEAVELPGRPVRRGDTV
+RVLPPRGTLTIGDTRHWVVTDLERTPDGKQAHLTEADVDPEVREPATSTAALEDLVVVAR
+FEDPIYPGLVETGRVENGGPDKPFHTVINAENFHALEMLTYTHRHKVDCIYIDPPYNTGA
+KDWKYNNDYVEADDDYRHSKWLSFMERRLQVARELLNPDDSVLIATIDEKEYLRLGMLLE
+QTFPEARIQMISAIINPKGSSRRDQFSRFDEYIFFVMNGSARPAAVAGDMTMRQARSKEK
+VRWAGLMRQGANGRRSARPNLFYPIFVANETGRVHSVGDSLPLDVPRSEVSPPPGTTAIW
+PLSKAGGESTWGRDPESLRKALSAGYVKIGRFTPGSERCGFTHLQSGQIKAIEEGALVVT
+GRDSDGSLQVEFAEGGQTAMPGTAWHRPAHSASEHGSTLLNAILPDRKFPFPKSLYAVED
+AVRFFVHGKPDAVVLDFFSGSGTTAHAVMRLNRQDGGRRQCISVTNNEVSAEEQKGLRKK
+GLRPGDPEWERWGICDYITKPRITAAITGKTPAGDPIKGNYKFTDEFPMADGFEENAAFF
+TLTYEAPRQVRRNRAFARVAPMLWFKAGSRGRIISSLPERGWDVAQAYGVLEDMDHAPEF
+LAALEADPQVGMAFIVTDSEVAFQSVARQLPEHATAVRLYESYLHNFQINRRA*
+>NZ_CP097650.1_107
+MSSLSDLLGQVRATNPDLAANLEREIKNRTRRQRQFGLVFEGHRPEAVELPSRPVRKGDK
+VRILPPRGETKKGDQTLWHVDHIDRTTGTARLTAVDGEQEAQAAISDLVVVAEFRDHMYP
+GLVETGRVENGGGKPFHTVINAENFHALEMLTYTHHRKVDSCRASDLGHV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000173.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..890ad2d2c1dfa20a148b19239d3820c09d1852d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000173.fa
@@ -0,0 +1,47 @@
+>NZ_CP040019.1_84
+MDLTYKLWEGSWDEGAVLQDKGGSRHADPEKVHKIHHVSERYRVEGPHLPAPSPQRTPVL
+FQAGSSGPGRAFAARNAEAVFLIAPSVEAARQQIEDPRRQAVEFGRRPEDIKFFQGLSFV
+IGDTEEEAQAKLEEYERYVSVDGYLAHAALVDPDGRVYPPDTPLRELETNTQKGFAESLQ
+KAITDREPVVADVAWRSHRDSRVVGTPEQIADELQRWQDAGVDGVNVINWVIPGSFEEFI
+EKVLPVLRERSLAQSDYGEGTLRHRLFGEGDRLPDRHPAAKYRGAFTGTPRSQRAPRTEP
+QGADPAPAA*
+>NZ_CP040019.1_85
+MTKTARRRPLHLNAFAMNTTSHIHHGQWRRPDARQHEFADLRTWTELARTLEDAAFDAMF
+FADVVGHYGDADADYAVYVEEGLQIPSNDPTVLLGALAAVTERIGLATTSNVFQAHPFQF
+ARQLSTLDHLSRGRIAWNIVTGT*
+>NZ_CP040019.1_186
+MMTPVHQSPGLWRHPESRIAEFDRLAYWTGLARTVEDGGFSALFLADVLGLYDVYGGGIE
+ATVRGGVQWPVLDPAVAVPAMAAATERIGFGVTASVTYERPYLLARTLATLDHFTGGRVA
+WNIVTSYQDSAARNLGLDRQIPHDARYDLADEALDALYRLWEGSVEPGAVAFDRAAGVVA
+DPDRVHPAAVAGAHVRVPDAALTHPGPQGTPYLFQAGASARGRRFALDHAEAVFAIGPTP
+AHVRRFVDQTRAGLTEAGRSADAIRVLAMVTVVVAETDEAAAQRLAGYAEHVDVAGALAL
+WGGWTGVDVAGLDPDAPLEHVVTDANRSALAAFTEDPSGRTWTLRDVAEFVAIGGRGPVI
+VGSPETVADELQRWQAETGVDGFNVSAAVRPADLERFAALVSPELRRRGVLREPEPGRTL
+RENLSGAGPALPADHRGHAFRTAG*
+>NZ_CP083691.1_124
+MTGTHPSTPRPRTADRQLILGAHFPGVNNTTVWSDPESGSQIAPESFIRFAEIAERGRLD
+FIFLAEGLRLREQRGLLHDLDVVGRPATLPILAALAAATEHIGLIGTLSTTYNEPYELAR
+QLAGLDALSGGRAGWNVVTSPDAFTGENFRRGGYLPRERRYQHAGEFLATAQQIWDAASG
+RPPHVDVDVEDFSVHGTVDAPAPVHGRPVILQAGDSDEGRDLAAREADAVFTRHGDWEAG
+QEFTADMRRRAAAAGRPDGAVRVLPGVTVVVGDTDEEAAAEAEQIRRAQVSGATAVLTLE
+RIWNRDLSGWDPDGPLPDVEPVLEDTGLSQGRVRHVADPHAEVARLREISQRQGLTLRET
+VIATGQRQDFVGSPETVAQELIRHVEHDVCDGFILIPHLTPGGLEPFVDRVVPLLQERGA
+LRTDYPEDGGGLRGLLGAAVHPTAGRAS*
+>NZ_CP083691.1_137
+MTATPAPAPFILSAFDMVTPVHQSPGLWRHPESRAHEFDRLSFWTDLARTVEEGGFTAVF
+LADILGLYDVHGGGVDATVRGGVQWPLLDPFTVVSAMAAVTERVGFGVTASVTYEQPYLL
+ARTLTSLDHFTGGRIAWNVVTGYQDSAARNLGLDRQPGHDERYDRADAYLDAMYRQFEGS
+VERDAVVADRESGVFADPAKVHPIDVEGPHVRLPGVALAHPGPQGTPFLFQAGASSRGRR
+FALEHAEAVFYIGPTTAHVRRFVEQTREGLREAGRPEDAIRVLAMVTVVVADTDEEAQAR
+LASYHEHVDVESALALFGGWTGVDLSGLDPDAELEHVESEASRTALAAFTTQSPDRRWTV
+REVAEFVSVGGRGPVIVGSPATVADELERWHRETGVDGFNISAAVRPTDLERFARLVSPE
+LRRRGVLREPEAGRTLRENVAGAGPLLPEDHRGAGFRR*
+>NZ_CP097650.1_194
+MTATPAPFILSAFDMVTPVHQSPGLWRHPESRAHEFDRLSFWTDLARTVEEGGFTAVFLA
+DILGLYDVHGSGVDATVRGGVQWPLLDPFTVVSAMAAVTERVGFGVTASVTYEQPYLLAR
+TLTSLDHFTEGRIAWNVVTGYQDSAARNLGLDRQPGHDERYDRADAYLDAMYRQFEGSVE
+RDAVVADRESGVFADPAKVHPIGVEGPHVRLPGVALAHPGPQGTPFLFQAGASSRGRRFA
+LEHAEAVFYIGPTTAHVRRFVEQTREGLREAGRPEDAIRVLAMVTVVVADTDEEAQARLA
+EYHEHVDVESALALFGGWTGVDLSGLDPDAELEHVESEASRTALAAFTTQSPDRRWTVRE
+VAEFVSVGGRGPVIVGSPATVADELERWHRETGVDGFNISAAVRPTDLERFARLVSPELR
+RRGLLREPEAGRTLRENVAGGGPLLPEDHRGARFR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000175.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000175.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c7a81b0dcfac0c14b93cb7f384f833b0006b343
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000175.fa
@@ -0,0 +1,39 @@
+>NZ_CP042169.1_2
+MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI
+EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL
+PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK
+EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV
+DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD
+DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV
+VSDYRYLVMPVRIA*
+>NZ_CP033200.1_1963
+MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI
+EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL
+PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK
+EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV
+DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD
+DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV
+VSDYRYLVMPVRIA*
+>NZ_CP040019.1_406
+MPVLSGLLITAEAGVVSIASFDYETSARLEIEADVETDGQVLVSGRLLNDIVRALPHAQV
+TVELDGGKVVVTCRSSRFALATMPVGDYPALPELPTPAGTVDGAAFAHAVAQVTVAASKD
+DTLPILTAVKVEIEGDTMTFLATDRYRLAMKEIRWTPADPSISTSLLVKARTLTEVAKSL
+GAGGDLEILLGEGTDLVGFSSGGRRTTSVLVDGEYPKIRSLFPETSPIQAVVDTAALVEA
+SRRVALVAERNTALRMVFTDGQVTLDAGTGDDASANESVPCTLEGEDITVAFNPSYLSEG
+LAVVDQPQVRFAFTSAPKPALLTGVNQEDGVVSDYRYLVMPVRIA*
+>NZ_CP083691.1_359
+MKFTVARDILSDAVSWAARSLSPRPPVPVLSGLLVTAEAGLVSIASFDYETSARLQIEAD
+VEDEGQVLVSGRLLNDIVRALPNAPVTLELDGGKVLVTCRSSRFQLATMPVADYPALPEL
+PEPAGTVDGAAFAHAVNQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMTEIR
+WNPADPAISTSLLIKARTLTEVAKSLGGGGRLEIMFGSSHDLVGFSSGGRRTTSVLVDGE
+YPKIRSLFPETSPIQAAVDTEELIAASRRVALVAERNTALRMVFTDGQVTLDAGTGDDAT
+ANESVPCTLEGEEITVAFNPAYLSEGLAVVDQPQVRFSFTAAPKPALLTGVHEEDGTVSD
+HRYLVMPVRLT*
+>NZ_CP097650.1_2
+MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI
+EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL
+PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK
+EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV
+DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD
+DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV
+VSDYRYLVMPVRIA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000177.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db206477543865705371c49c3700ed3cecfadecd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000177.fa
@@ -0,0 +1,23 @@
+>NZ_CP042169.1_4
+MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTPSAGRERQD
+RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED
+SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR
+GPRDTYG*
+>NZ_CP033200.1_1965
+MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTPSAGRERQD
+RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED
+SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR
+GPRDTYG*
+>NZ_CP040019.1_404
+MSSVFGRLIRDRGWSTPVAVGSVLTRWDELVGPEIALHCRPESFEDSVVRVRTSSTAWAT
+QLRLMTPVLLQRFDDALGPGVVTRLEVAGPQAPSWRKGPRTVRGGRGPRDTYG*
+>NZ_CP083691.1_357
+MRERSPEPDALAELPPDRPDLALVQLRRVRDAARQRGEAPLNRRGTAAGLAQSMAGSEAA
+AAAGGAVARSGHRRPGAPADRDPAVVSSVFGRLIRDRGWSTPVAVGSVLTRWADLVGPEI
+ALHCRPESFEDSVVRVRTSSTAWATQLRLMSPMLLSRFDEALGPGVVTRIDVAGPAAPSW
+RHGPRTVRGGRGPRDTYG*
+>NZ_CP097650.1_4
+MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTTSAGRERQD
+RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED
+SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR
+GPRDTYG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000182.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000182.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ec1a8022dacc770df4d9ecdcdda1bf9bf20b39a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000182.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_9
+MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGVVAFLVGSLLNASIVVRLKERMKERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR*
+>NZ_CP033200.1_1983
+MNTTTHAPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMKERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR*
+>NZ_CP040019.1_372
+MVLDGPVNTTIDTPSPDQPVSGQGTPAYARVPASYYDIFVGVFVALLILSGVTAAKLFYG
+PTVPVFSDVFYGGGPLIFDGGAFLFPFAYIIGDILAEVYGWRRARRAILLGFAMLVLAAL
+TYTVVSWTTPVEGFEVWDQALAPMLRITVAGFVAFLAGSLINATIVVRLKERMRERHVAF
+RLILSTIVGQFFDTLIFCTIAFAGTITLLELANYTFTGFLYKTLVEILIVPITLLVIRRV
+KASEPTYRPASSPARAAADAA*
+>NZ_CP083691.1_2132
+MNTTPASRSEPTSGQGAAASAAAPHSHYDIFVGVFVALLILSGVTAAKLFYGPTVPGVSD
+VFYGGGPLIFDGGAFLFPLSYVVGDILAEVYGLRRARRAIYIGFAMLVVAALTYRLVALT
+TPVEGFEAWDQALAPTLRITLAGLAGYIVGSLLNATVVARMKARMAERAVAWRLIASTLV
+GEFFDTLIFCLVAFAGTITLADLANYTVTGYVYKCLVEICIVPVTLLVIRWLKRHEPTYR
+AQPTPAPVSAPTA*
+>NZ_CP097650.1_9
+MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMRERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000188.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000188.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0d7a6603ed2e365dd987eef90801cedfcb8c07f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000188.fa
@@ -0,0 +1,66 @@
+>NZ_CP042169.1_17
+MDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGPDRAV
+AWTRGVLEALEHAHEEDIVHRDVKPANVMVTDTGTVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPPAP
+SDVDPDLPPAFDPVVLRALRKDPQDRFPTGAAFLAALEEAAADPHAGPGRHTPPLDAVHP
+ALVGAGGAVLGATPAEHGADVADVPTAAVPLTRPAPSVPAEPDTAQPQAVNHAVAGAGLP
+GAASAAQLAAAAAMDGPRPVTGGQPVTPGAAATPRPEPPPRDTPAPATATPRRVRRRVRR
+RTLLAAGVVLVALALVLAPWLAAALRTTAEVPAVVGLQQDEAVAALEDAGLVAVVSSAYM
+ADAPDGTVTQSDPPTGTEVPRGAEVRIRVSRGEEGIALSDSLHGLSEDAARRELERLGLR
+VSSVQYQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQL
+ALSAPELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTTSSWIAPTAEPSEPAP
+PSSEAPEPTPSASTSPSPPSSESPEPSESPEPSESAEPSPSPSASATPSPEPTTTATPSP
+TQSPSPPSAAPSTSSEPTEQSPSTSPTATPVDPLPTLTPDPEPSIDPPPST*
+>NZ_CP033200.1_1991
+MSVDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRK
+EARSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDR
+AVAWTRGVLEALEHAHEEGIVHRDVKPANVMVTETGAVKVMDFGIAHALADTSATTSQTQ
+AVVGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPP
+APSDVDPDLPPAFDPVVLRALRKDPEDRFPTGTAFLAALEEAAADPHAGPGRHTPPLDAF
+PPALVGAVLGAAAAEHGADVPTAAVPLTRPTPSVPAEPDAAQPQAANHAVAGAGLPGAAS
+AAQLAAAAAMDGPRPVTVGQPVMPGAAATPWPEPQGDTPAPATATPRRVRRRLRRRTLPA
+AGVVLVALALVLTPWLAAALRTTVEVPAVVGLQQDEAVVALEDAGLLAVVSSAYMADAPD
+GTVTQSDPPTGTEVPRGAEVRIRVSRGKEGIALSDSLHGLSEDAARRELERLGLRVSSVQ
+YQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQLALSAP
+ELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPYSEA
+PEPTPSASASPSPPPSESSEPSESAEPSPSPSASATPSPEPTTTATPSPTQSPSPTSAAP
+SEPTEQPPSTSPTATPVDPLPTLTPDPEPSIDPPPST*
+>NZ_CP040019.1_363
+MEEQWTLNGRYRIDALIGRGGMADVFRGTDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSVASLNHPSIVSVYDTGEVSLEDGHHPVDCPYLVMELVTGRSLREVLHAEGAVGTERAV
+AWTREVLEALEHAHQEGIVHRDVKPANVMVTDAGSVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYATGCVLFELLTGRPPFTGDTPLAVAYQHVREAPPAP
+SEVDPDLPRAFDPVLLRALEKDPEDRFPTGAAFREALEAAAADPHAAVDADTAALDLVRA
+GAAGAGGAAVAAGREVRRDGARDSADVPTAAVPLTPAPAPAAPAEPAEPPGGEPRRGRGR
+AARRRLRRPAGGRRLRGRPAPGHRLPTPPSRGPRRPAPRPPPGSALPPPLPPPDGAAAGG
+AACRSPGCCWPASSC*
+>NZ_CP083691.1_345
+MQGQRILHERYRVDELIGRGGMADVFRGHDLRLNRTVAVKMMRPDLARDPAFQARFRTEA
+RHAAALNHPNIVSVYDTGDALLDDGPQSVECPYLVMEHVDGRTLRELLDAGEVAWRDAVE
+WTRGLLHALDHSHRQRIVHRDVKPANVMVTRDGGVKVMDFGIARALSDTSAHTGQTQAVV
+GTALYLPPEQAQGARVDARSDLYAAGCVLFELLTGRPPFTGETPLAIAYQHVREEPPAPS
+AVDPSLSTEFDSVVLRALQKDPGLRHQHAREFLSALDFAAARAARAADDDAPTRVVPASG
+AAPLATGSGALAAAVAGSTAAGPTASGSTALGAGGAPEARPATGPPATTPLGAAAGPTEP
+LIAGHAVAGAAVPGAPSASQLAAAEAVETAPAAASTTGGSAGAGATSGAERAGRRHRLSW
+AVLAAVAAVAAVAAILALGAALLIGSRDPGPVTVPALAGRTEAEAVSALTGLGLRSAISP
+DYHSTEPDGRVLKVHPGAGAAVEPGSTVNLSVARGGEGVVLPTSLRGASEARVRQELARL
+GLNVASVEDTPSGELDRGALVQTDPVLGSRVPPGSAVVLHLADGTARVPSLVGMTGADAR
+TTLAALDPEMTVRFQGAAGADPDTGVVVLQDPAAGTVVDNTAMITLITSAEATPTASAVT
+VAPPDPALPSATTTTAPAEPSPGVPAPTTPAAPAVDTPAPAPATTPAPAPESSSTPGAGT
+DPAPTESAPTPDDGPGSTGTPSTEAPTEAPTDPVGTPAPSPSGEPVPQPSPSVEPLPEPT
+APTEAPTADPAG*
+>NZ_CP097650.1_17
+MDEQRTLNERYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDRAV
+AWTRGVLEALEHAHEEGIVHRDVKPANVMVTDTGTVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPPAP
+SDVDPDLPPAFDPVVLRALRKNPQDRFPTGAAFLAALEEAAADPHAGPGRHPPPLDAVHP
+ALVGAVLGATPAGHGADVPTAAVPLTRPTPSVPAEPDTTQPQAANHAVAGAGLPGAASAA
+QLAAAAAMDGPRPVTAGQPVTAGQPVTPRPEPPPGDTPAPATATPRRVRRRVRRRTLLAA
+GMVLVALALVLAPWLAAALRNTVEVPAVVGLQQDEAVAALEDAGLVAVVSSAYMADAPDG
+AVTQSDPQTGTEVPRGAEVRIRVSRGEEGIALSDSLHGLSEDAARRELERLGLRVSSVQY
+QDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQLALSAPE
+LRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPSSEAP
+EPTPSASAPPSPPPSESPEPSESAEPSPSPSASATPSPDPTSATPSPTQSPSPPSAAPST
+SPEPTAQSPSTSPTGTPVDPLPTLTPDPEPSIDPPPST*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000190.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26b3a76639c7725b814de300bdd1869f60057b29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000190.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_19
+MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN
+ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA
+ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTIVSGMKAIMEAVVT
+E*
+>NZ_CP033200.1_1993
+MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN
+ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA
+ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT
+E*
+>NZ_CP040019.1_361
+MNEAIRRTWTVMAAMMLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHDPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRVAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN
+ALSSHSATEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWPLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVKLGQDRIREVA
+ERFGFNDSFDYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRPDLTTVEEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGIGHQTIVSGIKAITEAVVT
+E*
+>NZ_CP083691.1_343
+MNEAIRRTWTVMVAMFLVLAVAASVIQVVAADSLKENKLNNRQLFLEFGAPRGPILVDGT
+PVAQSVPSGDAYNYQRVYRDSLLYAPLTGHYSLAYGTAGMEKAMNGELAGTSSSQFLDRA
+LEIVTGSTPEGDQVELTLDSELQKLAYESIPDGVKGSVVATDPKTGRVLAMASKPSYDAN
+TISSHTRSEATAAMSAYEGVPGLTVGQNRPTQQRVAPGSTFKLIDLVAMLESGDYAPDQV
+LDVPAAWTLPGTRTQMSNFDGGRCNGVGRATLTWIVANSCNTPFAQAAVALGQDEIRSVA
+ERFGFNQDGSMPLPVTASVFPEDLDDAALAQSAIGQRDVQATALQMNMVAAGIANDGMVM
+EPNLVQAVRRPDLTTVSEFSPREHGRAMDPDVAHQVRDMMVATVEDGTASAAKSSTLQIA
+AKTGTAEKDGTANVNTWVTGFAPAQDPKVAVTIVYEDQNSSSAHTQAVESMQRIMEAVVA
+E*
+>NZ_CP097650.1_19
+MNEAIRRTWTVMAAMLLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSGDAYHYQRVYHETELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN
+ALSSHSPAEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREAA
+ERFGFNDSFEYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIEAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT
+E*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000199.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000199.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16d75f485ce9fe732ce5409a57b31565c0aa1557
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000199.fa
@@ -0,0 +1,33 @@
+>NZ_CP042169.1_37
+MAKGVKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQL
+VNHDDAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDVDPRHVHLVGVYSE
+LPVVCVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSPEPMDAAELPGAGERM
+ALEIAASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQ
+ARAEAEAGAAVVDGADPAGHGDDDARHPVWDVALAWLKAADSELVQAFVGVARGRRGASS
+R*
+>NZ_CP033200.1_2006
+MAKGVKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQL
+VNHDDAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGGVDPRHVHLVGVYSE
+LPVVCVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSAEPMDAAELPGAGERM
+ALEIAASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQ
+ARAQAEAGAAVVDGADPAGQGDDDARHPGWDVALAWLKAADSELVQAFVGVARGRRGASS
+R*
+>NZ_CP040019.1_347
+MGPRRGLPEGEGPLSGARGGRGAGRQRASRGGPARSTRTGGRAGAKGGGPQRAGSGSRAG
+GEGRRRAPSAPADLAAPPETLFLATIPGATPSTWVDRFTTRQRVVQLVNHDEASQLAHLA
+HDDAGMPRHPLPQLGYVRRRRDVEAEEMLRAAGVDPRRVHLVGVYAELPVVCVGRDHLLA
+AWDAEADGPVPLAELDSHEELDPARFAAAPVEDPLDSAELPGAGERMALEIAASGAGHVV
+LPMSVARMFGRKDVVVLPLASALDDTVGMSRADREAAATRAEVEADAGDAGTAAAGPGEA
+DDDAARHPGWDVALAWLKEADSELVQSFVGVARGRRGNSSR*
+>NZ_CP083691.1_288
+MPAAPADLPTPPETLFLATIPGATPSTWVQRFSSRARTVQLVNHEEAQQAAHLAHDAAGA
+PLHPLPQLGYVRWLRDAGVESVLRESGVDPRFVHVVGVYSELPVVCVGKEHLLAAWDLEA
+DGPVPLAELDPAEHMDPARFAPEPGAASNPLDSAELPGAGERMALEIVASGVGHVVLPQS
+VARVFGRKDVVVLPVACELDDVVGLSRADREAAATRAEVAEEGDGVVPDGADAPATTAPR
+HPGWDVGLAWLKEQDSELVQSFVGVARGRRGGTSR*
+>NZ_CP097650.1_32
+MKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQLVNHD
+DAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDIDPRHVHLVGVYSELPVV
+CVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSPEPMDAAELPGAGERMALEI
+AASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQARAE
+AEAGAAVVDGADPAGQGDDEARHPGWDVALAWLKAADSELVQAFVGVARGRRGASSR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000200.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000200.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e66a9c371fbb16b4ecca85a3ca470202a0d5864
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000200.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_39
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAATTIGGTGAALGGILV
+TGLLLTVIGVIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVAFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVREAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMAAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEQFEASEAGRLG*
+>NZ_CP033200.1_2008
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIGGTGAALGGILV
+TGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEQFEASEAGRLG*
+>NZ_CP040019.1_345
+MSSSPSRPAPGFGWRLHGDGRTITSGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGVGTLLFLLLTGNRLPSYLGSSFAFIAPITAATTAGGVGAALGGVLV
+TGVLLAVIGLIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPLTTFGTAL
+AIVLTAVLFRGLLGRLSILVGIVVGYLLALAQGQVDFTAVGEAGWLGLPPFHAPELHWNL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTTLSGLGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGVMG
+VRIWVQNRVDFSSTINLMTAGAGLIIAIADPQLVLGGLVFGGITLGTIAALVVYHLMTAI
+ARVRGTEPVSEDDEAYEASEAGRLG*
+>NZ_CP083691.1_287
+MSSSPTPSAPRAGHVPGPGPAVRSWRLHGDGRTITPGTVVAPDERLSWGRTVGIGVQHVM
+AMFGATVLVPAITGMPATTALLFSGLGTLLFLLITGNRLPSYLGSSFAFIAPLTAASASH
+GVGAALGGIAATGVLLMVIGVVVGWAGTGWIHALMPPAVMGTIVALIGLNLAGATTQAMQ
+EVPLTTFGTALAVVLTAVLFKGLLGRLSILVGIVVGYLLALAQGQVDFTAVGQAAWVGLP
+PFHTPELHWSLLPLFLPVVLVLIAENIGHVRTVGLMTKRDLDPLTGRALLADGLATTLSG
+LGGGVGTTTYAENIGVMASSKVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG
+IILYGMIGVMGVRIWVQNRVDFSNTINLMTAGAGLIVAIANPELVVGGLVFGGITLGTLT
+ALVVYHLMTLVARVRGTEPVDEDTEDPASYRAAEAGRLG*
+>NZ_CP097650.1_34
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIGGTGAALGGILV
+TGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEEFEASEAGRLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000206.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000206.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24d6f3c6b2c3c776b61928c05ec4ef6a5c90574e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000206.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_47
+MAALTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPLAGLGAETATLDLTD
+ETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEADYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKATRDAETPLRS
+AAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGT*
+>NZ_CP033200.1_2016
+MAALTDRAVLIAGATSASGRAATRTLLDAGAHVVPTGRDAAKLAPLAALGAETAALDLTD
+EAAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLTGQTEDDYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKAARDAEAPLRS
+AAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD*
+>NZ_CP040019.1_340
+MGTLTGRTVLISGATSASGLAAARALLAAGADVVATGRSPERLAPLAALGADTAALDLSD
+EAAVRGLVEDLHARGVRVDGLLHLVGGWRGGGGLAGQSEEDYRALESSLTALRHVSRALD
+DDLRASSAGRLAIVSSTAVARPLAGGAAYAAVKAASEAWTRAVAQGWDKAARDAGTELRG
+AAVVLRVKSLAGLEDRLAEQFVRLWSADAAQLNDSILAVQEKETA*
+>NZ_CP083691.1_1195
+MSAPAAPDLTGALVLVTGASSGIGSALARGLAAAGADLVLVARRAGRLAALADELRAAHR
+TEVTVLPRDLAAPDAGPALRAELSSRGPRVTGLVNNAGFGSGLPFGREDPARLEAMPAEE
+ERGRERVLCVSPSSTGTEFFDVAGTPGAGGGFARRAAPDDVAAAVLRVLARRGGPAEVVP
+HDRAVTVAARLLPRTVLRGMGAMHRRGAARR*
+>NZ_CP097650.1_42
+MAALTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPLAELGAETAALDLTD
+ETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEEDYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKAARDAEAPLRS
+AAVVFRVRSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000208.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000208.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c003d4e355cd3cec20f02efc3bf83abfb99aee36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000208.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_52
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGRDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGHAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHRQQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLKQVQAEAQKLVDAVIG*
+>NZ_CP033200.1_2021
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYRTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGQAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLTQVQAEAQRLVDAVIG*
+>NZ_CP040019.1_329
+MTEHTAAPPASERPGTPALPQDLIDVDALLTAYRTGRPDVSDPAQKVVFGTSGHRGSALK
+TSFNDDHIAAITQAVVEYRAEHGITGAVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRDLTPAGFSADGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANALLAAGLEGVRRVAAADVDGHAKLGGFDFLDRYVTDLPDVID
+VEAIREAGVRIGADPMGGASVAYWGEIARRHGLDLTVVNPDADPRFGFMTLDWDGKIRMD
+CSSPHAMASLIERMTPDADGQAPYDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHRERWPADAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVKLDGGPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGSPAYARIDAPA
+TAEQKARLKTLSPDDVTVTELAGETILATLTNAPGNDAPIGGLKVVTQNAWFAARPSGTE
+DVYKIYAESFRGPEHLKQVQEEAQRLVDAVIG*
+>NZ_CP083691.1_268
+MSTPAAGRAGTPALPEDLIDVEALLAAYRDLHPDPADPAQKVVFGTSGHRGSALKSSFND
+DHIAAITQAVVEYRAEHGITGAILVGKDTHALSGPAQDTAVQVLLANDVEVLVDSRGGFT
+PTPAVSHAILHLNAGRDLTAAGFSADGDNAGLVDGLVITPSHNPPADGGFKYNPPHGGPA
+DTDATSWIAARANDLLAARLDGVTRLAPEDVEGHAKLGSFDFLDRYVTDLPQVIDLDAIR
+EAGVRIGADPMGGASVAYWGEIGRRHGLDLTVVNPDVDPQFGFMTLDWDGKIRMDCSSPN
+AMASLIERMTPDADGHAPFDVATGNDADSDRHGIVTPDGGLMNPNHFLAVSIDYLYRNRS
+QWPQNAGVGKTLVSSSMIDRVATDLGRELVEVPVGFKWFVPGLLSGTGVFGGEESAGASF
+VKFDGGAWSTDKDGLLLCLLAAEIQAVTGQSPSERYRDLVALHGDPAYARIDAPATAEQK
+AALKALSPDDVTATELAGETILAALTNAPGNDAPIGGLKVVTKNAWFAARPSGTEDVYKI
+YAESFLGEEHLKQVQQEAQAIVDAVIS*
+>NZ_CP097650.1_47
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGQAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLTQVQAEAQKLVDAVIG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000218.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000218.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2dadea532c046d132de5cb15eb2ff626f943668a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000218.fa
@@ -0,0 +1,46 @@
+>NZ_CP042169.1_66
+MGQVDTGRTGRRDRRTERPRSRSLHAVLLAALAAVLVACGPVTAPPAPSSAPASSTTAAP
+TSSSPSAGPTAAEVAAAVEPGLETSPGTASAEFRDLATGEVLYARDADEPVAPASSLKVL
+AAAAIVSALGPETTLQTTVVAQPTADDAATELVLVGGGDVLLGTGASDSTHVSGRAGLRT
+LAQRTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPESGNIAPVQPLATYGGRE
+APGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTLPATEVPRATVLAAAPVA
+AVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATRLLTATVEDLGVDTAG
+MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRPGEDSTLGDRFPDAPARQ
+AVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL*
+>NZ_CP033200.1_2035
+MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACGPVTAPTAPSSASASTSTAAP
+TSSSPSAGPTAAEVAAAVEPGLETSPGTVSAEFRDLATGEVLYARDADEPVAPASSLKVL
+AAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLGTGASDSKAVSGRAGLRT
+LAERTVAGLVEDGVTGRVVVSTDLRLFADRTALNPRWTSDIPESGNIAPVQPLATYGGRE
+APGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTFPATEVPRATVLAAAPVA
+AVESAPVGQQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATQLLTATAEDLGVDTAG
+MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALGTVLEGLPRPGEDSTLGDRFPDAPARQ
+AVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL*
+>NZ_CP040019.1_310
+MTPGSPFASLLAALAAALLSAAPVLTPLAGPAALAPGNPVTAEAVAAPSPDARALASAVD
+AALDASPGRVAAQVRDAATGEVLHARDADFLAAPASSLKVLTAAAALRTLGPERTLRTRV
+VAVPAADDGATELVLVGGGDVLLGDGASDPDAVAGRAGLRTLAERTVAGLAEAGVSGDVV
+VSVDLRLFDGAAVNPAWTPDLLEDGHVSAVQPLATWGGREVPGVDEERIEDPAGHAALVF
+QRLLDEEIERTGADLDLGLRDSIPATTAVRDDVVAAEPTAQVESAPVAEVAAYMLAHSEN
+QVAEALGHLSAYAVGRPATHEGAADLLEDVAADLGADTAGMAVLDASGLAEGSLVSPAQL
+AAVVSAASRVPWLAPVLDGLPRPGEDSTLDERFRGTAAEGAVAAKTGTLDHTVSLTGTVT
+TQDGRVLAFSIVASDLDWRLDEAREAVDAAVTAMAGL*
+>NZ_CP083691.1_252
+MTPSNRAARVAAVTRVLLALAICALLGLLAHDVLLPRLPTPAAPAASAPSAPVPAASPSG
+GATAPSSTALASVAPVDPADVAAAVAPALAQAPGTASAEVRDAATGEVLYARSADQAVAP
+ASALKILTAVTAVDVLGADRALTTSVVALPGGGATELVLVGGGDALLGAGASDPGRVDGR
+AGLRTLARRTVAGLRERGVTGPVAVSTDLRLFTDASPLNPAWSAGLVESGNITAVQPLAT
+YGGRTAPGTGEDRIADPAAFAALAFQRELTAAVADSGADLSVRARDVVPATSAPRGDVLA
+TEPVARVESAPVGQQVAYLLAHSENQVAEVLARVAAAADGRPATHAAVPGLLRDRAAAHG
+VDTAGMRLVDASGLSPQNRVTAHQLAGLVEAVQADPALAPVRDGLPRPGEDSTLAERFPG
+SPAREAVAAKTGTLDQTVSLTGTVTTGSGRVLAFSIVCSGVDWRIAPARAAIDEAVSALA
+AL*
+>NZ_CP097650.1_60
+MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACGPVTAPPAPSSAPAASTTAAP
+TSTSPSAGPTAAEVAAAVEPGLATSPGTVSAEFRDLATGEVLYARDADEPVAPASSLKVL
+AAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLGTGASDSTHVSGRAGLRT
+LAERTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPESGNIAPVQPLATYGGRE
+APGTGEDRIEAPAQFAALTFQAALDDAVAASGADLEVGLRDTLPATEVPRATVLAAAPVA
+AVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATRLLTATAEDLGVDTAG
+MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRPGEDSTLGDRFPDAPARQ
+AVAAKTGTLDQTVSLTGTVTATSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000221.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91192412c5c657ee175984288002a434d4b9d245
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000221.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_69
+MDAQDVQNDLTHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL
+HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS*
+>NZ_CP033200.1_2038
+MDAQDVQNDLTHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL
+HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS*
+>NZ_CP040019.1_307
+MDAQDVQNDLTHVLMRREEVQETVKDLAAQIDRDYEGKDLLIVAVLKGAIMVVADLTRAL
+HSHVQIDFMAVSSYGSGTKSSGVVRILKDLDADLTGRDVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPDAMKVEIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS*
+>NZ_CP083691.1_249
+MDAQDVQNDLTHVLMSKEEVQDTIRDLAAQIDRDYEGKDLLIVAVLKGAVMVVADLTRAL
+HSHVEMDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+TRGPASVEICTFLRKPDAMKVDIDVKYVGKDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS*
+>NZ_CP097650.1_63
+MDAQDVQNDLSHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL
+HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000223.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000223.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0deb0b94e4e434842e0b16a67854f711864d302c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000223.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_72
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG*
+>NZ_CP033200.1_2041
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG*
+>NZ_CP040019.1_305
+MTEQTHHDDAARGPVPAADGSAAAPTASTPAAAGVPGTFDPDSTAIDRPRIEAAVREILL
+AIGEDPDREGLQDTPKRVAKAYAEFFAGLHQGPEQVLGTTFDIAHEELVLVKDIPFYSTC
+EHHLVPVHGTAHIGYIPSAAGRVTGLSKLARLVELYARRPQVQERLTTQVVEALMEHLAP
+RGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG*
+>NZ_CP083691.1_246
+MTEQHRDAALADAHLHRPHEAAADVAPTTGAGAALAGAVPGVPGTFDPDQDTVDRPRIEA
+AVREILLAIGEDPDREGLQDTPKRVAKAYAEFFAGLHQRPEQVLGTTFDLSHEELVLVKD
+IPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVVEA
+LMEHLQPKGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRAEAMSLIMHG*
+>NZ_CP097650.1_66
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000225.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000225.fa
new file mode 100644
index 0000000000000000000000000000000000000000..79cd2576c7722b39259f2cbac6e8f1ce236b02af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000225.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_75
+MSTVDWSHLAEGPAPVPALGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTAPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVVPLRPACPDALGREDT*
+>NZ_CP033200.1_2044
+MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVAPLRPARPDALGREAT*
+>NZ_CP040019.1_302
+MSGVDWRHPAEDPAPTPALGARPAEPVAAVLALGANLREPAQTLDAAVAALSALPHVTDV
+QASPRAVTAPVGGPPGQPDYLNQVLTLRTTLSAWELLAVAHRLEQEHHRRREVRWGARTL
+DVDVIAYGDLVSDHPDLTLPHPRAAERGFVLLPWLWLDPDAVLAGRPVAELAALAADAPG
+VRRAEPERHRLLAGRDDVVPVRPRAVRAPGRDAIDGSGP*
+>NZ_CP083691.1_243
+MSRPEAAHPAEGPAPTPELAARPSSPVTAVLALGANLGDPSETLDASVAVLTVTPGIEAV
+AASPRALTAPVGGPPGQPDYLNQVVRIRTALSPWELLGVAHRLEQDHHRRRTVRWGARTL
+DVDLIVYGDLTSDHPDLVLPHPRAAERGFVLLPWAWLDPEAELAGESVAELGARAADAPH
+VRREPARTAHLDGPRPDVLRPDSTPGLPSAPLPDGAAIARPWSDPT*
+>NZ_CP097650.1_69
+MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVAPLRPARPDALGREAT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000227.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000227.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9268d4d2340c93bfb23b93f65ec11595aa131bcf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000227.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_77
+MPGIDLSGVAFTPASPRLTTVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL*
+>NZ_CP033200.1_2046
+MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL*
+>NZ_CP040019.1_300
+MPGIDLTGVTFAPASPKLTPVKLISSSIGHLIWLVVFSVPLVLKLLGPWEGLWAWTAWGL
+PAIVVVSWLVDLVLIPRRVRAMGWAEREDDVLWREGLLFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAASGSDVTLEGLPRETADELREVLMARGQARLAGL*
+>NZ_CP083691.1_241
+MPGIDLQGVEFTPVSPALVRVEAVRELIALVIWLAVVSVPLVLKLTGVWPDMWSWTAWGL
+PALVLAWSLVELVLIPRRVVAKGWAEREDDVLWREGILFRRVVAVPYGRLQYVDVTDGPL
+LRWAGLQKLTLKTAGGADVELVGLPRETCDRLREVLMARGQARLAGL*
+>NZ_CP097650.1_71
+MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000228.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000228.fa
new file mode 100644
index 0000000000000000000000000000000000000000..679913621328b8887931ca5dcc919eedd48bd523
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000228.fa
@@ -0,0 +1,56 @@
+>NZ_CP042169.1_78
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGMLGGAGADAS
+APERAAEPGLPDADAADAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVAL
+LPEAVLDEGETLTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETT
+HQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVLRVLT
+VVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRTGFTT
+TRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDED
+VAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVVGGA
+VVGEESGAHVPAVRGEEER*
+>NZ_CP033200.1_2047
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGVLGGAGADAS
+APERAAEPGLADADPDAVDADAGELLLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLAL
+VVALLPEAVLDEGETLTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGL
+TETTHQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVL
+RVLTVVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRT
+GFTTTRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRD
+LDEDVAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGV
+VGGAVVGEESGAHVPAVRGEEER*
+>NZ_CP040019.1_299
+MSAAAPVPATRPADDDGWARVHPASPWVRGWTFLLLILFFLGRNAVEDFAAGRFGAGAGG
+GSGEGEGSLLVAGGILLGVTLLVSLAFFFSWWFTRFRIGEDQIELRQGWLFRTRRQMKYD
+RIQAVDLQHPLVARLLGLAVVKVEAADGGESALELSFLPKARAEQVRREILDRASGVLVG
+PASAPRIAEGADAAAGVIPGVMPGVMPGAEAGPGVAPPGADADPTTPRADAPEGAAPSSS
+DPGLARRADDEGELMLRVPSGRLIGSVLLSGGVAGTVAVYLVVVLGTSLFFALAPGTWLE
+GEDTPLTGIVVAWGLPLAFAVVGQAWSGLNGGWGFQVRRSADGLRLRHGLTETTHQTVPP
+GRVQGVTVSQPLFWRPFGWHRVKVSVAGYGEDAAGKRSTALPVGPWEDVLRVLTVVAPDP
+GLDGDPREAEGLTPARLMHLGLHGSGTEGGFHHIPHRGRWWFNWFAWRRRGFTTTRALLV
+VRSGRWNRVLQTLQHERVQTAALDQGPVQRRLRLATVHVRTAGGRAVLPDLDEAVALELF
+AEEARHAAVSRRLADRDRWMRPEELARFEQRTREVAATEVGREELARAGVARPAAPAGGV
+AGTDPEPRTSHEERP*
+>NZ_CP083691.1_240
+MSAPAPRPEGLASGPSPEDGRIAPAPAADDAGWVRVHPASPWIRGWVMVATFLFFALRDV
+VERWIGGLFGADAGGGPGVDGRGLLIGGGIALGVLLLVGLAFFFSWWFTRFRIGAEEIEL
+KQGWLFRSRRQMHYDRLQAVDLQHPLPARLIGLAVVKVEAADGGGDSALELAYLPKAQAA
+AVRRQILDRASGAAAARPVPSAAPEAAGGPAAAGPVRGLLVDPEEQGPVLLRVPAGRLIG
+SVLLSSTVMGLLGAVVAVPAVLSLLLLLFPDANAGEEAGVWAVTLGSTFPLLFSLAGAVW
+SGLNKGWGFTVRDSSDGLRLRYGFTETVSQTVPPGRVQGVEISQPLFWRPFGWHRVKVSV
+AGYGGLEAEGRRRDVALPVGPWEDVLRVLQVVAPDPGLGGDARAAGELMRTAMTGSGEEG
+GFRHVPRRAAWWWHWLTWRRHGYALTPTLLVVRHGRLSRSVQTVQHERLQAVALTQGPVQ
+RRLRVATLRVHMAGGAARLRGLDEDVLAELFEVESRHAAVSRRLTDRNRWMLPEELERFE
+RRTAEVARTEVGRAEMAAAGVVPMETGPRPGDTPPVATTEHRGEETA*
+>NZ_CP097650.1_72
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGMLGGAGADAS
+APERAAEPGLPDADAADAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVAL
+LPEAVLDEGETLTGIGAAAALPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETT
+HQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVLRVLT
+VVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRTGFTT
+TRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDED
+VAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVVGGA
+VVGEESGAHVPAVRGEEER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000231.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000231.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77aa016a7f4b831fb18916d6ba2ca0514c6e0356
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000231.fa
@@ -0,0 +1,41 @@
+>NZ_CP042169.1_83
+MTSVRRHAARGLVALAAAVAVSAPLAAPAAAAPAAPTTPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARYGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEYGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDGLRDYDFYETAAGMREVRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDPNARGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDTWMQGKKEHPGRGVGKTAQRGLKVR*
+>NZ_CP033200.1_2052
+MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDVWMQGKKEHPGRGVGKTAQRGLQGR*
+>NZ_CP040019.1_292
+MISVRRHAARGLVALAAAVAVSAPLAAPAVAAPAAPTAPAAAQSATGKPVVRPEVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYNGRYQVPTFEEVLELRER
+LSDRYGRQIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGTPYDSVAAGDTVRDYDFYETAAGMREVRAAGVDTLGPAFAQ
+VITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSADSNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDTWMQGKKEHPGRGVGKSAQRGLQVR*
+>NZ_CP083691.1_237
+MTALRTTARGLAALTAAVAVAAPLAVPASAAIPAKEPITQAERPDVVAHRGASAYRPEHT
+LAAYELAVAQGADVIEPDLVSTKDGVLVDRHENDITGTTDVSERPEFADRKTTKTVDGVE
+ITGWFTEDFTLAELKTLRAKERLPEARPGSAAYDGMYQVPTFEEDLKLREELSAKYGREI
+GIIPEIKHPSYFDGIGLSQEEEVIELLEEHGLNHADGRAVVQSFEFSNLAEMNTRLGLQA
+DTAYLLWYEGSGYDAVLSGDTARDYAYFSTPAGAAEAAFNGIDIYGPELRQVIALNQDGS
+LGAPTGLVEVAHDAGLTVVPYTFRAENQSLPLQFRSSENPVEHGDLAAYITEVLDAGVDG
+FFTDFPDVGVAARDAWLAEKPAEQPSEQPSDGSHAVPGKVQTGDAAAWLPAGLAAAAAGV
+LVALRRRLTAAR*
+>NZ_CP097650.1_78
+MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDVWMQGKKEHPGRGVGKTAQRGLKGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000238.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000238.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6fca0e908f1a059d2d512cbbbfc8c6b4b31a443a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000238.fa
@@ -0,0 +1,65 @@
+>NZ_CP042169.1_90
+MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGTGFDPAQARVQATAAAGAHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+LDAFHEAFGTREGDPMWLAPEERVTIW*
+>NZ_CP033200.1_2059
+MTATAEPRVPSPREDLYRHVNTGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEGAVR
+EVGAGFDPAQARVQATAAAGAHRDAPLAPLDAEDTEGMEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVTTPAELLTLSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLTLAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHMTPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPVEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTREGDPMWLAPEERVTIW*
+>NZ_CP040019.1_285
+MTATAEPRVPAPREDLYRHVNAAWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGAGFDPAQARVDATAAAGAEHHTPLEPLDAEETEGMELPEVKRRIAALYASFMDDETV
+EARGLEPVATDMAAVASVQTPAELLELSGRLQRQGVSGLVNTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHAGRLLGLAGIGADSAEAAEAGVRVVELEKRIAAL
+HWDVVRSRDAVARYNLMTHEQLVELFPLAEAWLEGVDAAGERSREVVVWQPDFLSGVQAL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRHRWKRAVAF
+VNGAAGEDVARLYVDRHFPEGHVAAMDELVNLLQEAYRRSIDELEWMSEETRQRALEKLS
+MFRPMVGRPVRWVDYSSLEVHAGDLLGNARAASEFEWERDLRKIEDGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEKSMAANLGAIGAVIGHEIGHGFDDQGSRYDGSGR
+LEDWWTQEDRAAFTELTSRLVAQYNVLSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFSAWAAVWRQLTRPETMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTQEGDPMWLAPEERVTIW*
+>NZ_CP083691.1_230
+MTATAEPRVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRRIAEDAAR
+DAAMAAPAPEVEAPAQDEASQDPAAAERAARERIAVLWSAFMDEEAVEAAGILPLAADLE
+AVDAVASPAELLALSGRLQREGVSGLIGTGALNDAGDPERMLLHLIQSGLGLPDESYYRE
+EAYAEILAQYTEHVGRLFALAGVGGDEAGAAALGERVVALEKRIAAHHWDVVRSRDAVAR
+YNLLTRDQLLELLPLAPGWLEGIGAADARADEVVVWQPDFLTGVQALLEGPDAADLADWK
+AWLTLQVLRSRAGFLPDAFVQENFSFYGRRLAGTQEVRPRWKRAVAFVNGGVGEDVGRLY
+VARHFPEGHVAAMDQLVGLLLEAYRRSIDALDWMGEQTRQSALEKLAMFRPMVGFPETWR
+DYSALELTPGDLVGCARAVDRFEWDRDLAKIETGPDPREWHMTPQTVNAYYTPLENAIVF
+PAALLQPPFFDPERSMAANLGGIGAVIGHEIGHGFDDQGSRYDGSGRLHDWWTEQDREAF
+AERTGRLVAQYSALSPAEAPDRQVNGEFTLGENIGDLGGLGIAHQALEIWREEQDGSTED
+ESSGDREFFQAWAAVWRQLTRPETMVTRIASDPHSPNQFRCNQVVKNLDAFHTAYGTREG
+DPMWLAPEERVTIW*
+>NZ_CP097650.1_85
+MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGTGFDPAQARVQATAAAGAHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTREGDPMWLAPEERVTIW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000239.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000239.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2464eaecee327d98e1afe116667786162d481a3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000239.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_91
+MADGAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSPALSVGAMKAFMM
+LANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE*
+>NZ_CP033200.1_2060
+MVDGAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMARYAEALSPTLSVGAMKAFMM
+LANEGTMTPSAVAEGMLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE*
+>NZ_CP040019.1_284
+MAERGHGDDRGLDGVGAERGDAGGEIDGFEAAVRGLEDAFARMVRQHRQVVTRQAAALKP
+GLSAGAMKAFITLCNAGTMTPSTLAEHLLLDRAQVSRMVRDLEDEGLITREPDPVDRRSA
+LLTATEEGRARLDAVRGGPAGEGLRADLAHWDRADIHTLVRLLGRLVEEQQARVDRTPDA
+G*
+>NZ_CP083691.1_229
+MADPADHGSDGRGTGADAFAPEAFDAAVRELEGSFNRLVRQYRATLARQAEAVHPGLPLG
+AMKAFVAICHRGPLTPSDLAEHLMLDRTQISRVLKDLEGDGLIHREPDPRDRRSALLTAT
+DEARARLDAVRQGPAGGGTRARLQRWDLEDVRALSALLRRFVDEREDPAADDACRP*
+>NZ_CP097650.1_86
+MADGAPDPGRGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSPALSVGAMKAFMM
+LANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000240.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000240.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1589329b8fe23ff406b04f70c46e84d18d8044dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000240.fa
@@ -0,0 +1,61 @@
+>NZ_CP042169.1_92
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTSAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDSLRVIFEDVYAQGIALAFLVAVPLAIVALIAILFLPNLPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRSVSAERPATAVADRPVVPAA
+LAVAGTALLAAVVTALVRARRG*
+>NZ_CP033200.1_2061
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTTAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDGLRSIFEDVYATGISHAFLVGVPLAIVALIAILFLPNIPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRSVSAERPATAVADRPVVPAA
+LAVAGTALLAAVVTALVRARRG*
+>NZ_CP040019.1_283
+MIDHRQSLTAVNHSDDPAEGPHEPHLPAVAGTAPAGAPSLERAAADAARHRAVLQALTGL
+LLGMFVSMIANTVVSTSMPVIISDIGGNQNDYTWVITAALLATAVSTPVWGKLADLMDRK
+MLFQVALVIFVGASAAAGFTNDPTFLIVCRVVQGLGGGGLAALSQVIMADIISPRERGRY
+MGLFGAVMAVATVGGPLAGGVITDLWGWRWNFFVAVPFALVALVMVQRTLHLPAREPRKV
+SIDYLGIVLLGVATSLLLIWVTTAGQQFPWASWTTAWMVGGAVLAAALFVVVELKVTEPL
+IPLTLFRNRTFTLATIASIATGLAMFGAGVYLAQYMQLARGATPTQAGLMTIPMIAGLLI
+TSTVIGRVITRTGVWKRWLIVGAVLLTAGMALLATLHYDTPFVLVSLHMLLLGAGVGMTM
+QNLVLVVQNTTDPRQMGVASSGVTFFRSLGGSVGVAAMGAVVANVVPSRFEARGADLAAA
+LQSLGADGPVWAQRLQSGTLPRVAEMPEPLRVVVEDVYATGISQAFLVGVPLAVVAVVAI
+VFLPNIPLGRMTTSERLDASRADLATVTAPAAMQKVPATGEIPVVAPAAGGAGGTDDACT
+AEDADGTEGVPAAQGPTTAPAEPTAERAERPAVQPAAESVPARVVAPAAAAPSTAAASGR
+SGGARPGARAAAAVALLTAIAVLMRQARRG*
+>NZ_CP083691.1_228
+MSTTTAPPATAGPAAVGNSPAVPSLERAADDAARHRTVLRALTGLLLGMFVSMIANTVVS
+TSMPVIISDIGGDQTAYTWVITAALLATAIATPIWGKLADLVDRKVLFQVALVLFVAASA
+AAGFTTDPTFLIVCRVIQGLGGGGLAALSQVIMADIISPRERGRYAGLFGAVMAVATVGG
+PLAGGIITDLWGWRWNFFVSLPFALVALVMVQRTLHLPARESRKVSIDYLGIVLLSTATA
+LLLIWVTNAGHQFDWASATTAWMLGGAALAAVLFVVVELTVAEPLIPLTLFRDRTFTLGT
+IASIATGLAMFGASVYLSQYMQLARGATPTQAGLMTIPMIVGLLVSSTVIGGVITRTGVW
+KRWLVIGAVLLIAGAAMLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQ
+MGVASSGVTFFRSLGGTIGVAVMGAVVANVVPDQVEQRRTDIGAALASLGPAGAEWAQRL
+QSGSLPRVAEMPDALRVIFEDVYATGISQAFLVGVPLAVVALAAILFLPNIPLGHMTTTE
+RIDAERADLATVSVPQAMQTLPATGSTPVVAQAQVQEAAPASTTTTPAPAARALRVPAGL
+RERRIAPAGTGRSTAWRATASALAAGAAAAAFVPLLRRSRRG*
+>NZ_CP097650.1_87
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTTAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDGLRSIFEDVYATGISHAFLVGVPLAIVALIAILFLPNIPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRAVAAERPATASPVAGRPVAP
+AALAVAGTALLAAVVTALVRARRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000245.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000245.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3256095823ee80284ad7f2315051dccb327c764c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000245.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_98
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVNKGVDGAQEKFLSGDEGEQQA
+*
+>NZ_CP033200.1_2067
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHADTVNKGVDGAQEKFLSGDEGEQQA
+*
+>NZ_CP040019.1_276
+MGIGDLNNLANQHSDKINEAVDGAQEQHGDKLGEHADTVNKGVDGAQEKFLSGEKNEGEQ
+QA*
+>NZ_CP083691.1_222
+MVGFDDVKNLANENSDKINEQVDAAQAQHSDKLGQHADLADKGIDGAQDKFLNGQSAENE
+GEQQA*
+>NZ_CP097650.1_93
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVDKGVDGAQEKFLSGDEGEQQA
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000258.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000258.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97e144c76b97b41e1cffc6738308a25267009adc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000258.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_112
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMLLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGVAQGRAGGESAGAKDDGGVLGAIRRALPGGKDEKDDRQKKGKPAA*
+>NZ_CP033200.1_2081
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMLLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGAAQGRAAGESEGTKDYGGVFGAIRRALPGGKDEKDKPAA*
+>NZ_CP040019.1_259
+MAKNSMIGRYTSGKVKDFALKSALDENGEPTEGFEKVVSKVLGIQRPLVLKHIQNVAAKN
+PELTAEQIAERLGQQYLNTVTGAGAAVGGTAIVPGVGTVAALGLSAAATVGFMEATALYA
+QSLAELHGITMEDPQRAETLVMALMLGDDAKELLREAAAKAGRPFDPNASLNALAGSAAG
+TGGGAGISAFVMDRLKRTFMKKMLVRQGAGFLGRAVPFGVGAVIGGVGNRAMGKAVMENA
+QELFGPLPTVIPGEIREGAARQAQEDDGEGGVFAAIRRALPGGDDKKDAAKA*
+>NZ_CP083691.1_191
+MAKNSIIGRYASGKAKDFAMKSAFDENGNPTEGFEKLVFTTLDIQRPLVLKNIQRLHESH
+PGETPEQLAERLADQYVTASTGAGAAVGGTAIVPGIGTVAALGLSAAATVAFLEATALYA
+QSLAELHGLTTKDPARSKALVMAVMLGDDTKELLKDISRKSGVKNTGTPDSAAGLAAMMN
+GGAAGQAAGGAGLGAVAIEQLKKQFVKKVLVRQGAGFLGRAVPFGVGAVIGGVGNRAMAK
+AVVKNSRDLFGPLPAQIPGEIVAASAKGQDVGQSAEDGKGGLVSGLIKALPLGKKDEKKA
+*
+>NZ_CP097650.1_117
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMRLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGAAQGRADGTKDDGGVFGAIRRALPGGKDEKDDRQKKGKPAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000259.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000259.fa
new file mode 100644
index 0000000000000000000000000000000000000000..944e6219f8cf43f80fd2d5cc11d61d28f77d9ccb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000259.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_113
+MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE
+KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD
+WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL
+AERLHAETLKYLAGIRRDREHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER
+LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA
+AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSVVGALAGLAIHGV
+ATLFL*
+>NZ_CP033200.1_2082
+MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE
+KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD
+WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL
+AERLHAETLKYLAGIRRDRQHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER
+LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA
+AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSIVGALAGLAIHGV
+ATLFL*
+>NZ_CP040019.1_258
+MSLSPDPARQLLSAGTLERERGLRRMKAVALGLLVALAVVFAVAFPLQDVHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGIPVPHTALIPRKKDQLGAALTEFVQENFLDSDVARE
+KVEGLEVAAAAGGWLRRPENAERAAREVATAARGAMAAADDDAVQELLRQLMQRHMVEPE
+WSPTLAGVLQDVVTGRHHERVVDLVVEHTGDWVAAHPEMFVETVRRRSPEWSPDLVDRLL
+AERLHAEALKYLAGIRDDRDHEARRAVDDWLTRLSAEMRDDPHTRASVERFKHSLFADER
+LRAWAGRAWTSLRDSLLDALEDPASDLHRALVAALRDLGARLQEDPVLRDRVDGHARAAA
+AYALSTYGPAVTGVIEETVARWDGDQTARTLELFVGRDLQYIRINGSIVGALAGLTIHAV
+ATLFL*
+>NZ_CP083691.1_189
+MAPSPVPADSPFPLTPAALERAAGLRRMKAVALGLLIVLAVVFAVAFPLQRVHPAWGFVR
+AAAEGGMVGALADWFAVTALFRRPLGLPIPHTALIPEKKDQLGAALTEFVQENFLDSDVA
+REKVAGLQVARAAGGWLRERPHAVHAAGEIAMAARGAVAATDDDAVQDLLQQLMQRHMVE
+PDWSPTLAGVLEDVLAGRHHEKVVDLVVEHTGDWVATHPEMFLETVRRRSPEWSPDLVDR
+LLAERLHAETLKYLAGVRADRDHEARRSVDDWLARLAGNMRDDPATRASAERFKADLFAD
+EQLRAWAGRAWITLRDSLLAALEDQDSDLHRALVDALVDLGVRLQEDPALQASVDGRARA
+AASYALSSYGPALTGVIEETVARWDGRQTADTLENLVGRDLQFIRINGSVVGALAGLAIH
+TLASLVF*
+>NZ_CP097650.1_118
+MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE
+KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD
+WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL
+AERLHAETLKYLAGIRRDRQHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER
+LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA
+AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSIVGALAGLAIHGV
+ATLFL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000261.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24acdbcf4ebbfe59198915d5228a636e651a28fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000261.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_118
+MATRADRGRPVHNPDIIGFTDAELNETPIRPKWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVILGVIFKIVLVEGVGRWYLSTGKTIFQGWRSLGSWTSWYFGPYILIWGFV
+YGATAMSSAALPLAALFPGVDMKVYAIGLGLVGLGLVWLNRYGLIEKLMAVLIGVMFLTV
+LLSAALTAPNVGDILAGLVPRIPSGDPDVMFYVLGLAGGVGGTITLGAYAYWLREKGWNV
+PKYMRVMKFDNATSYILTGIFVIATMIMGVELLHSAGLAISSGDRGLLDVGNVLAERYGQ
+AYSVVFLVGFFAASFSSLLGVWHGVSLMFADFWTNFRRPADELDQDDAPSLASKPGRFFL
+LWLTFPPMTLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNKKEVPAQFRNGWIRNTL
+LGLTAAVFVAIGVNELWKALQPLIGG*
+>NZ_CP033200.1_2088
+MAHAVDPGRPVHNPDIVGFTDAELNETPIRPRWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRYYLSTGKTIFQGWRTLGAWTSWYFGPYILIWGIV
+YGATAMSSTALPLAALFPGVDSKVFAIASGLIGLGLVWLDRYRLIEWLMTVLIGVMFVTV
+LLSAALTVPNLGAILAGLVPRLPSGDPQAMFYVLGLAGGVGGTITLAAYGYWLREKGWNV
+PKYLKVMRFDNATSYILTGIFVIATMVMGVELLHSAGLAISSGDKGLLDVGDVLAERYGS
+AWSTVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPAEELDQDDAPSLSSKPGRFFL
+LWLTLPPMALLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNTKDVPRQFRNGWVRNTL
+LGLTAAVFVAIGVNELIKALQPVLGG*
+>NZ_CP040019.1_251
+MPHTADRGHPVHNPDIVGFTEAELNETPIKPRWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRWYLSTGKTIFQGWRQLGSWTSWYFGPYILIWGFV
+YGATAMSSTAIPLAALFPAVDAKVFAIAAGLIGLALVWLNKYGLIEKLMTALIGVMFVTV
+LISAALTAPNVGEILSGLVPRIPSGDPQVMFYVLGLAGGVGGTITLGAYAYWLREKGWNV
+PKYMKVMKFDNATSYVLTGIFVIATMIMGVELLHSAGLAISSGDKGLLDVGNVLAERYGQ
+VWSYVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPADELDQDDAPSLASKPARFYL
+LWLTILPMSLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNRKDVPVQHRNGWIRNIL
+LGLTAAVFVAIGVNELIKALQSVLGG*
+>NZ_CP083691.1_185
+MSHTTPPGHGLVDRHHPVHDPDIVGFTEAELNETPIKPKWNSLGPGIVAAATGVGAADLV
+ATLTAGSRYGYMLLWAVVLGVVFKIVLVEGVGRYYLSTGKTIFQGWRGLGSWTSWYFGPY
+ILIWGFVYGATAMSSTALPLAALFPGVDSKVFAIASGLVGLGLVWLNRYGLVEKVMTVLI
+GVMFVTVLISAALTVPNLGDILGGLVPRIPSGDPDVMFYVLGLAGGVGGTITLGAYGYWL
+REKGWNTPKYMRVMRFDNTVSYVLTGVFVIATMIMGVELLHSAGIAISSGDKGLLDVGDV
+LAQRYGDVWATVFLIGFFAASFSSVIGVWHGVSLMFADFWTNFRRPADELDQDDAPSLAS
+KPGRFYLLWLTFPPMVLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNSRRVPGKFRN
+GWVRNVLLALTTAVFLVIGGNELLKALKPLIGG*
+>NZ_CP097650.1_126
+MATRADRGRPVHNPDIIGFTDAELNETPIRPKWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRYYLSTGKTIFQGWRTLGAWTSWYFGPYILIWGIV
+YGATAMSSTALPLAALFPGVDSKVFAIAAGLIGLGLVWLDKYRLIEWLMTVLIGVMFVTV
+LLSAALTAPNLGEILAGLVPRLPSGDPQAMFYVLGLAGGVGGTITLAAYGYWLREKGWNV
+PKYLKVMRFDNATSYILTGIFVIATMVMGVELLHSAGLAISSGDKGLLDVGDVLAERYGS
+AWSTVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPAEELDQDDAPSLSSKPGRFFL
+LWLTLPPMALLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNTKDVPRQFRNGWVRNTL
+LGLTAAVFVAIGVNELIKALQPVLGG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000262.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000262.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93facce6d4e4758e0897df8aaf34d15978e3eb06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000262.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_119
+MIVAFSVAPSGQPADSAHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDWD
+EVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHSGELDGKLERLEAALAEDGNGDAADAR*
+>NZ_CP033200.1_2089
+MIVAFSVAPSGQPADSAHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDWD
+EVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHTGELDGKLERLESALAEDEGRRAAPAPH
+DGDAG*
+>NZ_CP040019.1_250
+MIVAFSVAPSGTPADAAHQPGDEDSASVHRAVAAAVAVVRESGLPHRTSSMFTEIEGDWD
+EVMDVVRGAVDAVAPYGSRVSLVLKADIRPGHTGELDGKLARLEAALASDDVS*
+>NZ_CP083691.1_184
+MIVAFSVSPSGAPADAAYAPSSDGDSASVHRAVAAAVAVVRASGLPHRTSSMFTEVEGEW
+DEVMGVVKRAVEAVEPYGSRVSLVLKADIRRGRTGELDGKLERLEAALTDGTPATPDRFR
+A*
+>NZ_CP097650.1_127
+MIVAFSVAPSGQPADAEHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGEWD
+EVMEVVRAAVDAVSPYGTRVSLVLKADIRPGRTGELDGKLERLESALAEDEGRRAAPAPR
+DGDAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000263.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000263.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af80bca9e9417ad6f3eca9e17036609a49e870fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000263.fa
@@ -0,0 +1,23 @@
+>NZ_CP042169.1_120
+MAVTVRPATSDDVEPLLRVKAQAWREAYGGLLPAAHLDAVDAGVPEQVPGWAALVGSDRE
+LWVADDGGRLLGMALAGPRRSQGGGLPDLELMALYVLAEAYGTGLGALLLDAVVGKRPAV
+LRVLAENPRAVAFYAKHGFAPEGGPEPMTGPWAGLHEQLMVRRG*
+>NZ_CP033200.1_2090
+MPESVTVRPAAPGDVEALLRVKARSWREAYGALLPSAYLDAIEARIPEDVPAWTALIGPD
+RDLWVADDGGRLLGVALAGPRRSAAETGRTGADDAAASPADLPDVELMVLYVLAEAYGTG
+LGARLLDAVVGERPAMLRVLAENPRAVAFYAKHGFAAVGAPEPMTGPWAGLHEQLMVRRR
+PHDGGAA*
+>NZ_CP040019.1_249
+MAVVVRPARREDAEALLRVKAQSWREAYGAHLPAEVFDRADARVPQDAPAWAALVGSDRD
+LWVAEDDDGGRLVGVALAGPSRIEDEGLPPRELMVLYVLAEAHGTGVGARLLDAVVGDGP
+AVLDVLAENPRARAFYAKHGFEDHGAPAPMDGAWAGLHEQRMVRRG*
+>NZ_CP083691.1_183
+MRETDGASDAVVRDVNPPSAPAPTVRPAGADDLPAVLAMKNAAWRETYAHLLEPGFLAAQ
+EAELPRAVEAWTRLLGEPGMEVWLAEGAGVVVGMAAAGPADDPALGPEGRELIALYVRAR
+LHGAGLGAALLRAAVGGRPARLDVLVGNERAIAFYERHGFVAVGEPAVLGGPWGDAREQR
+MVRR*
+>NZ_CP097650.1_128
+MPESVTVRPAAPGDVEALLRVKARSWREAYGALLPSAYLDAIEDRIPEDVPVWTALIGSD
+RDLWVADDGGRLLGVALAGPRRSAAETGRTGADDAAASPADLPDVELMVLYVLAEAYGTG
+LGARLLDAVVGDRPAVLRVLAENPRAVAFYAKHGFASVGAPEPMTGPWAGLHEQLMVRRL
+PHDGGAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000267.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000267.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80a75e9b0e5eb6e6cd41c6fa743194b8dcbf7c83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000267.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_124
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAQQAELTAAVVELLRTAREAGRPVFLVR
+TEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRDE
+MRQPLLGQDEALTLLRTGLVPDRG*
+>NZ_CP033200.1_2094
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAQQAELTAAVVELLRTAREAGRPVFLVR
+TEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRAE
+MRQPLLGQDEALTLLRTGLVPDRG*
+>NZ_CP040019.1_245
+MPDSAPAPEPIAGERPSGGETALVVVDMQYSYFEHPDLAARQAELTEAVVELVRTAVEAG
+RPVVLVRTEHERDRSTWTLNMLEDGEGFAFPGTRQAAVLDEVARAARGAVEVVKTRDSAF
+HRTDLDAQLRRRGVGRLLLCGVSTHSCVFQTATDAFARDFHAATAVDAIASEDPRLSAAM
+LEFLRDEMRQPLLGREDALALLRTGLVPDQG*
+>NZ_CP083691.1_635
+MNTLQNPALIVVDVQRGFDDVEYWGSRDNPDCETNISSLLTHWRDRSWPIVFVRHDSTNP
+ESTLAVGTPGNEFKEVITGDPDLLVSKTVNSSFHGTPDLDDWLRAEGIEQVVICGITTNH
+CCETTARIAGNLGYDTYFAIDATHTFDRPALDGTVLPAATVSAMTAANLHGEFATVVSTR
+TLIDGNSYAPRYEQEK*
+>NZ_CP097650.1_132
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAHQSELTAAVVELLRAAHEAGRPVFLVR
+TEHARDRSTWTLNMLADDEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRDE
+MRQPLLGQDEALTLLRTGLVPDRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000268.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a297bd1ece4f340a735f008307338db60402ad4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000268.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_126
+MSDPTPPSTEPMIPEQPGNHPSSATAPDAGVAPATSAAAGRDRVLLPWVFWPSAVIVLSF
+VGATLLAPAQMTVGIGLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK
+PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTQAEAAQSALATTFL
+HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYVMIGAVTCVVLYTVVSGVERGMKWLSN
+TNLILAAGLLLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS
+AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR
+PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA
+TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS
+LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA
+AGVPASEGPRRPRLRRHEH*
+>NZ_CP033200.1_2096
+MSDPTPPSTEPMIPEQPGNHPSSATAPDAGVAPATSAAADRDRVLLPWVFWPSAVIVLSF
+VVATLLAPEQMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK
+PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTQAEAAQSALATTFL
+HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSN
+TNLILAAGLLLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS
+AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR
+PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA
+TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS
+LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA
+AGVPASEGPRRPRLRRHEH*
+>NZ_CP040019.1_243
+MSESIPPSHPSAPPGPASAHPAAPAAGAADAREASGAVAPASSDAATGARVLLPWVFWPS
+TIVVLLFVGATLLFPEPMTAAIGTVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGAIT
+LGKPDEKPEFSTLSWFALLFAAGMGIGLVFFGMTEPLMHFVSPRPDLAATDPNPAQAAQA
+ALATTFLHWGLQPWAIYAVVGVAVGLAIHRRGRPLALRWAFEPLLGERRVRGGWGHLIDN
+IALIGTVFGVATSLGLGVTQMSAGLRSLGVVPEESAWVEYAMIGLVTLVVLYTVVSGVER
+GMKWLSNVNLVLAAGLLLFIAIVGPTAFLFKEMVQSFGAYLQTFFGASLNVSAFQGAEGD
+AWQAGWSAYYWGWWMSWTPFVGIFIARISRGRTVRQFLAGVLLVPTLIGVVWFGVLGGTA
+IYLETVRPDGYTSVVGADGSIDSNTALFQVVEQLPAGALLVIGAIMLSAIFFVTSADSGA
+LVMGMLATGGDVNPKVPVKIFFAIATALMSAALLAAGGLSAIQTLAITIGLPFSVLMLVM
+CLATFRSLGYSVARVEAVRRQAMLASIKDRFGLDTDDDEVVDGGPVAASQWWASLSRDRQ
+RTIAQAASAGPDDEIRLAGSSAEEPAGSPDARR*
+>NZ_CP083691.1_179
+MTPAPAGRDADAPAANRPHRTGPDPDVKHPAPATADQADRGHAGLLPWVFWPSTLIVLLF
+VVATLAFPAQMTDVIGDVQAAIIRNFSWWYAIVAFAFVVFCAYLVFSRKGSITLGKPDEK
+PEFSTMSWFALLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTEAQAAQSALATTFL
+HWGLQPWAIYAVVGVAVGLAIHRRGRPLSLRWAFEPLLGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMAAGLRSLGIVPADSPWLEYAMIAAVTCVVMYTVVSGVERGMKWLSN
+INLVLAAGLLLFIALVGPTPFLLKETVQSFGAYLQNFFADSLNVSAFYGAEGDAWQAGWT
+AYYWGWWMSWTPFVGIFIARISRGRTVREFLMGVLLVPTLVCVVWFGILGGTAIWLETVR
+PAGYTSVVGADGAIDSNSALFQVLEQLPAGLLLVIGAIILSGIFFVTSADSGALVMGMLA
+TGGDVNPKTAVKIFFAIATAFMAAALLAAGGLSAIQTLAITIGLPFSVLMLVMCVATFRS
+LGYSAARVEAVRRQAMLASIQDRLGKDTDDDEVVEGGPVAASQWWASLSRDHQRTIARLA
+SPGPDDEIRLHEDATATSARPDTTRGGSTAR*
+>NZ_CP097650.1_134
+MSDPTPPLKNPLDPERADTRPSSAPTADGAVAPATSAAAARDRVLLPWVFWPSAVIVLSF
+VGATLLAPEQMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK
+PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDVAAANPTQAEAAQSALATTFL
+HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSN
+TNLILAAGLLLFIAIVGPTAFLLKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS
+AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR
+PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA
+TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS
+LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA
+AGVPASEGPRRTRLRRHGH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000275.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000275.fa
new file mode 100644
index 0000000000000000000000000000000000000000..398c56af4802bb29ff41669b37a1b6260acc6b4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000275.fa
@@ -0,0 +1,37 @@
+>NZ_CP042169.1_134
+MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE
+DALAGGERAKLDRYGEDSFMVLHPARYIDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA
+AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR
+RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL
+SEQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNSALELDSTLASKRLAEQSIAQNEQ
+VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW
+L*
+>NZ_CP033200.1_2104
+MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE
+DALAGGERAKLDRYGEDSFMVLHPARYVDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA
+AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR
+RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL
+SDQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNNALELDSTLASKRLAEQSIAQNEQ
+VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW
+L*
+>NZ_CP040019.1_234
+MIDNAVYVDGRRVHAPSTLEDTWEAAEASGGMAWLGLYRPDADELRAVADELHLHPLAVE
+DALEGGERAKLDRYGEDLFMVLHFQHAIRALPVIVEQLQGGARARLREEEHRREVGAPRT
+GDVHEWDQDELSEEGVFEVENLRRLRDVHDHAVQINERVAAMRQMLANALELDSTLASKR
+LAEQSIEQNEQVKQISSWAAIIFAPQLVGSIYGMNFDGMPELHWAFGYPFALGLMLAVAL
+TLFVLFKRADWL*
+>NZ_CP083691.1_168
+MTLIDNAVYVDGRRVFAPTSLSDTWDAIERTGGMAWLGLYRPHPDELQEVADELPLHPLA
+VEDALTPGQRAKLERYGDDWFMVLHPARYIDATETVEFGELDVFTGKDYVVTVRHAEEPD
+LADIRAGMEQRHTDRLAQGPSQVAFEILDHVVDAYFPVAEGLEQDIREIEDQIFSGDAAV
+SRRIYELSREIIGFERATRPLPRMIEQLQEDMRARLGDAANGSHASHLEAPEPEPGEEER
+AELVETLRALRDIHDHAVQVTDRVAAMRQMLENALELDSTLASKRLAEQSIAQNEQVKRI
+SSWAAIIFAPQLIGSVYGMNFQHMPELEWPLGYPWALGLMLGVAVALYALFKKADWL*
+>NZ_CP097650.1_142
+MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE
+DALAGGERAKLDRYGEDSFMVLHPARYVDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA
+AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR
+RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL
+SDQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNNALELDSTLASKRLAEQSIAQNEQ
+VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW
+L*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000276.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000276.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1acf63f47c3cae841da65b86ca5a5510b331b311
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000276.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_135
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR*
+>NZ_CP033200.1_2105
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLATRGPAVTGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR*
+>NZ_CP040019.1_233
+MNSPRHAAPVVRDGRTLLPAHAVTTAPIAAFGLIGGYLTARETGIRPLGGVVLAAAGAYA
+GRTWLAKRGPAVAGGLTALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDREGA
+R*
+>NZ_CP083691.1_167
+MSKDTSTPVARDGKTLLPADAVTTAPIAALGLVGGYLVARETGIRWLGGVVLGAAGLYAG
+RTWAAKGGPAVAGTLGALYLGGFGASHPLAKKIGAWPSVLSVAAASAGAAYAAVDRKDGR
+R*
+>NZ_CP097650.1_143
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000278.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000278.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8115e56563b507164500b485cabbbca3c9debe8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000278.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_137
+MRAEQVTDPIAYHGEGPVWAASWGAAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTLAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG*
+>NZ_CP033200.1_2107
+MRAEQVTDPITYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG*
+>NZ_CP040019.1_231
+MRAEQVTDPITYHGEGPVWAEHWGTAASGLAAGGGLRWVDMLAGDVLSLRADGAVERTHV
+GDVAAVVRPRAGGGAVLAVERGFALMSPEGELTTLPELWGPEAGLRMNEGGCDPDGRFHA
+GTMAYAKTPGAASLHRLSPGPDGGAGEVDVVLTGATTSNGLEWSPGGSLAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGEDLGTLYITTSWENMERGEDPLAGALFAVRPGVTGLPARPFAS*
+>NZ_CP083691.1_165
+MRADQVTDPLCYHGEGPVWAESWGGLRWVDMLAGDVLSLGADGGVTRRNVDPKVCAVVRP
+RVGGGAVFAVERGFALEDPDGTLHRLPPLWDDAAGLRMNEGGCDPDGRFYAGSMAYAKTP
+GAASLHRLSPAPEGGAGEVDVVLEGVTTSNGLAWSPDGSLAYYDDTPTRQVAVFDYSREE
+GLTNRRVLVDVLDGEGKPDGLCVDAEGGIWVAVISHGRIHRYTPEGVLDEVVEVPVQKTT
+ACTFGGDDLGTLYITTSWEGMERGEDPLAGALFSVRPGVAGLPTLPFAG*
+>NZ_CP097650.1_145
+MRAEQVTDPIAYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRTDGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000283.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000283.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17243551d6ec5b6395e9695f6ffb56e1709122ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000283.fa
@@ -0,0 +1,39 @@
+>NZ_CP042169.1_143
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSASASASPSPSTSGD*
+>NZ_CP033200.1_2113
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSASASPSPSTSGD*
+>NZ_CP040019.1_224
+MREARESASAEGTPRAQPRQALETLGPGIRDGAATTAWENTAAVRNDTVSVMDCTRDVLD
+QRTLDAVATHIPDGSNIEIVQLFAAQDETHEFLTCAYNGYFEYSPGMPLAQVQYQHNLDS
+TRLDWCEDEPATVADEYTFDPETGKGLLALLRPGMIGGQDGAPLMPQRTAWACSEDGTEL
+VSVTMGSMEGYGDANGGLTQVENSPVAGSTTLVTEARDHLADTVLKDASRFHEVIKLSSP
+FFLNASMDEESLAKAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPPRPFQGAAREA
+AESQRAAEASASAAEASASRAASGSGTPSPSSTPASRTPSPSGTGG*
+>NZ_CP083691.1_163
+MTHPTSAPHRAAAALGAAALALTLAGCSDSGQPSPASSTSTATAAAGSSASATGDPQSPA
+SAAASEIRAARASEKADGSERPQPREALETQGPGITSGAASAGWKSVAARYNDTVSVMDC
+TQDVLDQTTLDAVATHIPVANDIGIVQLFASRDQTHEFLTCQYQGSSSRSEGAPLVMVHY
+QHNLDGRRLEWCRPEAPVMADEYSYDESTRKGLLALLRPGMVGGADGAPLLPQRTAWACN
+EDGTQLVSVTFGAMKGYGSVNEGLTQVTNSPIANSTTLATQARDHLADTVLKDPSDFQAD
+IETSSPFFLNAQTDQETLDKAKGLPTGIIPQDQLSDQSTIDRPEGAPEPVAPGQPPRPFV
+GAARDAAESAAAESAASSSGSDSASPSDDGDGNPVVSESGTPSPSNTTD*
+>NZ_CP097650.1_151
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSTSASPSPSTSGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000284.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29a09fcf2b5bf523d435efe78e3654298f266a0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000284.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_144
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEAGQGRARG*
+>NZ_CP033200.1_2114
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNHGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEAGQGRAQG*
+>NZ_CP040019.1_223
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDVVPVAPESSLVWALMAEDAWSEGR
+TVDSYAYARVGYHRGLDALRKAGWRGAGPVPYDHEPNRGFLRALYSLGRAAAGIGESEEV
+ERIRTFLKDSDPTAAEKIEATQGRSGS*
+>NZ_CP083691.1_162
+MSESLIGKNLMEPPATLLPEEPEVLARLDAGDLPEDLVPLAPESSLVWALMAEDAWSEGR
+AVDSYAYSRVGYHRGLDALRRAGWRGAGPVPWSHEPNRGFLRALYALGRAAAGIGESAEV
+DRIRTFLKDSDPTAAQQIEAAQA*
+>NZ_CP097650.1_152
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEADQGRAQG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000285.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7960334e3904aa072632c1d122a09376f0d5a835
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000285.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_145
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG*
+>NZ_CP033200.1_2115
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG*
+>NZ_CP040019.1_222
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEDEVVSRLGVTRTVDF
+LVPAGAGVRELFRRHASGDDPDALVDHVDAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRCFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVNPATGAEHF
+VFEGDQVAIDGVEVTYESLCGSCYLAESGGRLG*
+>NZ_CP083691.1_161
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPAVDTKGDAAVVSRLGVTRAVDF
+LVPAGADVLALFRAHAAGDDPDALVDHVDAPPVACLLVDEAQFLEAGQVDDLLRIAVLED
+VPVMAYGLRTDFRTHSFPGSARLLELAHSLEELKTICRCGRKAVLNTRKVVDAATGRSRF
+VFEGDQVAIDGVEVTYESLCAACYLEESGGRLG*
+>NZ_CP097650.1_153
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000287.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000287.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1f33d062e5f18f8716edefa13a87d18de3eceb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000287.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_161
+MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR
+LADRWERQLEIACGKPTAEATSMERLTAYILTCSTAASRAEFQMILDSQHTQHMAIWEDL
+IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV
+HESEAKPNG*
+>NZ_CP033200.1_346
+MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR
+LADRWERQLEIACGKPTAEATPMERLTAYILTCSTAASRAEFQLILDSQHTQHKAIWEDL
+IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV
+HESEAKPNG*
+>NZ_CP040019.1_2288
+MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR
+LADRWERQLEIACGKPTAEATPMERLTAYILTCSTAASRAEFQMILDSQHTQHKAIWEDL
+IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV
+HESEAKPNG*
+>NZ_CP083691.1_660
+MAKTTEQLLDDAIAVLRRGGVVTIDSVASEAGMSKAGVVHHFSSKEALMVGVVNRVMDLW
+EGQLAATIGEVTDPVERLRAYVDFEVLSDFDGGDLALLADVKLRDTLAAQWRERLRPWFG
+EDAPGDAGQKAALQSARLIADGAWTDQALGLLSMTGEQRALVRGIAQRLIDEGVQK*
+>NZ_CP097650.1_1956
+MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR
+LADRWERQLEIACGKPTAEATPMERLTAYILTCSTAASRAEFQMILDSQDTQHKAIWEDL
+IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV
+HESEAKPNG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000289.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000289.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7874aac147948cefe589378ea4e1566e5deb9df9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000289.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_172
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNAVPVIGNGVVVNLEALFEEIDGLESRGHSCEHLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS
+NPTAGGAAVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT
+GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ
+TEFHHAKPVYEHFDGWTEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV
+VQVRDLIQD*
+>NZ_CP033200.1_2124
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNAVPVIGNGVVVNLEALFEEIDGLESRGHSCEHLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS
+NPTAGGAAVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT
+GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ
+TEFHHAKPVYELFDGWTEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV
+VQVRDLIQD*
+>NZ_CP040019.1_213
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNATPVIGNGVVVNLEALFEEIDGLESRGHSCAHLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEVAEYFLGYAERLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS
+NPTAGGASVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT
+GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIESIPVCVAYDVDGVRHDRMPMTQ
+TEFHHAKPIFEHFDGWTEDISGAREFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV
+VQVRDLIDG*
+>NZ_CP083691.1_159
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNAVPLIGNGVVINLEALFEEIDGLEARGHSCANLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATFLDVDHGTYPFVTSS
+NPTAGGASVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRMTGGEFGVNT
+GRPRRTGWYDAVLAHYAARVNGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ
+TEFHHAKPIFEHFDGWTEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDEV
+VQVRGLIED*
+>NZ_CP097650.1_169
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNAVPVIGNGVVVNLEALFEEIDGLESRGHSCEHLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS
+NPTAGGAAVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT
+GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ
+TEFHHAKPVYEHFDGWAEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV
+VQVRDLIED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000292.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000292.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27797988d1d2de61d70a81876e6fbaee3f2cca14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000292.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_175
+MTINADGSHAVQPHTANAHTTPARPVRHAVVEEEVLEPLRPVDGWGFTNRVILVSVLVVI
+IGNVVRVLTGGLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVVYGSGVHLFWMLPVAGLLGGLWAGLVSSRR*
+>NZ_CP033200.1_2127
+MTINADGSHAVQPHAANAHTAPARPVRHAVVEEEVLEPLGPVEGWGFTNRVILVSVLVVI
+IGNVVRVLTGDLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVLYGAGLHLFWMLPVAGLLGGLWAGVVSSRR*
+>NZ_CP040019.1_210
+MTINADGSHAVQPHSANAHTAPASPARHAVVEEEVLEPLRPVDGWGFTNRVILVSVLVVI
+IGDVVRVLTGGLGDPNGSVALGETGRGWVVLVQSFMFGLVGGALAGAAGYLIVLLMGGAA
+RSVVPYVVGGVVGGFLGAVGVFAVFSNTALYGSGLHLYWMLPVAGLLGGLWAGVVSSRR*
+>NZ_CP083691.1_155
+MNTQAHGAHAVQTVGGTAAPQAPARRAVVAPEAVEPARPVDGWGFVNRILVVATVLIVAF
+ELWRAATGLLSDGPRVLGEDGVGWVAVLEAFMFALVGGAIAGAAGYGIVLLMGGAARSAA
+RYAIGGLIGGFLAAVGVIFVFSNTAALSVGGHLFWMLPLAGLIGGVWAGITSAKS*
+>NZ_CP097650.1_172
+MTINADGSHAVQPHAANAHTAPARPVRHAVVEEEVLEPLGPVEGWGFTNRVILVSVLVVI
+IGNVVRVLTGDLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVLYGAGLHLFWMLPVAGLLGGLWAGVVSSRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000293.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000293.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91f1b7cbf04afd1e334c5ae9db1991a4e0446a97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000293.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_176
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVATPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKARS*
+>NZ_CP033200.1_2128
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATGELAHLLGAADTPRERPADSPGKPKASS*
+>NZ_CP040019.1_209
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPASAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATDELAHLLGAADTPRERPADSPGKPKASS*
+>NZ_CP083691.1_154
+MPTTPPASTRTVDRALALLAAVVAQPRLSLAEAARATDLPASTALRLLRSLETAGFVDRQ
+EEGEYRPGARLIQLGARAFSREPLVRLARAPMDGVAEATGESVYLSLRNGAQEAVYIAIV
+EGTHSVRHASWVGRTVPLEGTAVGEVYRGEVPPGGYAHGGHSVEQDVTALSSPVVVGGRV
+VAALSALVPDYRCTAEHADRCGRALAGATTRLASALGEEAPPEDAD*
+>NZ_CP097650.1_173
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKASS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000295.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000295.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c1137838d587d9b14ebe3bfe4856773e69eaa68
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000295.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_178
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF
+GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPEQAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLGARFVIGVVCVSAIIFFSAVVPAI
+LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT*
+>NZ_CP033200.1_2130
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF
+GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAAGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLVVTFAVTAITVRIPPLSRIPDEVYPGAVHSPELAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPIPLWKLVVIWAERVALTILLAMPVAHLVAALT*
+>NZ_CP040019.1_207
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIATGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF
+GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFSALVVTFVVTAITVCIPPLSRIPDEVYPGAVHSPEQAVTRDRFRVALRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGMIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT*
+>NZ_CP083691.1_152
+MTHAHPADGELHTDTTAMAAIEADSPRPPARWRMVVYSLIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRYVALALIAAGAVFPFATGRWRQSVTTTVFAFLGVVGLLTACMVVF
+GFGPSWVLDKGIGPFLLDKLVIPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+DLMDHWLWYFFGTLVVTFVVTAITVRIPPLSRIPDEPFPGAVHVPEEAVTQDRFRVARRA
+AEQTLAEAPSLGRNVWLNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWVGLIFQPV
+FWALGFSDPALMASASATSIAEMFIPATMLAGHEDFVARFVIGVVCVSAIIFFSALVPAI
+LATDIPVKLWHLVVIWVERVVLTVLLATPLGHLVAALTS*
+>NZ_CP097650.1_175
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF
+GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPELAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPIPLWKLVVIWAERVALTILLATPVAHLVAALT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000296.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000296.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1806e5a45f0570f21954e19c421cd2aa464c9b9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000296.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_179
+MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPEADDRVSVEGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDARLAELVRGRVADAVA
+GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLAAVREHVGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDADVEALAGTWADWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGALGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV*
+>NZ_CP033200.1_2131
+MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPEADDRVSVEGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDARLAELVRGRVADAVA
+GGTTYLETKTGYGLTVAEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLAAVREHVGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDADVEALAGTWADWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV*
+>NZ_CP040019.1_206
+MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPDADDRVSVEGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDDRLAELVRGRVADAVA
+GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLEAVREHAGWADVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDTDVEALAGTWTGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGALGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV*
+>NZ_CP083691.1_151
+MASTLITDIAELTTVDPEGRVLRDAAVVLDDEDVAWIGPAAQAPAADERVSVAGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGLTMEATRAASDERLRELVLGRVADAVR
+GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDVEDYLDDVV
+GPMLEAVREHVGWVDVFCDTGAFDAAQTRRVLAAGVAAGLRARLHGNQIEQGPGVALAVE
+FGAASVDHVNHLSDADVEALAGTWSGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV*
+>NZ_CP097650.1_176
+MRSTLITDIAELTTVDPEGRVLQDAAVVVEDERIAWIGAAADAPDADDRVSVGGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDDRLAELVRGRVADAVA
+GGTTYLETKTGYGLTVAEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLEAVREHAGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDADVEALAGTWTGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000297.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000297.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b20c4681c683f4cfedb92236192655bba42ceb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000297.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_180
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGTDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH*
+>NZ_CP033200.1_2132
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGEDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH*
+>NZ_CP040019.1_205
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGADGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAWKSEGTEAEGH*
+>NZ_CP083691.1_150
+MTTTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTG
+FGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVV
+VETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGADGALRPAGEALAE
+AGIEPVELREKEGLALVNGTEGMLGMLIMALADLDELVDTVDLTAAMSVEALLGTDRVFV
+PELHLPLRPHPGQAASADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTL
+AYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTD
+RMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQEDH
+VSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGVPGP
+GPDQYMAPQLAAAEQALRDGSVLAAVAEALAGASADAEPQDLAEESAGAEAEGH*
+>NZ_CP097650.1_177
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGTDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000301.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000301.fa
new file mode 100644
index 0000000000000000000000000000000000000000..688f81752cfc50cbc6ea93b53f2597cde8c2fd94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000301.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_188
+MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGIPDPCAPDGAAAL
+VRLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRTDLDGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIADGDHLVRPPWTPTGRADPVATVSELS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRGARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG
+LVRRRLARTR*
+>NZ_CP033200.1_2140
+MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGIPDPCAPDGAAAL
+VRLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRTDLDGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIADGDHLVRPPWTPTGRADPVATVSELS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRGARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG
+LVRRRLARTR*
+>NZ_CP040019.1_195
+MTARAPLPPALARAAFGVDELLDAGLPWDRTRAADLHRIWRGVYTAADPAALTWDRAAAL
+CRVTGGVISHTTAAAWHGIPLPRRLEASEELHLTVDRGRRQHRSARPGVVTHRLRLPPQE
+IRQVGGGLRVTSPERTWLDLAVLLRPWELDWLVVAGDHLVHHPWHPDGRRPSATTPALLD
+AALGRHVGRHGIRRAREALADVRVGADSAPETRLRLALIRAGLPEPALQIAVDPSDPRSP
+EADLGYRDARIALQYDGAAHRTPEQQARDARREAYCLELDWLPLRCTQEDLREGFIRVIG
+LVRRRLGPRGAFGATSRR*
+>NZ_CP083691.1_143
+MTARTPLPPALAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGVPDPCAPDGAAAL
+ARLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRSDLGGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMFRPHEVDWLIAAGDHLVRPPWTPTGRADPVATVPGLS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRAARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG
+LVRRRLARTR*
+>NZ_CP097650.1_188
+MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGVPDPCAPDGAAAL
+VRLTGGVVSHVSAALWHGLPLPPRLTRPAGLHLTFDRSARTHRTDLGGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIAAGDHLVRPPWTPTGRAHPVATVPGLS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRGRAWPSSTTAPATARLSSRRGTPVGTRTASSGNGRPCAAPGRTSALGSGGSWG
+WSGVGSPARADPPPRPTRVELSRVPSNAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000307.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b3b85fa7bd2a88af5a3f3fd4b76a7f97e538a65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000307.fa
@@ -0,0 +1,27 @@
+>NZ_CP042169.1_201
+MAAAPCLGRQQPQEENMQRRRAVRAAGLGVVGALALAGCASEPQSAGEAWHQARTQLDEA
+ETVRLETAYTTGRQGPHSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR
+VDVDGSDVPDDVQVMYSDPQWRRVPAGEGQEPPLKALLDQVGFPAADALDGAEVRAEEVD
+WDDGTAYRYAVPEEVADAAMVEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ
+IEPAEAPEEVAE*
+>NZ_CP033200.1_2150
+MQRRRAVRAAGLGVVGALALAGCGSEPQSVGEAWHQARTQVDEAETVRLETAYTTGRQGP
+QSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVRVEVDGSDVPDDVQLMY
+ADPQWRRVSAGEGQEPPLKSLLDQVGFPAADALDGAEVRAEEVDWDGGTAYRYAVPEEVA
+DAAMAEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQIEPAEAPEEVAE*
+>NZ_CP040019.1_174
+MQRRRAVRAVGLGVAGVLALAGCAAEPQSAGEAWQQARTQLDEAQTVRLETAHTTGRQGP
+NTVRWDIAGRLDGSNGDAKGVIQAGHESHMTMETRTVGEDSYVRVSIDGADFADDVQLAY
+ADPQWRRTPAGQEQERPLKELLEQIGLPSADALEGAEVRAEEVGWAGETAHRYAVPQEVA
+AAAMGQGDSTLLHSFTVDDDGGLLALTVDDGRSLRQYALSDWNEIDPAEAPEEVAE*
+>NZ_CP083691.1_120
+MQRRRAVHAAGLGVVAALTLAGCGTDQQDVGEAWQHARAQIDGAESVRMTMASVNDSQGP
+SVVAWDVAGPLEGADGTTTGRMQVGRDSWMTVRSVSADGKTWARVDTEGQDVPEQIASMY
+RTDGWTETQQSGQNALRATLDAVGLPAADALDGVDVQPEKVDWSGGTAYRYAMPGDVASA
+ARGDSQFSVRAFTVDEDGDLVGLRVEDGGVIQEFALSDWNEIEPAEAPEEAQH*
+>NZ_CP097650.1_201
+MAAAPCLGRQQPQEENMQRRRAVRAAGLGVVGALALAGCASEPQSAGEAWHQARTQLDEA
+ETVRLETAYTTGRQGPHSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR
+VDVDGSDVPDDVQVMYSDPQWRRVPAGEGQEPPLKALLDQVGFPAADALDGAQVRAEEVD
+WDGGTAYRYAVPEEVADAAMAEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ
+IEPAEAPEEVAE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000309.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000309.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09b3ddf3d49513c4ff4a26fccefdae73aa2c0efe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000309.fa
@@ -0,0 +1,19 @@
+>NZ_CP042169.1_203
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNITSAARHGAEPDTISDPSTPLGD
+EGPLTR*
+>NZ_CP033200.1_2152
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNITSAARHGAEPDTISDPSTPLGD
+EGPLTR*
+>NZ_CP040019.1_172
+MRLITLGLGAALGYLLGSAEGRRNLEKMSQNAQKFWNDPKTQQKVGNLQETAQQKFADVK
+NSEQVQKATAKVEDTMNKNGSKDQVRDDRVTESNNENTTTASAHGADPDIVSDPSTPLGD
+EGPQTR*
+>NZ_CP083691.1_118
+MRWFTLAVGAAAGYLLGSAEGRQNLQKMTANAQKVWNDPKTQDKVGVVKDKAQVVASDAK
+DKAASAASDAKQAVQEKTSSNQPSPASNNETVTTGNAHGADPDVVSDPSTPLADEGPAA*
+>NZ_CP097650.1_203
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNVTSAARHGAEPDTVSDPSTPLGD
+EGPLTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000310.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000310.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d465eb04b42fb1eb43a7b86330da51d5b36832e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000310.fa
@@ -0,0 +1,70 @@
+>NZ_CP042169.1_204
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQDL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG*
+>NZ_CP033200.1_2153
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQDL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG*
+>NZ_CP040019.1_166
+MSQQFSIETVADAAANPDIEQPWAELGLKENEYAQIREILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGLGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFAGSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPDNVAAFEAVMAKWDVEYSWL
+GEVTGDGRLVITWDGEVIVDVDPRTVAHDGPVYERPYARPGWQDRVQADTFRASEAGADL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTAMAAPDDAGVVRVDEETGMGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPENPDVMWQFAEA
+VRGLADGCQVLGIPVTGGNVSLYNQTGATPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGVPPKVDLAKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRHGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYTVTRIGVVDADSAALEVQDAFTLPIAELREGWEATLPKHFG*
+>NZ_CP083691.1_115
+MSTQFTIETVEQAAANPDVAQPWAELGLKEDEYARIREILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGDTLTEEMKEHMMVGIGENAGVTDLGDGWAVTFKVESHNHPSFVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAVDHPDTARVVHGVVAGIGGYGNSLGLPNI
+GGEVAFDPSYQGNPLVNALAVGVLRHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDDGGKPAKRPSVQAGDPFAEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEHSWL
+GEVTGDGRLVITWDGETIVDVDPRTVAHDGPVYERPCHRPSFQDALQADTFRSSAAGQDL
+PATGEELKAAVVELMASPNMADVSWITRQYDRYVRGNTALASPDDAGVVRVDEETGMGVA
+VATDCNDRYAYLDPYAGAQLSLAEAYRNVTTTGAVPLAVTDCLNFGSPEDPEVMWQFAEA
+VRGLADACQVLGVPVTGGNVSLYNQTGGVAIHPTPTVGVLGRFDDVLRRTPSGFGTDADG
+QAVYLLGVTADELDGSEYANLRGHLGGVPPKVDLAQERLLGELLVNMSRDGMVDAAHDVS
+KGGLAATLADMVLRFGVGARIVLDEVVRRDGVDVFTALFSETQGRTVVSVPRTEEVRFTD
+MTTARGYTVTRIGVVDAQSDALEVQGQFTLPIAELREAWEATLPKHFG*
+>NZ_CP097650.1_204
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQHL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGMGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPITELREAWEATLPKHFG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000311.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000311.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6035500c4b39e46cd39497431b6b7a7564206778
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000311.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_205
+MTELPLIGDYSTPATPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT
+LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQELVVESTDTVWTRDFEQGQTITVPLKNQDGQYVADET
+TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVETGFGPDTAAGP
+RSGVDGLGFFTSVLTTLASRGGHA*
+>NZ_CP033200.1_2154
+MTELPLIGDYSTPTTPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT
+LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQELVVESTDTVWTRDFEQGQTITVPLKNQDGQYVADET
+TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVETGFGPDTAAGP
+RSGVDGLGFFTSVLTTLASRGGHA*
+>NZ_CP040019.1_165
+MTTDLPLIGDYSTPTTPLNGARIGVITFPGTLDDVDALRAVRLTGAEPVSLWHADEDPQR
+TLAGVDAVVIPGGFSYGDYLRAGAISRFAPMMDAVATAAGGPEGAADGLPVLGICNGFQI
+LTESHLLPGSMIKNDHLHFICRDQELTVENTDTAWTRDYERGQTITVPLKNQDGQYVADD
+ATLDALEAEGRVVFRYRGWNPNGSRRDIAGIANAAGNVVGLMPHPEHAVEPGFGPDTADG
+PRTGTDGLGFFTSVLTTLASRGGHA*
+>NZ_CP083691.1_114
+MTEIPLIGDYSTPSTPLNGARIGVITFPGTLDDVDALRAVRLTGAEPVSLWHAEADAAAT
+LATVDAVVIPGGFSYGDYLRAGAISRFAPMMGAVAQAAGGPEGSEDGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQQLAVESTDTAWTRDFEQGEVITVPLKNQDGQYVADEK
+TLDALEAEGRVVFRYVGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVEAGFGPDTEAGP
+RSGTDGLGFFTSVLTTLATRGGAA*
+>NZ_CP097650.1_205
+MTELPLIGDYSTPTTPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT
+LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQELVVESADTVWTRDFEQGQTITVPLKNQDGQYVADET
+TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVEPGFGPDTAAGP
+RSGVDGLGFFTSVLTTLASRGGHA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000316.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000316.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1349dce249e09d054728607c02487f6e9c4892d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000316.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_213
+MPEPHTAPAPSETLPPAVVALPADVWRAHARAHRERIARRTDPLVALRMRGQKHPVQDFL
+FGYYTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGATPRGEWKHYRRVEAGEVAGAV
+VDGRPVGGWLVDVAAVLADRASGVAFTRELLARTAERAPRLGCFGLHEWAMAYRSDVHGV
+RHSQLPLRLGAEGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMRKMEQ
+PGCLHAGMDLYKWAYKLVPVVDSDLLADCFDLAWDIRRLDMEASPYDLTGVDDLSDGRGG
+YAAVRIEEPAGRAEYARRQREFAARGQSLRVRLLAVLDAAAGAAPGARPDTEWTSSARP*
+>NZ_CP033200.1_2182
+MPEPRTDPAPPPTAVVALPADVWRAHARAHRERIARRTDPLVALRMRGEKHPVQDFLFGY
+YTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGTTPRGEWKHYRRVEAGEVAGAVVDG
+RPVGGWLVDVAAVLADRASGVAFTRDLLARTAERTPRLGCFGLHEWAMAYRSDVHGVRHS
+QLPLRLGAGGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMREMEQPGC
+LHAGMDP*
+>NZ_CP040019.1_151
+MAGTCLHTPPPSPAAPRTAPTDPTAVVVLRPEEWLARSAAHRERIEARTAPLLELHGRGE
+RHPVQDFLFGYYTHSPAALARWHPGAGVVLADPDGAAAAAEAERDGAPHRGGWRHLRATE
+PGEIPGAEPDGRPTVGWTVDADAFAADRATGIAFTAELLERTAARPARLGCFGLHEWAMA
+YRSDLHGVRHSRLPLRLGAEGTDAVVESQRIRCTHFDAFRFFAPEARGLNEGADGVLPTR
+AGMRDMEQPGCLHAGMDLYKWAYKLLPWVSSDLVADCFDLAWDIRALDMRASPYDLRGVT
+DLAGGDYPPVRIETPEGRAEYVRAQRGFADRGQALRARLLAALAPLLGDDARG*
+>NZ_CP083691.1_109
+MTSAAPSPVPLVLAPEDWRARARAHRERIAARTAPLMARRTRGEPHPVQDFLFGYYTLTP
+GALQRWHPGAGVVLADDDGAAATAEAAELGTAPRGEWRHWRRVEPGEVVGVVLDGREVGG
+WTVDVPAFLADRASGVAFTRELLERTAGRPARLGCFGLHEWAMAYRSDVHGVRHSQLPLR
+LGAAGTDAVVEDQRIRCTHFDAFRFFAPEAVPLNEGAEGVQPTRAGMRDMEQPGCLHAGM
+DLYKWAHKLLPLVDSDLVADCFDLAWDIRRLDMEASPYDLTGVDDLSDGLGGYTPVRIET
+PEGRAEYARRQRGFAERGQALRARLLAALEAGARAAGDRRPTEDPSTPDPEEHHG*
+>NZ_CP097650.1_214
+MPEPRTAPAPPPTAVVALPADVWRAHARAHRERIARRTDPLVALRMRGEKHPVQDFLFGY
+YTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGTTPRGEWKHYRRVEAGEVAGAVVDG
+RPVGGWLVDVAAVLADRASGVAFTRDLLARTAERTPRLGCFGLHEWAMAYRSDVHGVRHS
+QLPLRLGAEGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMREMEQPGC
+LHAGMDLYKWAYKLVPVVDSDLLADCFDLAWDIRRLDMEAAPYDLTGVDDLSDGRGGYAA
+VRIEEPAGRAEYARRQREFAERGQALRARLLAVLDAAVGAAPGTGPDAEWTSSSARP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000317.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000317.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c5299a618a52a615dda592e396003ac690fbf79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000317.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_215
+MSLIVQKFGGSSVADAAGIQRVARRIADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR
+VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW
+IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI
+DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG
+MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAESKLDDAVRAVHAAFGLDAEEEA
+TVYGGTGR*
+>NZ_CP033200.1_2184
+MSLIVQKFGGSSVADAAGIQRVARRIADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR
+VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW
+IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI
+DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG
+MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAESKLDDAVRAVHAAFGLDAEEEA
+TVYGGTGR*
+>NZ_CP040019.1_149
+MSLIVQKFGGSSVADAAGIQRVARRVADTVRAGHRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMMTDTSYGRARIVKVNPHR
+VQEALDAGGVAIVAGFQGVSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPSARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPIHVRSSFSDHEGTW
+IMPDPNDTITLKEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAESNVNI
+DMIVQNVSREGSGTTDISFTLPIVEGKDAMAALRAAQERIGFQDIVSDKEIGKLSLIGAG
+MRSNPGVSATFFKALSDAGVNVDLISTSEIRISVVTAEDKLDDAVRAVHTAFGLDAEEEA
+TVYGGTGR*
+>NZ_CP083691.1_107
+MRLIVQKFGGSSVADAEGIQRVARRIVATQQAGNQVCVVVSAMGDTTDELLDLAAELTAD
+APAREMDILLSAGERISMSLLAMAIDAQGVPARSFTGSQAGMMTDAAYGRARIIEVNPHR
+VRAALDEGAVAIVAGFQGMSRESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVSSARKLPQLSSEETLELAASGAKVLHLRSVEYARRFGVPIHVRSSFSDHEGSW
+IMPDPNDTIHLKEGAPMEQPIVAGVAHDRSEAKVTIVGVPDVPGKAAEIFRVIAESNVNI
+DMIVQNVSRQDSGRTDISFTLPIVEGKAAIEALRAAQESIGFEEIVPNKEIGKLSLIGAG
+MRSNPGISATFFKALSDAGVNVDLISTSEIRISVVTSEDKLDDAVRAVHTAFGLDTDVEA
+TVYGGTGR*
+>NZ_CP097650.1_216
+MSLIVQKFGGSSVADAAGIQRVARRVADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR
+VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW
+IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI
+DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG
+MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAEDKLDDAVRAVHAAFGLDAEEEA
+TVYGGTGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000320.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..642c866ba9334b15b5fc77b8f84e7a2280a867c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000320.fa
@@ -0,0 +1,107 @@
+>NZ_CP042169.1_219
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV
+RLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADITNLALTDMVGATSPRLHLELLMA
+RLLLPASDETHRGLAARLEALERRLELGGAAPVEDGAPEGTTTPARSGTPAKDGGGSAGD
+ADGSGPLTGAALARAAMRRPEEPAPTAPTAPPERWTPPAPQSVAEAPEGDAAAGATGSER
+PQQPPQPKRPEPAEVGARSGDTRRPEAGSRAEPEGRPEGRPQAQDRTGAAPSSPAPAPAA
+SQVEMIRRAWPDILTALEDASRLVWMLVKDNASVAGYDGSLLTIGFQQDGPRQSLLGRGG
+DRVLGEAVHQVLGIRPRLDLILGGDAPTGDARAQSGARPAGPARTDRPERPAPQQGRPDR
+PTAQPNRPAPAPGQAPREPESSRPTPPRSAAPSTAEDDPAPPAAPPRATQQRQTPEPSPA
+WTPAAPATSWGPTPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPEEDPWDSLPAFDPDA
+EQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAPAPGGAAPDAGQDSP
+VQPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELRAEFAKRFGATRPAG
+FDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSSDEQRRPTGAPTADA
+TPDPGVPADDADATPRTAAGPTGSDFPGSGHPASMYPRLMERLRAGGPLEPPVNAGSSGG
+GGTGGGPGAPGGPDPDASPGSPAGGRPSAASLGARPADVEPAGGASAPPSLDARAAAIHA
+AREAAQGRGPTRPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLVGRAVVERVLGGRLL
+EERPNDA*
+>NZ_CP033200.1_2188
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV
+SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLLLPTSDETHRGLAARLEALERRLELGGAAPVEEGAPEGTTTPARSGTPAADGGGSAEN
+AEGSGTLTGAALARAAMRRPEEPAPTASTAPPERWTPPAPQSVAEAPEGDAAAGATGSER
+PQQAPQPKRPEPAEVGARSGDARRPEAGSRPEPEGRPEPEGRPQAQERTGAAPAPAHGPE
+ETAAPSSPTPAPAASQVEMIRRAWPDILAALEDASRLVWMLVKDNASVAGYDGSLLTIGF
+QQDGPRQSLLGRGGDRVLGEAVHQVLGIRPRLDLILGGDAPTGDARAQSGARPAGPARTD
+RPERPAPQQGRSDRPTAQPNRPAPAPGQAPREPESSRPTPPRSAAPSTAEDDPAPPAVPP
+RATQQRQTPQPSPAWTPAAPATSWGPAPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPE
+EDPWDSLPAFDPDAEQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAP
+APGGAAPDAGQDSSVRPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELR
+AEFAKRFGATRPAGFDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSS
+DEQRRPTGAPTADATPDPGVPADDADAAPRAASGPTGSDFPGSGHPASMYPRLMERLRAG
+GPLEPPVNAGSSGGSGTGGGPGAPGGPDLDATPGSPAGGRPSAASLGARPADAEPAGGAS
+ALPSLDARAAAIRAAREAAQGRGPARPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLV
+GRAVVERVLGGRLLEERPNDA*
+>NZ_CP040019.1_145
+MSTALYRRYRPDRFEEVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAHLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQDGGVSYELAV
+SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLLLPASDDTHRGLAARLEALERRLELGGVPVASADESAGGTTTSARPGAPAAAGGGSAG
+SGGAGGGEPLTGAALARAAMRRPEVQEAPTPPAQETARSEKAPAQPEPTPMPSPVGQAAP
+PAQPAQSEHPRPERWAPPAAASSPEADAPAQRPDAARPEQPAQQDRPQRQTPPPAPAGQP
+EQRQQQTAQAERPTTTERPAERPAAGAPEASPASTRPQAAERAAERPQAEADAAGSAVPS
+SAAPAPTPSQVEKVRRAWPDILAALEDASRLMWMIVKDNASVAGYDGSLLTIGFQQDGPR
+QMLLGRGGDRVLAEAVHQVLGIRPQLDLILGGDAPQGGSRHAQGQAQTPSAPRAESRADA
+PTSRPDAGEAAPTRQDRPQQQGGEPDRGQQQDRGQQQGRGQASDLGPAQGGSPSGRPTGQ
+AAAPTPGRGPSSPAPAQRPTAPQAASTTPPGAPPSDGWGRADEEPPAWDDAPPPEEDPWD
+SLPEFDPDADMDDSDGPEGWTPPAAGQDDAPVGAAGWDGPVPAAEDWGAPPQGGAPAPDG
+RRDERPAAAQGSDAPSEQPTPQGSADAGPAAETDAEPSAEEVRRAYDPGPLVREEEHTIP
+VFARPEAELRAEFAQRFGATRPAGFDDGAGAGADAESTRAAAPSPGPDDLPPGQGDDPDA
+TARRDTHPAASASGPSSAADHGSSGEPTADGTPDPGVPAEDHEHTSASDADDDGSPERAA
+GSGHPASMFPRLMERVRAGGPLEPPVNAAPPGGATPPGGGPGGGAGPSGPGSAPGSDQGP
+RPGGAPSDAQGPGAPGPDAPRGGRPSAAALGARPGGETGSPAGASAPPSLDARAAAIRAA
+REAAQGRGPARPAGNGPAAPSAPAVGWEDEVASDDDVALEDSGLVGRAVVERVLGARLLE
+ERANSA*
+>NZ_CP083691.1_103
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLERLCQEEGVRVEPGVLPLVVRAGTGSVRDTLSVLDQLIGGAQQGQVSYDLAV
+SLLGFTPEALLDDVVDAIAADDTPTVFRVADRVVQSGQDPRRFVEDLLERFRDLVIARAL
+PDEASSILHGMPEDQVRRLAAQASQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLMLPATDDTHRGLAARLEALERRVAGGAAFSPDDDASSGAEGPAAGGAGQGGAALSGAA
+LARAAARRAEPEQAREQEPGAGSDKRAAEPATPKPATPEPVAAAPAPERPVERPAEAPAP
+SSSAPAAPAAPTAHTPSQVEKVRRAWPDILAALESDSRLMWMLVKDNATVAGYDGELLTV
+AFPQEGPRRTLQSRNGEQVLGEAVHRVLGIRPRLDLILGGDTPRGEERPKAEGRPAAAVS
+EAPAAPSTSAPPPAPQGQPTQAQPPRAQPSPEDGRRPAASAPRPQDVAVATSWDQAPAPS
+AAPWQPAPSRPAAASPAPQTGPAAPSTPDPRQDAHPGTRPGPADTTPPAAPPSDGWGHVD
+EEPPAWDDAPPPPEDPWDSLPEFDPDADMEDSPGPEGWTPGAGDDAVHGSAGSAPTSAPE
+AWGGAVPTPQDWGAPRPQDPVESPAPQGPEAGTQGTAPDAAAQGAPSPAAPAEAVPEDPE
+TARRAYDPGPLVREEELTIPVFAKPEAQLRAEFAARFGGTRPAGFDSTAASDAAAPDAQG
+PGAAARAAAHGEPVRGGQDAAEPAADREAEPEEDPQAAASAPEHPVRPSPARPTADDTPD
+PGVPQEDHAEDAAPPSATAPDDRGSGHPDSHYPALMERLRASGPLEPPVNARPAGQGGAR
+EEQVPAPVDAAPSPGRPSAASLGRPTGDPQAAIAPPAEDPRASGARAAAIQAAREAARGA
+GPRPADGAPGGPATASGPSVDWQDEVASDDDVALEDSGLVGRPVVERLLGARLLEERPLE
+PGL*
+>NZ_CP097650.1_220
+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_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000325.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000325.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cec0c142827d4a3698c232a33166cd66e38dbfb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000325.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_225
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAVVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLLAYAVWQFLASAQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLMWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR*
+>NZ_CP033200.1_2194
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAVVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLLAYAVWQFLASAQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLVWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR*
+>NZ_CP040019.1_130
+MSTATDLGPHRSTFGPDAAGRVPSSGTGLASTGGRVAMLLVVLAALVAAFLGAGVVAGFT
+PVAEASGGWLGPDATWVAPASPAFSIWSVIYAGLLAYAVWQFLPSAQSARHDRLRPWILV
+SVLLNAAWIWTVQLGLLGLSVVVIVLLLASLCRILMLLESARAHSWGERILLDGVQGLHL
+GWVSIATVANVAAWLASTGWTGDPFQPTTWAKIMIVVAVLVGAFTAVYDGGRPAPAFALA
+WGLVWIGVGRADGSGLLSGSLAVLAWGGAAIVLLCWVAALLLSRRSATGEARDLVLDALD
+GGDDPVDGRR*
+>NZ_CP083691.1_95
+MSTAIDAGPQGTVPIDAAQAPSSGRGLASPGGRWAMLAVVVLGLVGAFLGAGVLPGMTPT
+SDAAGGWLGADSTWIAPATPAFRIWSVIYLGLLAYGVWQLAGSAQSARHDALRTWIMASI
+VLNVAWLWVVQVGWLGLSVVVIFLLLAVLCRILVLLETGRPRGWAARILLDGVQGLHLGW
+VSIAAVTNVAAWLASLGWFGAPLEPTRWAQIMIVVAVLVGAFTAVYSGGRFAPAAALAWG
+LLWVGVGRSDGSGLLSGAVALTAWGAAAIVMLCWLVSLWLSSRSATGEARDLVLDALDGG
+GDPVDGVR*
+>NZ_CP097650.1_226
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAIVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLFAYAVWQFLPSGQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLVWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000329.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000329.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc935b9e301f68940e405d16878ecd5c76c0b486
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000329.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_230
+MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV
+ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT
+VSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELIGTVATSDADVRAAVALPAVASLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKI
+TDDGTAAERLVEFLAGRGLV*
+>NZ_CP033200.1_2199
+MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV
+ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT
+LSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELTGTVATSDADVRAAVALPAVAGLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKV
+TDDGTAAERLVEFLAGRGLV*
+>NZ_CP040019.1_125
+MKILVLAKQVPDTWQERELSLDTGWVVRDGAAEPVPDEISERVMEVALGWRDAGTDAEIV
+ALTVGPEDSSKTLRKMLAMGADAAVQVTDDALVGSDAVETARVIAAAVEREGADLVLAGT
+VSTDGGTGVVPAMVAELLDRPYLPHAEAPQLADGELTGTVATSDADVRAAVALPAVAGLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGAKV
+SDDGTAAQQLVDFLAGRGLV*
+>NZ_CP083691.1_90
+MKIAVLAKQVPDTWQERTLDMETGMAVRDGAAEPVPDEIGERVMEVALAAREAGLEAEIV
+AVTMGPADATKTLRKMLAMGADSAVHVVDDALDWSDAVQTARVLAAAVEHLGVDLVLAGS
+ESTDGATGVVPAMVAELLDRPLLPSVEAVEITPEEVRGVLVTEDARLRASVPVPAVVALT
+EKTAEPRFPNFKSIMAAKKKPLETLTLADLGLTAGPLDADRRSVMVSAAARRERAAGEKI
+VDDGTAGEQVAAFLAARGLV*
+>NZ_CP097650.1_231
+MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV
+ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT
+LSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELTGTVATSDADVRAAVALPAVAGLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKV
+TDDGTAAERLVEFLAGRGLV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000340.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000340.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62a959d222fd574510c80752d0ffdbf0481210b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000340.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_249
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYAWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMAAPTDVAVGKRLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEVRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG*
+>NZ_CP033200.1_2219
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYAWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMGAPTEVAVSERLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEIRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG*
+>NZ_CP040019.1_104
+MTHVAARARVPKKGLLVFLVVAAVLLLLGALTVVRGIAADAARVNIVSVVDGNTVVVNQG
+GTQRTLVLAGVTSAGRNPEGLKVGPELCMGEQSYAWLRDRLPQGAVASVDTSREGAPEGM
+ESALVHIGGKTVNVDMAEAGMTAPTGIGVDDDMAEEIAAANRVAVGRGVGLYDVEEPCTY
+QNRLYEAQFALDQIPKDAEDSIRRIDERSVEYAAGLDQVRLVQQEIQALDPENGTFEDLA
+YGPARESLLAEADPVVEEGLQVLRDLNARRNEIAARG*
+>NZ_CP083691.1_72
+MTHVAAQARVPKKGLIVFLVVAGVLLALGAASAVRGLVVARDTVEVVRVVDGNHVVVNAD
+GEERTLTLAGVRSAIRNPEGLRVGPEYCMGEEAYAWLRDRLPQGATVRVDRSDEGAPEGE
+QSAVFTVAGKEVNVDMAKAGMAAPTGLGVSGDLEEQIAQANQQAQTAGGRNNGVGLYNRD
+ETCTLGYQLYAAQTELEKVPTAPAANTVVEIDKKSVEYANALDAVRLVQQRIEGLDASSG
+DFTGLAYAPAKDRLLARANPVVDEGMQVLRDLNAQRNALAGG*
+>NZ_CP097650.1_248
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYSWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMAAPTEVAVGKRLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEIRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000344.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000344.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f9b6615f49de1dc0ce69b98188dc95f42dbae50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000344.fa
@@ -0,0 +1,22 @@
+>NZ_CP042169.1_256
+MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLSADASLWILGALLALE
+LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV
+VAVVVGLWLLARRFRARRTRGRAAAVPGGPEWTA*
+>NZ_CP033200.1_2225
+MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLSADASLWILGALLALE
+LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV
+VAVVVGLWLLARRFRARRTRGRAAAVPGGPEWTA*
+>NZ_CP040019.1_91
+MLEFLTGTGLATSAGLNAYIPMLALGLLDRFTGLVDLPAGWTWLSADASLWILGVLLLLE
+VVADKFPGVDAVNDAVQTVVRPAAGGIVFASGVGTETTAVHDPGTLFGGSGWVSVLIGAG
+IALAVHLAKAGTRVGANTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLVVAVVVG
+LWLLARRFRARRTRGRAAAAAGGSEWTA*
+>NZ_CP083691.1_62
+MLALGLLDRFTPLVDLPPAWAWLSSDVALWVVGILLVLEVVADKIPAVDAVNDVVQTVVR
+PAAGGITFASGVGAQTVTVQRPDTLLDSQVWVPTLIGAAMALLVHLTKAGTRAAANTVTM
+GTAAPLLSTAEDASAVVLTAAALFLPVLVLVVLLAVLVGLWAVPRRFRAGRRGGRRATMA
+S*
+>NZ_CP097650.1_254
+MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLAADASLWILGVLLALE
+LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV
+VAVVVGLWLLARRFRDRRTRGRAAAVPGGPEWTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000353.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000353.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0862032a7ae0d24ba3aa0e4d0e84cbea70009290
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000353.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_270
+MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR
+TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH
+AVALVYVVPVTGECQPRQNALELTWLTPEEALGEDIQAEFIGGRGDLVRQALAHVGWGR*
+>NZ_CP033200.1_2241
+MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR
+TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH
+AVALVYVVPVTGECQPRQNALELTWLTPEEALGEDIQAEFIGGRGDLVRQALAHVGWGR*
+>NZ_CP040019.1_67
+MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR
+TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH
+AVALVYVVPVTGECQPRQNALELTWLTPEEALGQDIQAEFIGGRGDLVRQALAHVGWGR*
+>NZ_CP083691.1_52
+MSVRTPDPNPGWLNEEDLYEARRRLPMVYVEAIPVRVDALGYVSEIGLLYVADEEGQFQR
+TFVSGRVMYRETIRGALMRHLEKDLGPLAFPQLPPSLVPCAVAEYFPAPSETGLTDDRQH
+AVSLVYVVPVSGECSPRQDALELTWLTPQEALGEDVQAEFIGGRGNLVRQALAHVGWGR*
+>NZ_CP097650.1_269
+MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR
+TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH
+AVALVYVVPVTGECQPRQNALELTWLTPEEALGEDIQAEFIGGRGDLVRQALAHVGWGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000354.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000354.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5155dd371ee80864d6c898bea0279b0e8736b19
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000354.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_272
+MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH
+RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR*
+>NZ_CP033200.1_2243
+MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH
+RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR*
+>NZ_CP040019.1_65
+MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH
+RAGEDAEAAEVARRMAEAVSGVAATGRLDVLRRDGGRWVPVPAGPGR*
+>NZ_CP083691.1_51
+MPSYRARLQIGDVLPGHRPEEVLDTAEAAIGATHEVAAKDVEVVARVPRIVLRFTVPAAH
+RAAEDAEAAAVAGRMAEAVADVATVGRLDVLRREGGRWLPVSAR*
+>NZ_CP097650.1_271
+MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQASHVLAAKDIEVVARVPRIVLRFTVHGSH
+RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGPGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000356.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5ecdfd2e8a314a5dbf3310258b1ec036b8d0dff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000356.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_275
+MAVPSPLPPRNGVNATRLRLPTSGWPTAQDYVLHRFGHVDPEGIRARFARGEVVAADGTA
+LTPTTPLGVHDDLWYYRDVPDEAPLPVTHTLLHRDEHLVVIHKPHFLPTTPGGRFVQETA
+LVRLRNELGLDDLVPLHRLDRATAGVVMFSANPATRGAYHLLFERRAVAKTYEAVALLPD
+APDDGARGPGAPTDPILGRFPLTVRSRIRKDKGVLRSVVEEIPAAASGRRAGAPVRTRRS
+NRPHAGANAESRVELLGVGVSAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFDP
+FYPDLLDLAPDDVARPLQLLSRSLRFTDPVTGEEREFTSPAELQERPR*
+>NZ_CP033200.1_2246
+MAVPSPLPLRNGVNATRLRLPASGPWASVQEYVLDRFGHVDPDGIRRRFASGQVVAADGA
+PIPADTPLGVHDDLWYYRDVPDEAPLPVTHTLLHRDEHLVVIHKPHFLPTTPGGRFVQET
+ALVRLRNELGLDDLVPLHRLDRATAGVVMFSANPATRGAYHLLFERRAVAKTYEAVVLLP
+EAPDDGARGPGAPADPVLGRFPLTVRSRIRKDKGVLRSVVEEIPAAASGRRAGAPVRTRR
+SNRPHAGANAESRVELLGVGVSAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFD
+PFYPDLLDLAPDDVTRPLQLLSRSLRFTDPVTGEEREFTSPAELQERPR*
+>NZ_CP040019.1_62
+MAVPSPSPARNGVNATRLRLPASGWDTAQDYVLHRFGHVDPDGIRARFAAGEVVAADGTA
+LTPTTPLGVHDDLWYYRDVPHEDPLPVAHTLLHRDEHLVVIHKPHFLPTTPGGRFVQETA
+LVRLRNELGVDDLVPLHRLDRATAGVVMFSVDPATRGAYHLLFERRAVAKTYEAVSALPP
+DADDDGLVLGRFPLTVRSRIRKDKGVLRSVVEEVPAAASGRRAGAPVRTRRSNAAHAGAN
+AESRVEVLGVGESAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFDPFYPDLLDA
+APDDFSRPLQLLSRSLRFTDPLTGREREFVSPAQLQERPR*
+>NZ_CP083691.1_48
+MAAPSPLPPRNGVNATRLRLPASGWDTAQDYVLHRFGHVDPDGIRARFARGEVVARDGSP
+LTPTTPLGVHEDLWYYRDVPHEAPLPFQHTLIHRDERLVVIHKPHFLPTTPGGRFVQETA
+LVRLRNELGIDDLVPLHRLDRATAGVVMFSADPATRGAYHLLFERRAVTKRYEAISALPP
+ARDHADDDAAAWLDRFPLVMRSRIRKDKGVLRSLTEEIPAAASGRAAGARVRTRKSNLSH
+AGANAETRIEVLDVGRSAGTLAGAPVVRFRLSPRTGRTHQLRLHLAALGLGIAFDPFYPD
+LLDAAPDDLARPLQLLSRSIAFTDPVTGEHREFVSPAELQERPA*
+>NZ_CP097650.1_274
+MAVPSPLPLRNGVNATRLRLPASGPWASVQEYVLDRFGHVDPDGIRRRFASGQVVAADGA
+PIPADTPLGVHDDLWYYRDVPDEAPLPVTHTLLHRDEHLVVIHKPHFLPTTPGGRFVQET
+ALVRLRNELGLDDLVPLHRLDRATAGVVMFSANPATRGAYHLLFERRAVAKTYEAVALLP
+DAPDDGARRPGAPADPVLGRFPLTVRSRIRKDKGILRSVVEEIPPAASGRRAGAPVRTRR
+SNRPHAGANAESRVELLGVGVSAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFD
+PFYPDLLDLAPDDVTRPLQLLSRSLRFTDPVTGEEREFTSPAELQERPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000357.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000357.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61bda6a5caeea7e1b4ba0325ebbf9ec00083cec9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000357.fa
@@ -0,0 +1,47 @@
+>NZ_CP042169.1_276
+MADPFPKDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDLAAEGWPLIT
+NPHQAPPAWVAPDARVSGSLLSPGCRIAGEVSDSVVGPGVVVAAGATVRGSLLLGDCEVP
+AGAVLDTVVVDVGGAVPAREVTGRAAPAEEVVVLTPQDRGPAEDETTGSGRPGRSD*
+>NZ_CP033200.1_2254
+MADPFPTDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLT
+NPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSVVVEAGAVVRGSILLGECTVP
+SGAVLDTVIADVGAAIPAEGATGRAEPADEVVVLEPGERGPASSDETTGSGAPVRD*
+>NZ_CP040019.1_61
+MPEGDSLVRLAHRLRPVLAGRALTHADLRVPQHATADLTGWTVVEVEPRGKYLLMRLTPP
+AGRPAARPLTLVSHLKMEGRWLVSALDARWGAPAWQVRAVLETADHRVLGAQLGMLTLVP
+TDREDTVLGHLGPDLLDPAWDGSEEAAAALLAEGTRRLTARPERPVGLALLDQRTTCGIG
+NIYRCESLLLAGIDPHRPVGAVPDVPGLLTIARDLLRANVPPAAPFLGWPRTTTGVRANP
+DRPYGIEVVVADRGFPPGLPAAVGSGTAADPAADPGADRTASGPALGRPPARPPADPGAA
+GRRRTGCTGTTAPPACAAAGACARRTSAPPRTTRGSCGGARPASGEPRPNRGPGGGAPYA
+ERRPSPQGRSARPPTPRRTRVADPFPDDPRSAVVALILAGGRGSRLAPLTDARSKPAVPF
+AGQYRLIDVALTTVAHSGLQDAWIVEQYRPFTLNQHVAGGRPWDLDGTRHGLRVLPPAQG
+RDEEGFAQGNGHAIHQQLAPLRRFGAKTVVIMSADHLYRMDLRPVLERHRERDAELTVVT
+TQVAEGASRFGVVSSDADGRVTAYDYKPDEPATDVVATEVFVADVDALTEVIESLLDSAS
+EEQVDDDDPAGAQLGDYGETIIPALVERGRVHEFRHEGYWKDVGTIDAYYQAHMALLRGD
+GLDLDDPRWPLISNFHPRPPAFIHPEAEVNGSMLCPGSRVRGTVTESVIGPGVVVEAGAT
+VHRSVLLGSATVPAGARLDAVIADVGARIPEGATGQTKPGPGNITVLTPDDRSTAEGDET
+TGHA*
+>NZ_CP083691.1_41
+MADPFPKDPAGSTVALVLAGGRGSRLDPLTAARSKPAVPFAGQYRLIDVVLSNLAHSGLK
+DVWIAEQYRPFTLNQHLAGGRPWDLDGTRHGLRILPPAEGREEEGFSAGNGHALAQQVPI
+LRSFGAERVVVLSADHLYQLDLRPVLAAHADSGAELTMVTTVTDEDPSRFGVVQADEDGA
+VTAYDYKPEDPEGRLVATEVFVFDVAALHEVVAELVAREKAAGEHADGEEDEDGDPVASS
+LGDYGETIIPAFVERGRVREHRLEGYWRDIGTLDAFYRAHMELLDGAGLDLAAPGWPLLT
+NPPAAPPARVGPRAEVSNALLSPGCVVKGTVEDSVLGPGVVVERGAHVRRSVLFGECIVP
+RGARLDAVIADVGAHIPAEEVGRSRPGPGNLTVLTPATRDPDSEDETTGGAAAKDG*
+>NZ_CP097650.1_282
+MADPFPKDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHTRSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLT
+NPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSVVVEAGAVVRGSILLGECTVP
+SGAVLDTVIADVGAAIPAEGATGRAEPADEVVVLEPGERGPASSDETTGSGAPVRD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000359.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000359.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d26d0b1c827b88358cc192862a5b3e53ed41a398
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000359.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_281
+MTSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGPLGANATALYGMRSSTGHTY
+ATLPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVAAFSV
+RSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGGQDLD
+REQVPLPGREVPDGGHAIPEEDRVQAIVDFFGPTDFLTMNRQMLPGACADYNRANRLKHC
+HLDDRSTKSDMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSLELYR
+AAETAGLRTAFYSVAEGSHDLGMMTAKTRSAEVLRNGVPASAVHATISWSAVASFLDAVL
+PR*
+>NZ_CP033200.1_2259
+MTSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGPLGANATALYGMRSSTGHTY
+AALPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVAAFSV
+RSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGGQDLD
+REQVPLPGREVPDGGHAIPEEDRVHAIVDFFGPTDFLRMNRQMLPGACADYNRANRLEHC
+HLDDHSTKADMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSLELYR
+AAEAAGLRTAFYSVAEGGHDLGMMTAKTRSAEVLRTGVPASAVHASISWSAVASFLDAVL
+PR*
+>NZ_CP040019.1_57
+MATSGRRGRLTRRAVLGLGAGALALGGGAAVANLAGVPPAPVGPDVNALFGMRSSTGHRY
+ADLPGRAGRVDVYRPQGPGPFPVVVWNAGSGWRDDRGYHDGQTVARGLVPHGYAVAAFSV
+RSSKQGRFPAQVEDATAAVRWVRAHAVELDLDASRLTVAGTSSGGWNALMAGLTGGRDLD
+RAHVPPPGREVPPGGHAIPEEDRVQAILDFFAPTDFLAMNAQMPPGACADYNRQRRLEHC
+HLDDHSTKSAMLGVPVLASYGLTRLASPIAHVRPDSPPMMIVHGLKDPTVPWRQSLELYE
+AAEAAGVRAAFYSVADAGHDLGMMGGGWGSAEVLRSGVPLSAVHATISWAAVAAFLDTVL
+PG*
+>NZ_CP083691.1_36
+MGGDTSTARAPRVRRRTLLGLGLGALAVGGTATALGHGSPVDSPALRQTMGALFGTTVIS
+GIVYADLPGAAGRMDLYLPEGEGPFPVLAWNAGSGWRSDRGFQGGDAVARGLVPAGHAVA
+AFSVRSAREDAFPAQVLDATAAVRHLRENAGELRVDPGRIAVGGNSSGGWNALMAGLTGG
+RDLDRSAVPAPGDEVPEGGHAIPEEDRVQAIVDCFAPVDFLQMNVQMPRGACEEYDRRNH
+TRHCHLDDASTKSRMLGAPVMARPELARLANPAVHVTPAAPPTLIVHGRADREVPYVQSR
+GLYQAYVGAGVPVAMYSVEGAGHDLQMMARRVGRTDVVRSGLPRQAVHGSISWSAVAAFL
+DVAMPRPRR*
+>NZ_CP097650.1_287
+MTSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGPLGANATALYGMRSSTGHTY
+AALPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVAAFSV
+RSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGGQDLD
+REQVPLPGREVPDGGHAIPEEDRVHAIVDFFGPTDFLRMNRQMLPGACADYNRANRLEHC
+HLDDHSTKADMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSLELYR
+AAEAAGLRTAFYSVAEGGHDLGMMTAKTRSAEVLRTGVPASAVHASISWSAVASFLDAVL
+PR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000361.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000361.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b4e91760e2124ff84901a84db4b913d34e70ef7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000361.fa
@@ -0,0 +1,26 @@
+>NZ_CP042169.1_283
+MDGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE*
+>NZ_CP033200.1_2262
+MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE*
+
+>NZ_CP040019.1_55
+MRVHLVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVEIQTPVAT
+TTGLRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTYAERLPAD
+LSGRHVFVLDPMLATGGTLIESIRFLYERGAARVTCICLLGAPEGIARLEESLGDVEVDL
+YLAAQDERLDENAYIVPGLGDAGDRLYGLAE*
+>NZ_CP083691.1_34
+MRLHVVDHPLVAHKLTVLRDERTPSMIFRQLTEELVMLLAYEATRGVAVTEVEVKTPVAT
+TVGTTLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTYAERLPAD
+LTGRHVFVLDPMLATGGTLIEAIRFLYERGAERVTCLCLLGAPEGVARLEEALGDVDVEL
+YLAAVDERLNEKSYIVPGLGDAGDRLYGLAE*
+>NZ_CP097650.1_290
+MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000362.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000362.fa
new file mode 100644
index 0000000000000000000000000000000000000000..449952852107456ab80a8c23c006f9d974ab6b25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000362.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_284
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI*
+>NZ_CP033200.1_1
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI*
+>NZ_CP040019.1_54
+MGQSAGYVHISVRNAQRRADGMSRRGQARADLRLAGGTDAPAAQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGSESHAAVALAPSGA
+EGRDLEVVRQVLGDPTVQGGAHPDLAQAPAPVSTREPGVLIDLSRREVQLDGESLNLTYK
+EFELLNYLVENGERTVGREELLEALWHNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI*
+>NZ_CP083691.1_33
+MGETAGYVHISVRNAQRRANVSRARRGDLRLAGGTSHEPTPPQTAPTPVLAPSGIPGPQA
+VARENEARGFVIYVGMDELMASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGAA
+GRDLEVVRQVLGDPTVQGAARPDLAQAPAPVSTRQPGVLIDLSRREVQLDGEALNLTFKE
+FELLNYLVENGERTVGREELLDALWKNSDEVPNERTIDVHIRRLRAKLGRLANTVRTVRG
+QGYRFYRHPEVVVWAAPEYSI*
+>NZ_CP097650.1_291
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000367.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000367.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b82b37179f3c7003d922a6a22bbf3a2643a70bb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000367.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_290
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETAGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAITALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPAVGEGVG
+EGQAVHEDFAGVATTVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER*
+>NZ_CP033200.1_7
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETAGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAITALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPAVGEGAG
+EGRAVHEDFAGVATTVTRMDGTTIAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER*
+>NZ_CP040019.1_48
+MTTSTSSLDLHESFKAYDVRGIVGETITADSVRAVGAAFVDVLGLAGETVLVGGDMRPSS
+PAFMAAFAEGATRRGADVVDLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAKA
+GAVPVSSDTGLYEIRDAAQALLDAGEIPAAEAVGTVTQQDILPAYAEYLRSLVDLSGVRP
+LTVVVDAGNGMAGKTTPAVLGDAALDALPLRIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVVDEKGAPVSPSAITALVARREIARAKGEGEETPVVIH
+NLITSRAVPELVAADGGRAVVTRVGHSFIKAVMAEESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGEQDQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPTVGEGAG
+EGRAVHEDFAGVDTAVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEAIR
+DAVLAIVRAER*
+>NZ_CP083691.1_26
+MVTLRPGRIIDRVTTAADAINLRDSFKAYDVRGIVGETITAETVRAVGAAFVDVLGLAGQ
+TVLVGGDMRPSSPEFIEAFAEGATRRGGNVQRIGLISTDMLYYAAGVEQAAGVMFTASHN
+PAAYNGMKMAKAGAVPVSSDTGLYEIRDVAQGYLDAGEIPAADAQGSVTESDILTGYAEY
+LRSLVDLSGIRPLKVVVDAGNGMAGKTTPAVLGGEVLEALPLEITPLFFELDGTFPNHPA
+NPLEPENLRDLQRAVVEHGADIGLAFDGDADRCFVIDEQGEPVSPSAVTALVARREIARA
+KASGEETPVIIHNLITSRAVPELVSADGGRAVQTRVGHSFIKAVMASEGAVFGGEHSAHY
+YFRDFFNADTGMLAAMHVLAALGEQDGPLSTLGAEYEPYVASGEINSQVEDKDAAVAAVL
+ARFAPQAADGGESGTAVEDAVAGTSTSVLRMDGTTVSAADGSWWFNLRPSNTEPFLRYNG
+EAKDRATMETVRDAVLAIVRAPR*
+>NZ_CP097650.1_297
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQASGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETTGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAVTALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVEDKDAAVAAVVAQFAPAVGEGVG
+EGQAVHEDFAGVATTVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000368.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab7667f076c161f12eba7aaba7567e932185c287
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000368.fa
@@ -0,0 +1,42 @@
+>NZ_CP042169.1_291
+MPPTTPPPPAGPPAVPPSGPAPAAPGEAAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLALSVVPWSVAGDRWGRRRAMVVSMVSASACALAGVLAPTF
+EAMLRLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY
+LQGALLMGGFVALYNFVGYRLLGPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTAPAR*
+>NZ_CP033200.1_8
+MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF
+EAMLGLRLLEGMAHGGVAGLAVALLAEEVVPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLTVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY
+LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALVSAVVVLRGRGTAPAR*
+>NZ_CP040019.1_47
+MPPQPPPAGPPAVPPSGPAPLAPGDPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSADL
+GVGAHRAALLVSAGTLGLALSVVPWSMAGDRWGRRRAMVVSMVSASLFALAGVLAPTFEA
+MLGLRLLEGMAHGGVAGLAVALLAEEVAPRAVATAAGTYIAGTTIGGLSGRLIALPVAEA
+FTWRTGMLAVTVVGVACTAAFLAVTPQARRFTPSPTSVARLVRIVRGHLGSAELVAVYLQ
+AALLMGGFVALYNFVGYRLLGPPFSWAPTAAGLVFLAYLAGTWSSPRAGRLAARFGRLPV
+LTGATAAMAAGAALTLVPHPAVLVGALVLTTGAFFAAHSVASAWSGTAAPHGRAQSTSLY
+NLAYYAGSSLFGWLGGVFHESHGWTGTVLMVVALALTALAIAVVVLRGRGTAPARCAGAV
+RGAGRRGIRRISRGRLRRRRWPSGAGRARPRGPRGPAARASRPSAGRSRSRCPARRTPPA
+WSAPRPG*
+>NZ_CP083691.1_25
+MPPALPAPLEPGTPLYRRLLLGLFLAGVATFAQLYAPQGLLPLVSSDLGVPSHRAALLVS
+AGTLGLALSVVPWSLAGDRWGRRPVMVASLVSASVLALVGVFMPSIELLMGMRLLEGMAH
+GGVAGLAVTLLAEEVAPRVVPVAAGTYVAGTTLGGLSGRLLAMPVGEWAGWRAGMLAVTA
+AGAACTVAFLFVTPPARRSTPVRLSLARLGRIIGGHLRTPGLVALYLQAALLMGGFVALY
+NYIGYTLLAPPFGWPPTAVGLVFLAYLAGTWSSPRAGRLAVRVGRLKVLTGSTALMAVGV
+VLTLVPSPFVLVPALVVATGAFFAAHSVASGWAGTAAPTGRAQSTSLYNLAYYAGSSLFG
+WLGGVFHEGVGWAGTVFMVAGLAAVALVVALVVLRGREDAGPPPPSAVAEGAAA*
+>NZ_CP097650.1_298
+MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF
+EAMLGLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSAAALVRIVRGHLSSPELVVVY
+LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTAPAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000371.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000371.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b8e4163005f1f402da1bb56ee630c48e40a549b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000371.fa
@@ -0,0 +1,61 @@
+>NZ_CP042169.1_295
+MSEPLVADRRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVAEVVEHRAEATALHPRPDGGARLELRDPDGSVSVLDADA
+VVLCLGHQPAELSPGQMRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPTGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALTARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWIAEGRIAEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLEPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAAAAVLAG*
+>NZ_CP033200.1_19
+MSEPLVAERRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVVEVVEHRAEATALHPRPDGGARLELRDADGAVSALDADA
+VVLCLGHQPAELSPGQNRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPSGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALAARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+AELMEQTCVEAALGEESPFMMAVGALHAGRLRIKAWVAEGRITEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLGPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAATAVLAG*
+>NZ_CP040019.1_26
+MPDAQEAVRRLAVVGAGPRGVMLLERLLARLEGSAPGAHPARLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVQRHQYPARAVY
+GRYLRHLYQDVVAGLRARPEVADVVEHRAEVTALHPTPAGGARLELRDADGAASELAADA
+VVLCLGHQPAELSPGQARMAAAARGRDDLHYQGPQIPSDVDWDTVEPGARVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALAYEPSGREPRLHLMSRRGVPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALSARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYTAPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWVAEGRIAEDSRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPVPVVDAEERAFSVRSPQVGAADSLGPAVVEGE
+WLVEAMMPPNRVQAASSPLIRGMLDDGVAAAGTWEDEEGVRVPAPGFDVTGRPHRLRAAD
+GAVHEDVYVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAVAQAVLAG*
+>NZ_CP083691.1_22
+MSPPSISEPTRAIAVVGAGPRGVMVLDRLLARLEAASEPRPTGSLAVHVVDPFPPGPGRV
+WRPDQDPLLLMNTPAFFPTACAADNPGLAPSSVSLSFDQWRLARPDRAAGLERTDYPPRA
+VYGRYLEDVVAAVLDALRARPEVVAVTVHAAQAVALRAAYEGGPVAAPESPSAWRLTLRP
+VDGTPPRELQADVVVLCLGHQDAEPSAAQRRLGEAADASPALHYRGPHLPAELDVDGIAP
+GATVLVRGMGLNAFDLQARLSEGRGGRFEPTGGEPGRALRYVPSGREPVLHLLSRRGLPY
+LPKAAVDAFVPRGVRMSYLTDTEAEALVARHGQLDLAEHLWPLLHRDVVRAYYATLARVH
+PERLGGPADAGRFVRELVGMFESAGRGAPVTARHGQELLHAFAPGMRFLDIRSWAAPFQG
+AVFDDAAAYQEAVAGVLEQACGEAAAGEDSPFMQAVGTLHAGRLRIKAWIAQGLLTDASR
+IRDVQGWFEPLVEGLASGPPLVRVEQMLALHRAGLLSWAGPGPQVEADAEAGVFRARSPQ
+VGADDAVAPAVTEAAWLVEAMMPPSRVEAAATPLVRQMLADGVAAVGRWEDEDGALRSSS
+GFDVTARPHRLRGADGTVREGVLVLGLQLSGVQWGTAIAAEAGADVRDRALFLADADAAA
+RVALGG*
+>NZ_CP097650.1_302
+MSEPLVAERRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVVEVVEHRAEATALHPRPDGGARLELRDADGAVSALDADA
+VVLCLGHQPAELSPGQNRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPSGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALAARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWIAEGRIAEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLGPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAATAVLAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000374.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000374.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70822cd8296f09cf58d39d9659fa384d957c5767
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000374.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_299
+MRGPFARFRQERADDRELGTGLWRRAHDRLGRAMDRYWQVLAGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGAGL*
+>NZ_CP033200.1_23
+MRGPFARFRQERADDRELGTGLWRRAHDRLSRALDRYWQVLEGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGAGL*
+>NZ_CP040019.1_22
+MRGPFARFRQSCSDDRELGTGLWRRAHDRFVRAMDRYWQVLEGDRGPDLLRTEQRNGVVH
+AGNVLAERLPAVRALCVRLHRDHAGDGEHIPPEAADVHRELSRAAHELAATAQALAMHRL
+GQGSSDSVGRHAERTLAHLDRAEELAARL*
+>NZ_CP083691.1_18
+MIRGPFARFRQGRSDDRELGTGLWRRSHDRYVRALDRYWQVLEDGRSAGGFTPEERNGLV
+HAGNVLAERVPAVRALAARLHAAHPGDGEQHIPPVTAPVHRELSRASHELAAAAQAVAMF
+RRGVSGSEAVSRHAQRTLDHLDRAEGLAADL*
+>NZ_CP097650.1_306
+MRGPFARFRQERADDRELGTGLWRRAHDRLGRALDRYWQVLEGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGARL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000375.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000375.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acee0edee147468b479873b7bcbeadbe474eac40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000375.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_300
+MSLPHAPRTPAPPAAASSAVPLRLAVVDMSGTSIVEHGLQDTAFARSLDQHGVPAGTPEH
+DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEATFDALLAEHGVRAVPGAEEALI
+RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD
+LEDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADHVLLAAGSDRVVPGLADVPDLV
+VRTR*
+>NZ_CP033200.1_24
+MSLPHAPRTPAPPAAASSAAPLRLAVVDMSGTSIVEHGLQDTAFARTLDQHGVPAGTPEH
+DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEAAFDALLAEHGVQAVPGAEEALV
+RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD
+LDDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADDVLLAAGADRVVPGLADVPDLV
+VRTR*
+>NZ_CP040019.1_21
+MSLPPRPPPRGRAPRADGPPAPPLRLAVVDMSGTSIVERGLQDAAFAHALETHGLAADAP
+AHADAVRVFRARRATSRTAVFAQVFPDRPAAAAAARTFEEAFDSLLAEHGVQPVPGAEEA
+LLRLRALGLRVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPFPDMILTALLG
+LDLDDVRGVLVVGDTAEDMTAGRRAGAGLVAGVRTGRDADAALLAAGAHHVVDGLADVPA
+LVGAGG*
+>NZ_CP083691.1_17
+MSLSTAVPALSVGTPVPLRLAVVDMSGTSVVEGGLQDRAFAEVVAARGLAEGSPEHERAA
+RLFRERRGTSRTAVFQALFEGRTAALEATRAFEAAFDRLLAEHGVTAVPGAEGALVRLRE
+AGLDLCLITGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMVLTALLALDHDDV
+RSVLTVGDTAADILAGRRAGAGLVVGVRSGQDTGGVLAGAGADQVVDSLAQVPDLVATLR
+G*
+>NZ_CP097650.1_307
+MSLPHAPRTPAPPAAASSAVPLRLAVVDMSGTSIVEHGLQDTAFARTLDQHGVPAGTPEH
+DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEATFDALLGQHGVQAVPGAEEALV
+RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD
+LDDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADDVLLAAGADRVVPGLADVPDLV
+VRTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000377.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000377.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc1cb6ce3fa0cb8f9c9d777f64165d70820f541a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000377.fa
@@ -0,0 +1,26 @@
+>NZ_CP042169.1_302
+MSTQTEHRGLFVAVEGPDGSGKSTQARALTEVLRAAGHEVVLTREPGGSDLGETLRELLL
+DPEHAPVDPRTEALLFAAARSAHAVRTLRPALARGALVVTDRYVDSSVAYQGAARGLGEA
+RIAALNEWATDGLVPDLTVLIDVDAATAADRRERRAAGGEGAPDRMERETADRHEALRAA
+FLARAAAAPERYLVLDGALPPQELTARALARVTAEAADR*
+>NZ_CP033200.1_26
+MSTQTEHRGLFVAVEGPDGSGKSTQARALTEALRAAGHEVVLTREPGGSDLGETLRELLL
+DPGHAPVDPRTEALLFAAARSAHAVRTLRPALARGAVVVTDRYVDSSVAYQGAARGLGEA
+RIAALNEWATDGLVPDLTVLIDVDAATAADRRDRRAAEGEGTPDRMERETADRHEALRAA
+FLARAAAAPERYLVLDGALPPQELTARALARVTAQAADR*
+>NZ_CP040019.1_19
+MSTETEHRGLFVAVEGPDGSGKSTQARALVAALRAAGREAVLTREPGGSDLGETLRGLLL
+DPAHAPVDPRTEALLFAAARAAHAVRTLRPALARGAVVVTDRYVDSSVAYQGAVRGLGEE
+WIARLNDWATDSLVPDLTVLIDVDAATAAARRTGRDGDGADRMEQETADQHEALRAAFLA
+RAAAAPERYLVLDGALDPEELTARALARVTAEADAR*
+>NZ_CP083691.1_15
+MSTPSPRPAPHPAPTPAADPADSPAAAAQGMPGRGLFVAFEGADGTGKSTQARAVAQALR
+DAGREVVLTREPGGSDLGEAVRALLLDPAHAPVDARTEALLFAAARAAHVARTVRPALAA
+GTVVLTDRYVDSSVAYQGEVRGLGAERVAELNDWATEGLVPDLTVLLDADAATAEARRAA
+RHAGGGDAPDRMEQETAQAHGTLRAAFRARAAAAPHRYLVLDAAGAPEELTAAIAARVLT
+AAADAARDGTGA*
+>NZ_CP097650.1_309
+MSTQTEHRGLFVAVEGPDGSGKSTQARALTEALRAAGHEVVLTREPGGSDLGETLRELLL
+DPGHAPVDPRTEALLFAAARSAHAVRTLRPALARGAVVVTDRYVDSSVAYQGAARGLGEA
+RIAALNEWATDGLVPDLTVLIDVDAATAADRRDRRAAGGEGSPDRMERETADRHEALRAA
+FLARAAAAPERYLVLDGALPPQELTARALARVTAQAADR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000384.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000384.fa
new file mode 100644
index 0000000000000000000000000000000000000000..56dd632991b9051c13c5a76b809d497df8bd7cd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000384.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_310
+MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD
+VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL
+SAGEKRMLAKARQVLVSELALAKKVTEEEAEGRLDKVLEG*
+>NZ_CP033200.1_34
+MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD
+VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL
+SAGEKRMLAKARQVLVSELALAKKVTEEEAEGRLDKVLEG*
+>NZ_CP040019.1_11
+MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD
+VVDSEGLEEVVEVLQAEQVEEPTNWSRRYKANLEKLASGDVKKVAEVVRDLWRRDQDRGL
+SAGEKRMLSKARQVLVSELALAKKVTEEEAEGMLDQVLEG*
+>NZ_CP083691.1_7
+MPDTRGVFRVSVVESTDRKGAFHMVFEVGETVVYPHHGAARIEEIKTRTIKGEEKMYLKL
+KVAQGDLTIEVPAENVDLVGVRDVVDDKGLEHVVEVLQAEHVEEPTNWSRRYKANLEKLA
+SGDVNKVSEVVRDLWRRDHDRGLSAGEKRMLSKARQVLVSELALAKKVSEEEAEGMLDKV
+LEG*
+>NZ_CP097650.1_317
+MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD
+VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL
+SAGEKRMLSKARQVLVSELALAKKVTEEEAEGRLDKVLEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000385.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000385.fa
new file mode 100644
index 0000000000000000000000000000000000000000..428466d816beef1bbdac223962a3f66b52aa8956
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000385.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_311
+MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLRHCLESVAAARAAGLDLDAVVVLTPP
+AGADAGRVAAEVDAGPRLDVPVHCVPGGAERADSVRAGLAAASHALADLAPAGAPRRVLV
+HDAARALTPPSVFGAVTAALETGAVAAIPGLPLTDTVKQVTPGRGGVDVVAATPARAGLR
+AIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFKVTAP
+ADLDLARLELARRAPQEEAPMDQPARPAAAPAPLPRVGIGTDVHAWAPEDAPRPLWLGGI
+HWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRPEMADASGADMLREVLRL
+LTEAGLAVGNVAVQVVAPRPKVGARRAEMEAALSAALGGAPVSVSAATTDRLGFIGRKEG
+LVGIATALVIPAA*
+>NZ_CP033200.1_35
+MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLRHCLESVAAARAAGLGLDAVVVLTPP
+AEADAGRVAAEVDAGPRLDVPVHCVPGGAERADSVRAGLAAASGALADLAPAGAPRCVLV
+HDAARALTPPSVFGAVTAALGTGAVAAVPGLPLTDTVKQVTPGRGGVDVVAATPARAGLR
+AIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFKVTAP
+ADLDLARLELARRAPQEEAPMDQPARPAAAPAPLPRVGIGTDVHAWAPEDAPRPLWLGGI
+HWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRPEMADASGADMLREVLRL
+LTEAGLAVGNVAVQVVAPRPKVGARRAEMEAALSAALGGAPVSVSAATTDRLGFIGRKEG
+LVGIATALVIPAA*
+>NZ_CP040019.1_10
+MPTALVIAAAGAGTRLGAGMPKALVPLADGRTLLRHCLDSVAAARAAGAAVDAVVVLAPP
+AEEDAARVAAEVDAGPGLGAPVACVPGGAERADSVRAGLAAAADALNALGPAAGPRRVLV
+HDAARALTPPAVFAAVEAALDAGAVAVVPGIAVTDTVKQVAPGPGGAEVVTTTPPRAALR
+AVQTPQGFDLDALLAAHEAVRADPALDAAALTDDAMVMEAAGHPVAVVAGDAAAFKVTAP
+ADLELARLELARRADAPTPEEDPAMDQYGTAPGTGPEADAATDPAGPRPGAALPRVGVGT
+DVHRWAPEDAPRPLWLGGVHWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVD
+RPEMADASGTAMLAEVLRLLTEAGLAVGNVAVQVVAPRPKVGTRRAEMEAALSAALGGAP
+VSVSAATTDRLGFIGRGEGLVGIATALVAPTA*
+>NZ_CP083691.1_6
+MPTALVIAAAGSGTRLGAGVPKALAPLTDGRPLLDHCLESVAAARATGLGLDALVVLVPP
+AADHARAVADVVARHETAVGAPVTCVPGGVERADSVRAGLAAADAALADRGHPAGQGVRH
+VLVHDAARAFTPPAVFEAVAGALVSGEVAAVPGLPLTDTVKEVTGADGREVVVATPARSA
+LRAVQTPQGFDLDVLLAAHAAAQADPAADAAALTDDAMAMEAAGHAVVVVPGDERAFKVT
+SPADLEAAARILAVRDAQSGPGTPSPAAVPAAPPLPRTGIGTDVHRWAPDDAPRPLWLGC
+VEWPGQNGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRWEMRGASGAAMLAEVLR
+LVTEAGCRIGSVAVQVVAPRPKVGTRRAEMEAAMSAALGGAPVAVSAATTDGLGFIGAGE
+GLVGLATALVVPAA*
+>NZ_CP097650.1_318
+MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLHHCLASVATARAAGLALDAVVVLTPP
+AEADAGRVAAEVDAGPRLDVPVHCVSGGAERADSVRAGLAAASYALADLAPAGAPRRVLV
+HDAARALTPPSVFGAVTAALETGVVAAVPGLPLTDTVKQVTPGRGGVDVVAATPARAGLR
+AIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFKVTAP
+ADLDLARLELARRAPREEAPMDQPARPAAAPAPLPRVGIGTDVHAWAPEDAPRPLWLGGI
+HWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRPEMADASGADMLREVLRL
+LTEAGVAVGNVAVQVVAPRPKVGTRRAEMEAALSAALGGAPVSVSAATTDRLGFIGRREG
+LVGIATALVVPAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000387.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000387.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9c873521ee89568535bccaae81a1370717abf47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000387.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_313
+MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE
+QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI
+ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN
+TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQIVSIP
+IDSTMESLNASMAVGISLYEISVQRAGGR*
+>NZ_CP033200.1_38
+MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE
+QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI
+ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN
+TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQIVSIP
+IDSTMESLNASMAVGISLYEISVQRAGGR*
+>NZ_CP040019.1_6
+MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGKGPTPKAEDRVYHKAYRAKQLSERSAA
+KRGGPVRPSRPKLTDETVSGRNPVVEALRAGIPAKALHVAVRIEMDDRVKEALRLCLEQG
+VPVMENTKPELDRLSGEAIHQGLVLQIPPYEYADAMTLATDALEKHEKGHLRTPPLLIAL
+DGITDPRNLGAIIRSGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLNTT
+LVELHRAGYFVLGLDGGGDVSLPGLSLATEPLVLVVGAEGKGLSRMVREHCQQIVSIPIN
+SDMESLNASMAVGISLYEISVQRAGGR*
+>NZ_CP083691.1_4
+MSTAPRSGGSRAPKGKKGPQKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KHGGGRVPVRDQVRGRVKLTDETVSGRNPVVEALRAGIPAKALHVATRIEVDDRVKEALR
+LCAENKVPVMENTRPELDRMSGEAVHQGLVLQIPPYQYADALTLGREAMEAQEKGHLRTP
+PLLIALDGITDPRNLGAIIRSASAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQA
+GNLNTTLVELHRMGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQI
+VSIPIQSEMESLNASMAVGISLYEIAVGRAGGRPVAS*
+>NZ_CP097650.1_320
+MSTAPRSGGSRKPKGKKGPVKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE
+QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI
+ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN
+TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRLVREHCQQIVSIP
+IDSTMESLNASMAVGISLYEISVQRAGGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000389.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000389.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a157283b26d123b08edac6c23117ff6fcf2dd18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000389.fa
@@ -0,0 +1,69 @@
+>NZ_CP042169.1_318
+MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT
+VVRAGDGQRVELTHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY
+RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSADEAVGTAFAVWAPNARAVRVVGDHN
+GWDGRTHAMRSLGSSGVWELLAPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA
+SRVLESDYAFGDRTWMERRRVTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG
+FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHQAGIGVIVDWVPAH
+FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID
+GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNMTVYRLHPGVHMIAEES
+TAFSGVTAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHGQWTFSMVYAYSENYV
+LPLSHDEVVHGKGSLLSRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE
+GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFAWVDGGDADGNTLVFL
+RMPAAQVVPEPRIDDDGDAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT
+DSTDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPHPDSTVTP*
+>NZ_CP033200.1_43
+MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT
+VVRAGDGQRVELTHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY
+RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSAGEAVGTAFAVWAPNARAVRVVGDHN
+GWDGRTHAMRSLGSSGVWELLVPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA
+SRVLESDYAFGDRTWMERRRLTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG
+FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHRAGIGVIVDWVPAH
+FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID
+GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNATVYRLHPGVHMIAEES
+TAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHEQWTFSLVYAYSENYV
+LPLSHDEVVHGKGSLLGRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE
+GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFAWVDGGDADGNTLVFL
+RMPAAQVVPETRIDDDGAAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT
+DATDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPTLDTTATP*
+>NZ_CP040019.1_1
+MLGAHPHPDGAAVTYRVLRPLARTVTVVRTGDGERVELAHEHDGVFAGVARMPRVAGAAA
+GDYRLEVAYETADGQTGPAQEQDDAYRHLPTLGELDLHLIGEGRHERLWEVLGARVVRTP
+AGEAVGTAFAVWAPNARAVRVVGEHNGWDGRGHAMRSLGSSGVWELLVPGVGHGHRYKFE
+ILGRDGRWRQKADPMARWTEVPPATASRVLESEYEFGDRTWMERRRTVDPHERPLSIYEV
+HLGSWRPGLDYRELAEQLVEYVQWLGFTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGS
+PDEFKHLVDALHRAGIGVIVDWVPAHFPKDEWALARFDGTPLYEHADPRRGEHPDWGTYV
+FDFGRTEVRNFLVANALYWLAEFHIDGLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLE
+AIDFLREVNATVYRVHPGVHMIAEESTAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLS
+QDPVNRRWHHGQWTFSMVYAYSENYVLPLSHDEVVHGKGSLLTRIPGDRRHQLATLRAYY
+GYMWAHPGKQLLFMGGEYGQPSEWSEAEGLDWPVSWDESHRGVQLTVRELNALYRSKPAL
+WSQDHSPAGFEWVDGGDADGNTLVFLRHPAERVVPEARIDDDGAAVSAAEPGGAPLLCIT
+NLSGSPRQGLRVGVPGAGSGPWSWTPTPPTSTGTAGGSRPGSPRC*
+>NZ_CP083691.1_2
+MTSPTLSPQSVDPAVLAAVAEGLHHDPHAVLGAHPHPDGAAVTYRALRPFARAVTVVREG
+DAARIELAHEADGVFAGVGALPRKAGVAAGDYRLEVVYPGADGEDVVELHDDAYRHLPTL
+GELDLHLIGEGRHERLWEVLGARVRRAADGALVGTSFAVWAPNARAVRVVGDFNGWTGRT
+HAMRSLGSSGVWELLVPGVEHGAAYKFEILGADGQWQQNADPMARWTEVPPATASRVMES
+EFAFTDRDWMERRRAEDPHERPLSIYEVHLGSWRPGLSYVDLAEQLVEYVQWLGFTHVEF
+LPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVNALHEAGIGVIVDWVPAHFPKDAW
+ALGRFDGTALYEHPDPRRGEHPDWGTYVFNFGRTEVRNFLVANALYWLGEFHVDGLRVDA
+VASMLYLDYSREDGQWTPNALGGNHDLEAISFLQDVNATVYRVHPGILMIAEESTAFSGV
+SAPVSAGGLGFGKKWNMGWMHDTLAYLSEDPVNRRWHHDQWTFSMAYAYSENYVLPLSHD
+EVVHGKGSLLARIPGDHRQKLATLRAYFAYMWAHPGKQLLFMGGEYGQPSEWSEERGLDW
+AASWDESHRGVQLTVRELNALYRAKPALWSADHSPQGFTWVDGGDADGNTLVFLRRPGAG
+VEGAPLLCITNLSGGTRQGLRVGVPSSGEWTVVLDTDSTDFHGDGRREQAGQLEVIEAED
+GQWQGQPAYLTLNVPPLTTLWLQPDED*
+>NZ_CP097650.1_325
+MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT
+VVRAGDGQRVELMHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY
+RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSADEAVGTAFAVWAPNARAVRVVGDHN
+GWDGRTHAMRSLGSSGVWELLAPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA
+SRVLESDYAFGDRTWMERRRVTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG
+FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHRAGIGVIVDWVPAH
+FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID
+GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNATVYRLHPGVHMIAEES
+TAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHGQWTFSMAYAYSENYV
+LPLSHDEVVHGKGSLLGRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE
+GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFSWVDGGDADGNTLVFL
+RMPAAQVVPEPRIDDDGAAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT
+DATDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPTLDTASTP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000397.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9bf81eaece8ef4109a5f0055fa82da3dfbdf1d3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000397.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_326
+MTFEPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADAHGRNTEVDVLDNTRL
+QRRVGAVMLAVAAVLAGVGVWTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP
+DGTVLRDEMVLVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP*
+>NZ_CP033200.1_51
+MTFAPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADEHGRNTEVDVLDNTRL
+QRRVGAVMLAVAAVLAGVGVGTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP
+DGTVLRDEMVLVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP*
+>NZ_CP040019.1_2575
+MAFERVDLTTPWLAYWAALLALVIGAALLAAGIWRERRHRRHAAAHGRNTEVDVLDNTRL
+QRRVGVVGLVAAVVLAGVGVWTHLAGLDALRQNLTAKYGYTDVERIRQSGTGFIIDLTQP
+DGTVLKDEMVLVDPSGEPFIGDDIFIDVIGGA*
+>NZ_CP083691.1_2423
+MTFAPVDLQTPWLLYWAAAVAAVVGVSLALAGRWRERDHRRRQAAAGSHVVMRVLENTRL
+QRRVGYGALVLALALAVWGAVAHVQGIDALRGNVRQKYGAEVEDVRQSGSGVTVDLVHPD
+GTREEDQYMAVEQDGEPVYGAELVESPPIGG*
+>NZ_CP097650.1_333
+MTFEPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADEHGRNTEVDVLDNTRL
+QRRVGAVVLAVAAVLAGVGVWTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP
+DGTVLRDEMVVVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000402.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000402.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bf83475c31651469a877aa9a851ec8b9a31db11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000402.fa
@@ -0,0 +1,56 @@
+>NZ_CP042169.1_331
+MQSSTPRSTRRIGALVAGAVLAGGTLTSSPALAAPSGAAPAAPAASPTVASPLAAAQVED
+PNADGYDSFIVTYKETAANAHAKGRANAWGKAAKEAGVSVKELRETALGSRVVTVDRKLD
+QAESAKFMADLKASGAVEAVEPDAILTATGLSPVDALYSQQWGFTGTHGMRVPGAWDRTT
+GSGATVAVIDTGITSHPDLDRNVVPGYDFISDSAAARDGGGRDSNPRDEGDWYAAGECGT
+AGASDSSWHGTHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGKCGGSLSDIADAVVWAAG
+GTVAGVPANPNPADVINMSLGGSGMCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVRP
+ANCQNTIVVAASTSQGARASFSNYGSAVDVTAPGANIISTVNNGATTPTTAGHAAYNGTS
+MATPHVAGLAALLLAAQPSLTPAQVESTLRSTARSMPVTCSAGCGAGLADASAAVSSLGG
+AQTEPGPAPVASLIVNGGFESGSTGWTGTPTGFVRTDAAKAASGQAFAQLNGVGRRNTTT
+VEQKVTVPASGATLTYALQVDTAETTASRSYDLLDVQVVTGATGTYTVASHSNLDKGGYA
+TRTVDLSRFAGTTVTLRFRGTEDSSAATTFRIDEVAVTAR*
+>NZ_CP033200.1_56
+MQSSTPRSTRRRIGALVAGAVLAGGTLTSSPALAAPSGGAPAAPAASPTAASPLAAAQAE
+DPNADGYDSFIVTYKETAANAHAKGRANAWGKAAKEAGVSVKELRETALGSRVITADRKL
+DQAESAKFMADLKASGAVEAVEPDALLTATGLSPVDALYSQQWGFTGSHGMRVPGAWDRT
+TGSGATVAVIDTGITSHPDLDRNVVPGYDFISDSAAARDGGGRDSNPRDEGDWYAAGECG
+TAGASDSSWHGSHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGRCGGSLSDIADAVVWAA
+GGTVAGVPANPNPADVINMSLGGSGVCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVR
+PANCRNTIVVAASTPQGARASFSNYGSAVDVTAPGANIISTVNNGATTPTTAGHAAYNGT
+SMATPHVAGLAGLLLATKPSLTPANVESTLTSTARSMPVTCSAGCGAGLADAARAVSSLG
+GSS*
+>NZ_CP040019.1_2562
+MKSSVQHSTRRRVGALLAGAVLAGGALTSSPAFAAPAEGARAEQAPRPVAAAPLATVDAA
+DPNADGYDSFIVTYKETAQNNNGKGRALAWGKAAKAAGVSVKELRETALGSHVVQADRKL
+DQSESARFMADLKASGAVEDVEPNAIMTATGLSPADALYSQQWGFTGTNGMRVPGAWDYN
+TGSGVTVAVLDTGITSHPDLDRNVVAGYDFISSSAAARDGNGRDSNPRDEGDWYAAGECG
+ASQPGNSSWHGTHVAGTVAAVTDTQGVVGVAPNAKIQPVRVLGKCGGSLADIADAIVWAS
+GGSVTGVPANANPADVINMSLGGSGTCGTTYQNAINAAVNRGVPVVVAAGNENQPAANAR
+PANCSNVITVAASTSQGARSSFSNYGSAVDVTAPGSSIISTINRGLTTPTTAGHASYNGT
+SMATPHVAGLTALMLAQQPGITPAQVESTLKSTARSMPVACSAGCGAGLVDATRAVAALG
+GGSTTPTPTGVIVNGGFESGATGWTGTPSDFVGNTAGYARSGSNYGVLNGYGRSNTGTVE
+QRVTVPASGASLSYWLQVGSDETTTRSQYDTLAVQVVDGSQTTTVKSHSNLEKGTSYAQH
+TVDLSAYKGKTVTLRFRGVEDYSNSTVFRIDDVAVTAK*
+>NZ_CP083691.1_2417
+MTALTSPSARRRVGSLLAAAVLAGTALTAAPTLAAAERPAEPARTSPAAAAPLADPNADG
+YDSFIVTYRETAANSTAQGRAKAWGRAAREAGVSVKELRETALGSRVIATDEKLTQEESA
+AFMADLRASGAVEAVEPNVIMTRAALSPADPYYADQWGFTGVNGMRVPGAWDVSTGTGAI
+VGVIDTGQTDHADLNANTVPGYDFISDATTARDGGGRDADPRDEGDWYLAGECGQSRASN
+SSWHGSHVAGTVAAVANTQGVVGVAPGAKVQHARVLGKCGGTLADIADAIVWSSGGSVPG
+VPANPTPVDVINMSLGGQGTCGTTYQNAINAAVGRGVPVVVAAGNENQSAANARPANCQN
+TITVAATDVNGNRASYSNYGSAVDVAAPGSGIISTVNAGTTTPTAGAYAQYNGTSMATPH
+VAGTVALMLAEDATLTPAEVESSLKTNSRPIPGVCAEGCGAGLVDAAKTLASLRGGTTDP
+HPVTPVPGAEKLVNGGFESGLTGWTATGRVAASSTAGLSATGSLHAALNGKGGTSTATLT
+QKAVLPAGAAATLSYAVRVDSAETTTARQWDKLTVSVSDGATTTTLRTHSNLDKGRGYLA
+QAADLSAYAGKTVTISFSGTEDGSGATTFRIDDVSVKAG*
+>NZ_CP097650.1_338
+MQSSPPRSTRRRIGALVAGAVLAGGTLTSSPALAAPSGDAPAAPAATPTAASPLAAAQVE
+DPNADGYDSFIVTYKETAATAHAKGRANAWGKAAKEAGVSVKELRETALGSRVIKADRKL
+DQAESAKFMADLKASGAVEAVEPDAILTATGLSPVDALYSQQWGFTGTHGMRVPGAWDRT
+TGSGVTVAVIDTGITSHPDLDRNVVPGYDFISDGRAARDGGGRDSNPRDEGDWYAAGECG
+TAGASDSSWHGTHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGKCGGSLSDIADAVVWAA
+GGTVAGVPANPNPADVINMSLGGSGMCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVR
+PANCRNTIVVAASTSQGARASFSNYGSVVDVTAPGANIISTVNNGATTPTTAGHAAYNGT
+SMATPHVAGLAALLLAEQPSLTPAQVESTLTSTARSMPVTCYAGCGAGLADATRAVSSLG
+GSS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000404.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000404.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51eb70b9cb500a69fa78cfce77c2ac046fbaee90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000404.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_333
+MEFIAPLDPGWEAALAPQAAAFEQVGERLRARRAGGEQVLPAPEHILRAFRQSFADVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGITPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLTAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD*
+>NZ_CP033200.1_58
+MEFIAPLDPGWEAALAPQAAAFEQVGEALRARRAAGEQVLPAPEHILRAFRQPFADVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGITPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLAAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD*
+>NZ_CP040019.1_2560
+MELIAPLDPGWEAALAPQAAALEQVGAALTQRRAAGEQVLPAPEHILRVFRRPFEDVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLVNIHRELQDDLGIAPPAHGDLSAWADQGV
+MLLNRALTVRAGAPGSHRGLGWEQITEAAVRALCERGTPLVGLLWGADARRMAPLLTQAG
+AGVVESPHPSPLSAHRGFLGSRPFSRVNRLLEEAGAEPVDWRLPD*
+>NZ_CP083691.1_2415
+MDLISPLDPGWAAALADQEEALVRVGAELTARRAAGEHVLPAPEHILRAFRQPFADVKVL
+IVGQDPYPTPGHPIGLCFACDRHVRPLPRSLANIHRELHDDLGVPPAAHGDLSAWTDQGV
+LLLNRVLTVRAGAAGSHRGIGWEQITEAAVRALVARGTPLVGLLWGNDARRLAPLLTAGG
+AGVVESAHPSPLSASRGFFGSRPFSRVNALLEAAGASPVDWRLPD*
+>NZ_CP097650.1_340
+MEFIAPLDPGWEAALAPQAAAFEQVGERLRARRAAGEQVLPAPEHILRAFRQPFADVRVV
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGIAPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLTAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000407.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000407.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cdd4dafc8c64847d4a64ea2eefc895d9d7aac08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000407.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_337
+MTVLIDPPAWPAHGTVFSHLVSDASLEELHAFARAAGLSERAFDRDHYDVPAHRRAELVA
+RGAVPVTGRELVRRLAASGLRVPARSRAEKRDVVLARRWARLFEGTAASPDAVTTAGRDL
+LARWAEPHRHYHDPAHLLAVLESVDLLERAGAKAGPDPRAVRLAAWFHDAVYAGDPTAPA
+GQDEADSAALARDVLTDPRLAVPADVVDEVARLVLLTAAHDPAPHDAAGAVLSDADLEVL
+GRSPEAYARYVAAVRQDYAHVCDADWARGRGAVLDALLDAERLYRTAPGRTRWEAAARRN
+LAAERAALSA*
+>NZ_CP033200.1_62
+MTVLIDPPAWPAHGTVFSHLVSDASLEELHAFARAAGLSERAFDRDHYDVPAHRRAELVA
+RGAVPVTGRELVRRLAASGLRVPARSRAEKRDVVLARRWARLFEGTAASPDAVTTAGRDL
+LARWTEPHRHYHDPAHLLAVLESVDLLERAGAKAGPDPRAVRLAAWFHDAVYVGDPAAPA
+GQDEADSAALARDVLTDPRLAVPADVVDEVARLVLLTAAHDPAPHDAAGAVLSDADLEVL
+GRSPEAYARYVAAVRQDYAHVSDADWARGRGAVLDALLDAERLYRTAPGRTRWEAAARRN
+LAAERAALSA*
+>NZ_CP040019.1_2556
+MTVLIDPPAWPAHGTVFAHLVSDASLEELHAFARAAGLPERAFDRDHYDVPAHRCEELVA
+RGAVPVSGRELVRRLVASGLRVPARGRAEKRDAVLARRWAALFEGTGARAEAVDAAGRDL
+RERWAQPHRHYHDRSHLLAVLEAVDLLERAGADPGPEPRAVRLAAWFHDAVYAGDPAAPA
+GQDEADSAALAARMLAAPALAVPAAVVGEVRRLVMLTASHDPAPQDAAGALLCDADLEVL
+GRSPEAYRRYVQAVRRDFAHVPDADWARGRAAVLESLLGAERLYRTAPGRARWEAAARRN
+LEAELADLRP*
+>NZ_CP083691.1_2411
+MAVLIDPPRWPAHGTVFSHLVSDASLEELHGFAAAHGLSPRAFDLDHYDVPAHRHAELVA
+AGALAVDGGELVRRLIRSGLRVPARRRDGRAEPVLRRRWARLFAGTDASPDAVTAAGAEL
+LGRWSEPHRRYHAPAHLLAVLQAVDLLSAAGEDLGPHPLAVPLAAWLHDAVYTADPARGP
+GADEEDSARLAERLLAAPGLALGDDVVAETARLVRLTAEHRPAPDDAAGAVLCDADLEVL
+GRAPHDYEAYVDLVRADFAHVPDEAWRTGRAAVLEGLLGADRLYATAAGRARWEDPARAN
+LERELAAHRPALS*
+>NZ_CP097650.1_344
+MTVLIDPPAWPAHGTVFSHLVSDASLEELHAFARAAGLSERAFDRDHYDVPAHRRAELVA
+RGAVPVTGRELVRRLAASGLRVPARSRAEKRDVVLARRWARLFEGTAASPDAVTTAGRDL
+LARWAEPHRHYHDPAHLLAVLESVDLLERAGAKAGPDPRAVRLAAWFHDAVYVGDPAAPA
+GQDEADSAALARDVLTDPRLAVPADVVDEVARLVLLTAAHDPAPHDAAGAVLSDADLEVL
+GRSPEAYARYVAAVRQDYAHVSDADWARGRGAVLDALLDAERLYRTAPGRTRWEAAARRN
+LAAERAALSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000413.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000413.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08db9a0bd01db237f7768eddbdfe6ae9e4ff0233
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000413.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_344
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVARVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVVAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPAFLDLATAVE
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPYV
+ARPEDRSAVICTVDFSDDVDAAAVAQVLRANGVVDVEPYRKLGRNQLRIATFAATEPEDV
+AALLRCIDHVVERLG*
+>NZ_CP033200.1_69
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVARVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVMAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVTEIKESGRWIPAFLDLATAVD
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPFV
+ARPEDRSAVICTVDFSDDVDAAAVAQVLRANGVVDVEPYRKLGRNQLRIATFAAIEPEDV
+AALLRCIDHVVERLA*
+>NZ_CP040019.1_2549
+MAAPAEITLPQDLLPADGRFGAGPSKVRSEQLQALQDAAGLLGTSHRQKPVKDLVASVRA
+GVAELFSAPEDYEVILGVGGSTAFWDAAAFGLVRERAQHLSFGEFGSKFAKATDKAPFLG
+ASDIRTAEPGSRPEPEAVAGVDVYAWPHNETSTGVMAPVARPEGIDEDALVVIDATSAAG
+GLDVDVSQADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPDFLDLSTAVD
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLAAMAARTADSSSRVYAWAEASSYATPYV
+ARPEDRSGVICTVDFSDDVDAAAVAKALRANGVVDVEPYRKLGRNQLRIATFAAIDPEDV
+SALLRCIDHVVEQLG*
+>NZ_CP083691.1_2404
+MTDPTAITIPPEMLPQDGRFGAGPSKVRPEQLQALQEAAGLLGTSHRQKPVKDLVASVRA
+GVAELFSVPEGYEVVLGVGGSTAFWDAAAFSLVRSKAQHLSFGEFGSKFARATDNAPFLE
+ASDIRSSEPGTRPQPEAVPGVDVYAWPHNETSTGVSAPVVRPEGIDDDALVVIDATSAAG
+GLDVDVSQADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPEFLDLSIAVD
+NCLKDQTYNTPALATLVMLDAQLRWMNANGGLGFTTGRTADSASRVYAWAEASEHATPYV
+ADPAERSNVICTVDFDDAVDAAAVAQALRANGVVDVEPYRKLGRNQLRIATFAAIDPEDV
+TALLACIDHVVARLG*
+>NZ_CP097650.1_351
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVASVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVMAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPAFLDLATAVE
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPFV
+ARSEDRSAVVCTVDFSDDVDAAAVAQALRANGVVDVEPYRKLGRNQLRIATFAAIEPEDV
+AALLRCIDHVVERLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000419.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000419.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2079e448efb425537eaf7453d495ee540cabea0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000419.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_352
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDTAEFFAL
+SQSKTGEDGKPKTRIIGPNCPGVITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILQAQA*
+>NZ_CP033200.1_77
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDTAKFFAL
+SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGTGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPIIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILEG*
+>NZ_CP040019.1_2542
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGSVTEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAKFFAL
+SQSKTGEDGKPKTRIIGPNCPGVITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILQAQA*
+>NZ_CP083691.1_2397
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDEDGNAVEL
+PVFGSVAEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAEFFAL
+SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LKDFGFSTAIGIGGDPVIGTTHIDALEAFEADPETKAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETADLMRE
+IMKGL*
+>NZ_CP097650.1_359
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAEFFAL
+SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILQAQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000422.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000422.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bcb3f49797aaaf4ff5a254ed6a6dc00ea262bae8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000422.fa
@@ -0,0 +1,33 @@
+>NZ_CP042169.1_357
+MQNTTLLPAPTAVDSRTETIVEIHDLRVDYGDFTAVDGIDLEIRRGEFFGLLGTNGAGKT
+TTIEVMEGHRAPTAGSVRVLGQDPSDRTLRRRVGIMLQESGFAPDLTVRETLALIGRLTR
+RDDDVDRVLDLVDLRRRRDTRTGQLSGGEKRRLDFATAIFGSPELIFLDEPTTGLDIEAR
+DALWHVVDRLRDEGATILLTTHYLEEAQERADRIALMHSGRIHRQGTVAELTSAFPSTIS
+FRLSGEPTVPFEDATIAPGGAVTIPTTNLQEDLYRLLVWSRSRDVELEGLNVGAEGLESL
+FRALNA*
+>NZ_CP040019.1_8
+MDGADVDGTADAVTEPALLHAEALECGYAGVPVTGRLDLVVRPGERVGVVGANAAGKSTV
+LRTLVGDQEPVAGRVRLEGLPVLPESAAHRRALSVLTDEDAYFPTLTVAEHLTLVALGHG
+VPEPDRVVDRELDFFALREAADAPPSRLSSGQRRRLLLAAALLRPFRLLALDEPEQRLDA
+GMRERLTARLAALEPASALVLVTHDPDVLAGAATRCLIVDGRVREAAVAEGAAWIRERT*
+>NZ_CP040019.1_2538
+MQNTTLLPAPTAVDSRTETIVEIHDLRVDYGDFTAVDGIDLEIRRGEFFGLLGTNGAGKT
+TTIEIMEGHRAPTAGSVRVLGQDPSDRTLRRRVGIMLQESGFAPDLTVRETLALIGRLTR
+RDDDVDRVLDLVDLRRRRDTRTGQLSGGEKRRLDFATAIFGSPELIFLDEPTTGLDIEAR
+DALWHVVDRLRDEGATILLTTHYLEEAQERADRIALMHSGRIHRQGTVAELTSAFPSTIS
+FRLSGELTVPFEDATIAPGGAVTIPTTNLQEDLYRLLVWSRSRDVELEGLNVGAEGLESL
+FRALNA*
+>NZ_CP083691.1_1157
+MSNAPALATRGLTRRFGPVRAVDGVDLTVPAGEVLALLGPNGAGKTTLLDMALGFSPPSD
+GTVRILGSDPVAAVRQGRVGAVLQTGGLLEDLSVRETVAMVAGCHRRHIGVSAALERAGL
+TGLAGRRVKKCSGGERQRLRFALALLTDPELLILDEPTAGMDVRARHDFWDTMHAEADRG
+RTIVFATHFLPEAEDFADRIVLMREGRIHADGTPAELATGGSVTLTGRWAGGGGDPDAPA
+RLAAALGLPRDAVQLEPQHLSPGRLRVRVPAGGRVTGDDVARHLLNERLVEDLAITHASL
+DDVFLSLTDAGQSAPSEPQESLA*
+>NZ_CP097650.1_363
+MQNTTLLPAPTAVDSRTETIVEIHDLRVDYGDFTAVDGIDLEIRRGEFFGLLGTNGAGKT
+TTIEVMEGHRAPTAGSVRVLGQDPSDRTLRRRVGIMLQESGFAPDLTVRETLALIGRLTR
+RDDDVDRVLDLVDLRRRRDTRTGQLSGGEKRRLDFATAIFGSPELIFLDEPTTGLDIEAR
+DALWHVVDRLRDEGATILLTTHYLEEAQERADRIALMHSGRIHRQGTVAELTSAFPSTIS
+FRLSGEPTVPFEDATIAPGGAVTIPTTNLQEDLYRLLVWSRSRDVELEGLNVGAEGLESL
+FRALNA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000423.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000423.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e6c63ba61c6b2b477ed09564fa13c89aefb06e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000423.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_359
+MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE
+GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA
+AAVTYVLGLLFGANVG*
+>NZ_CP033200.1_92
+MSAAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRILLGEHAENPPRPSFRRVLLRWLARIFGSVFVLALAQRAESDTPYEKDQDAPE
+GMAADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGAALLFTGGVVGLLSGSSPLARGLRQLAIGYGA
+AAVTYVLGLLFGANVG*
+>NZ_CP040019.1_2528
+MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRALLGEHAENPPRPSVHRILLRWLARIFGSVFVLALAQRAESDTPYAKDQDAPE
+GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELTLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGYGA
+AAVTYVLGLLFGANVG*
+>NZ_CP083691.1_2396
+MSPAHAATPAALPEPTREQVRRWRRYLADEIAEGQIYRDIAASKDGVERDILIGLAEAEK
+RHEEHWRALLGEHAAHPPRPSVHRILLRALARVFGSVFVLALAQRAESDTPYAKDQDATE
+HMAADEQIHEEVVRGLASRGREQLAGSFRAAVFGMNDGLVSNLALVMGIGATGVASSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAEHLDLDRNELELVYLARG
+MTPEDAKHRALERLGYLSCDCNPQFSARPDGSKGPVDHSESFAEIGSAWGASLSSFCFFA
+SGALIPILPYLFGMTGLGALVVAAVLVGIALLFTGGVVGLLSGSSPLWRGLRQLMIGYGA
+AAVTYLLGLLVGGSIG*
+>NZ_CP097650.1_365
+MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE
+GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA
+AAVTYVLGLLFGANVG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000430.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000430.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ed7ec1a375f10e8280b3a6f4ad33d2ed0dbb536
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000430.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_368
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLGRVGHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD*
+>NZ_CP033200.1_101
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLRRVRHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD*
+>NZ_CP040019.1_2520
+MTPQHHDTADAPSMQRPDPVAEPGDHLMFEHPDGEPVLVLDEDQVWRLLRRVRHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGTHPERNESQTD*
+>NZ_CP083691.1_2387
+MTEHTTPSMQRPDPAVGPGSMFPHPEGEPVLKLTDEQIWKLMRGVRHARLGLAVGGEPDI
+VPVNVRAVDGVVWFRTAPGSKLAELTVNPRVVVQADGILSDQAWSVLLHGTARRADTAEE
+IAEAESMGIRPWVPTIKDFYVKVEVDSATGRHFLLGEQPERDGAEPTD*
+>NZ_CP097650.1_374
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLGRVGHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000434.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000434.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d510ded3a5071135479d437abc19e6e706a9a09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000434.fa
@@ -0,0 +1,37 @@
+>NZ_CP042169.1_373
+MTLLSDHSRALLPGRGPLLCAADPHDGAARRRLERAWTRGVLVRLCPRVYISVSDWAALR
+PWDRTVVSAVALSIARPETVFTGLTAARLHGLGPAVEPPALELRAPSPGHHGAGPLTRRP
+FAPSLMAHDRRPPGLPRRRPRWGLPEADPAAPQRVEAVLSDGQSLGTVLADPLPTVLLVL
+GAATPFRDAVATLDALVRARPEEAARWARQAESRLGSAAALRRFERAWHFADARAESAGE
+SYSRAIVHELGFVPPTALQHRHRDANGREVARTDFWWEQVRVYGEFDGLGKYDLSFFDGD
+DTARRASIRREKEREVALQLVTRAGAHWTWGDLLRPDRLARILTAAGVPRSV*
+>NZ_CP033200.1_106
+MTPLSDHSRALLPGRGPLLSAADPHDGAARRRLERAWTRGVLVRLSPRVYISVSDWAALR
+PWDRAVVSAVALSIARPATVFTGLTAARLHGLGPAVEPPALELRAPSPGHHGCGPLTRRP
+LAPSLVAHDRRLPVPPRRRPRWGLPEAAPTGPQPVEAVLSDGQSLGTVLADPLPTVLLVL
+GAATPFRDAVAPLDALVRAWPEEAARWARQAESRLGSAAALRRFERAWHFADARAESAGE
+SYSRAIIHELGFVPPTALQHRHRDANGRGVARTDFWWEQVRVYGEFDGLGKYDLSFFDGD
+DTARRASIRREKEREVALQLVTRAGAHWTWGDLLRPDRLARILTAAGVPRSV*
+>NZ_CP040019.1_163
+MDDAPDPRLAPLRHDGHLLPGHGPLLRAAPGAPTRARKALARLWAQGVLVRLGAGLYVPL
+AHWCALAPWDRYTLACAGYALLHPAARFTGTTAAHLHGLPLAQTPPEIRLRSPAPGHRAR
+RPLAASAFSDLADARGRRLPAPPAVRWTWNGVQAPADDGGELRRRRLASGGPEGEAPPPG
+PLPPVTVEAALSDGTLLGPVTVDALPTVQLALGSGPVFREAVVPLDGLRRRLPGPSAAWA
+ERHADRLPTRAARERFERAWGFSDPRAESAGESLSRALIHELGFAAPHLQRTVFGRDGRA
+IGRTDFWWEEVDVVGEFDGIGKYDVDLHASAAERRQAITREKEREVALRRVCRDVARWTW
+ADLREPAGLEAELVRAGVPRRR*
+>NZ_CP040019.1_2515
+MTALADVADLRPGTGPLLHVARREDLAARRRLERAWTRGDLVRLAAGVYLPAPTWTALSP
+WDRSTASAAALALARPATVFTGLTAARLRGLPVALELPALDLRATSPGHRGAAPLTSRPF
+SPALLATGGRLPRPPRRRPRWGLPQAPGMAPEPVEIRLSDGTGLGWGLADASATLLLVLG
+AATPFRNAVAPLDVLLATHPEAQSWAQAAEEALPTRAARERFERTWSFAAAGSESAGESY
+SRALMHELGFASPTALQHRHRDATGREVARTDFWWADARVAGEFDGIGKYDLGLHRGDDA
+ARRASIRREKEREVALQLVTRAVAHWTWEDLRAPERLARILTAAGVPRTVCPEPTDAQRH
+HRRAERR*
+>NZ_CP097650.1_379
+MTLLSDHSRALLPGRGPLLSAADPHDGAARRRLERAWTRGVLVRLCPRVYISVSDWAALR
+PWDRAVVSAVALSIARPATVFTGLTAARLHGLGPAVEPPVLELRAPSPGHHGAGPLTRRP
+LAPSVVAHDRRLPVPPRRRPRWGLPEAAPAAPQPVEAILSDGQSLGTVLADPLPTVLLVL
+GAATPFRDAVAPLDALVRARPEEAARWARQAESRLKSAAALRRFERAWHFADARAESAGE
+SYSRASIHELGFVPPTALQHRHRDANGREVARTDFWWEQVRVYGEFDGLGKYDLSFFDGD
+DTARRASIRREKEREVALQLVTRAGAHWTWGDLLRPDRLARILTAAGVPRSV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000435.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000435.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01a29cac07bd2ac14aa434ee15971629192c4996
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000435.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_374
+MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII
+FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ
+YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG
+NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS
+RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS
+GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV*
+>NZ_CP033200.1_107
+MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII
+FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ
+YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG
+NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS
+RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS
+GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV*
+>NZ_CP040019.1_2514
+MNHALETLRDEVFARNPGEAEFHQAVSEVFEALDPVMERHPQYVEAGVLHRLCEPERQII
+FRVPWIDDNGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIIKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGGREIGYMFGQ
+YKRLTNRFEAGVLTGKGLTWGGSLVRTEATGYGAVMFADSMLKTRGESMDGQQVLISGSG
+NVAIYAAEKAASLGATVLTASDSAGYIVDPDGLDLDLLKQIKEVERARISEYVERKGGRA
+RYVAGGSVWDVEGTVALPCATQNELDESAAKTLLGNGVKAVAEGANMPCTEAATRLFLHA
+KTLFGPGKAANAGGVATSALEMQQNASRDSWNFEYTHDRLEAIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV*
+>NZ_CP083691.1_2382
+MHQVLQTLRDEVFARNPGEAEFHQAVSEVFEALDPVVERHPHYVDAGVLHRLCEPERQII
+FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIIKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGGREIGYMFGQ
+YKRLTNRFESGVLTGKGLTWGGSLVRTEATGYGAVMFADSMLRTRGESMDGQKVLISGSG
+NVAIYAAEKAAQLGATVLTASDSAGYIVDPDGVDVELLKQIKEVERARISEYAERKGGKV
+RYVAGGSVWDVEGTVALPCATQNELDESAAKTLLQNGVKAVAEGANMPSTEAATHLFLDA
+GTLFGPGKAANAGGVATSALEMQQNASRDSWDFDYTHDRLERIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV*
+>NZ_CP097650.1_380
+MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII
+FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ
+YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG
+NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS
+RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS
+GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000438.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000438.fa
new file mode 100644
index 0000000000000000000000000000000000000000..754cb4d60c946eb73007037b8c2e09551d6a16f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000438.fa
@@ -0,0 +1,19 @@
+>NZ_CP042169.1_378
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCGASALTV
+RAQQACADEFTRQVEERTGVPQLRP*
+>NZ_CP033200.1_111
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCGASALTV
+RAQQACADEFTRQVEERTGVPQLRP*
+>NZ_CP040019.1_2511
+MVLSLSLVLPWKLAALVLGLVALVLGVRVWLTSRGERRAGLPRAVAAGGMALALFGTTTA
+ALPLLAWDATVELERCTSSALTVRAQQACADAFTRAVEERTGVPQLRP*
+>NZ_CP083691.1_2378
+MSALPPVPPSAPDRRPADAAARARVGRLLVAQSAALLAMLGAFTLVLPFKVLTLAAALAA
+LVLGVLVFTASRRTAQSLVPRAAAGAGMALALMGLTVGVFPLLLWNETAGFERCTASAVT
+VRAQQTCADDFTATVERRTGVAQLGG*
+>NZ_CP097650.1_384
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCSASALTV
+RAQQACADEFTRQVEERTGVPQLRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000444.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000444.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a61dfcadf3e7e3011615463ba698c2055704259b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000444.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_385
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKRAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFTDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARVRALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGLGGPVATSGGES
+HDGSPWLSWIGADDIAGAFAHAVIDDGVTGPVNAVAPEPVTAREFATVLGRVLHRPAVIP
+VPDAGPRLLLGEEGRVETVAADQKVVADRLVASGYDMRDPELEGALRHVLGR*
+>NZ_CP033200.1_117
+MTEITVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKKAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFSDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARARALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAETSGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGVGGPVATSGGES
+HDGSPWLSWIGADDIAGAFAHAVLDDGVTGPVNAVAPEPVTAREFATVLGRVLRRPAVIP
+VPEAGPRLLLGEEGRVETVAADQKVLADRLVASGYEMRDPELEGALRHVLGR*
+>NZ_CP040019.1_2503
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPSDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGEDLLGRVPGVGAAASRRAHEAF
+EAELSRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VVRLVRSPKKAGALDAALWDPGRETVDEDALAGADVVVNLAGEPIAGRFTDEHKEAVHDS
+RVRGTRTLVDALARITAREGDDARARALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGVGGPIASSGGES
+HDGSPWLSWIGADDIAGAFAHAVLDDGVTGPVNAVAPEPVTAKEFATVLGRVLRRPAVIP
+VPEAGPRLLLGEEGRVETVAADQKVVADRLVASGYDMRDPELEGALRHVLGR*
+>NZ_CP083691.1_2367
+MTETRVFEHRTLLRHPRRTVFDWLAAPGALQRMNPPFASELAAGPSDGLREGSQTRLRIG
+APGSLGLFAGAVDGALRAALPAAVSRRIPAALSPRLPWRARHTAYEEGRMFRDEMASGPL
+SAWRHTHSVEDAAPGEADTAEGEPGAVVVDRVEYALPGVGTAGRLPVVGRPAADAAHRVF
+EAELRRQFEFRGRVMAEDLDFHAGHPGPLVGGPARTVLVTGAGGLVGTQLCALLTGGGHR
+VIRLVRSPAQAEAEDAVLWDPAGGTVDTAALRAADVVVNLAGEPLAGRFTEKHRRAVHDS
+RVDGTRTLVDAIARLPEAERPTVLVNGSAVGWYGADAGAGPDGRGLTEDLPAGDDFLAGV
+VADWEAQARRAEELGLRVVRVRTGIVLSPTGGMLAQLLPLFLAGAGGPVATRGGRSHDGS
+PWISWIGVDDIAGVFAHAALAEGVVGAVNGTAPEPVTAKEFARVLGTVLHRPAAVPVPEF
+GPRLLLGEQGAAELVRADQKASAELVLDSGYAFRDAALEGALRRLLGR*
+>NZ_CP097650.1_391
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADMADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKKAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFSDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARVRALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGLGGPVATSGGES
+HDGSPWLSWIGADDIAEAFAHAVLDDGVTGPVNAVAPEPVTAKEFATVLGRVLRRPALIP
+VPEAGPRLLLGEEGRVETVAADQKVLADRLVASGYQMRDPELEGALRHVLGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000445.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000445.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be1028e88521388ab2a567f721307d3acdbf6780
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000445.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_386
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAVPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALSQLIRETGALQD*
+>NZ_CP033200.1_118
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLMVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVFVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMAAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTTRVLTAQVMVALQEGFPQLALALWEALARDAF
+TALGQLIRETGALQD*
+>NZ_CP040019.1_2502
+MTTPVQKHLDRLTSAHTGEGDVPDGLGVAMLMVDGHRYVSGSMTSVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSDTTDENALGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVLELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEIRELMAAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSQHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALSQLIRETGALQD*
+>NZ_CP083691.1_2366
+MKSPVQDRLDRLTAAHTPGTAADADATSDAGTGLALSVATVGGDHYSAGELVAVPLAGLA
+GPVVHALALEDLGVERVGEAVGTVPRPDLRTRLELEPGTGRPLTPLQDAGTMALAALVKG
+RGGRDRAARLLQQLAGLIGRETAPTDAAVRAADRAQHRARAAAWLLRSVGVLEADPDGLL
+ADVATLRAAPVTVADLALLAGTLAAHGVHPVSGERVLAEETVRAVLSALDACGMDTVDGA
+WALDVGQPGWSSARAGTVIAVVPGHMGIAVQGPADPDDADAPSPAALAALRTLVRDFELH
+PSQAAGSPRAAFRTHYRVDQAPSGSVRSAEVLELLSAHGDTAHVLELGGHVGFSQVDALA
+HVARNLPAALETIIVDVRSVSSTSHAAAVLAAQWFAYALHHGLDVVVVDRDTAAVDQVMA
+TAEASGVTLPDPLHDADDADPGHQDLGPAFRFFDSRSRAVQWAEQRLLARHAPHLLPASE
+EEAAMAPLLQHLSSEDARLLESMMDERVYEDGQIIRRAGQPFGGIYVITSGRVELTGQGT
+GGRRVRRTVLTPGMTFGEMALGQPGRQPSTVRARGRVTTRVLTAQVMYALQEGFPSLALT
+LWEALARDAYTALGQLIRETGALQD*
+>NZ_CP097650.1_392
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSAMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSNTTDENGLGAAAMTALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAALAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALGQLIRETGALQD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000448.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9506426b99159fb420214e25a30ee80d32efc2bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000448.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_393
+MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD
+LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL
+DFPGKRLVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA
+AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS
+TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG
+*
+>NZ_CP033200.1_122
+MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD
+LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL
+DFPGKRIVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA
+AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS
+TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG
+*
+>NZ_CP040019.1_2498
+MSTAVSAPAPEGRAPEGRGPEGRAPRRRGTGKATALWWILTVVIGVWCLFPLFSIFATSF
+KTPADLANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAY
+AIARLDFPGKRLVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWIGLIIPYLSLTLPIS
+IWTLAAFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFG
+ISLTSTETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTN
+GAVKG*
+>NZ_CP083691.1_2362
+MSTGNPIPAPQEPVTTRPDGAAERTEAGTAVGDRGVAPTTTRRTRKGSSSWIWWLLAVLI
+GVWCLFPLFSIFATSFKTPADLSNGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGIT
+VIATLIAVVLATLCAYAIARLDFPGKRIVLTVSLMVSMFPVISLVTPLFNVWRTLGLYDT
+WLGLIIPYLSLTLPISIWTLAAFFRQIPWELDQAAQVDGATPLQAFRKVIVPLAAPGVFT
+TAIIAFFIAWNDFVFGISLTSTEAARTVPAALAFFTGASQFESPTGAISAAAIVVTIPIV
+ILVLLFQRQIVAGLTNGAVKG*
+>NZ_CP097650.1_396
+MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD
+LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL
+DFPGKRIVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA
+AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS
+TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000457.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000457.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b3bf1f57caf046582c79bf0f92e64f71e2e0db9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000457.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_405
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VSGTVIG*
+>NZ_CP033200.1_135
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VSGTVIG*
+>NZ_CP040019.1_2484
+MSQPLTTGSGETRRGPRAGLRVGSVGFAAMIVILIVAIMFAANQNDVIGWLVVAVAAGWL
+VFALVVFLQMRRGVQAAGRKVDAAMENARADVAALRGQGAAAAPQAAAHAPAGDPMRDTK
+LDHSFKIAQVQVKVVREQLAAGGAMDREMVDRALETIDITAANARDMIKESRGQGGSEGP
+VSGTVIG*
+>NZ_CP083691.1_2350
+MPQSIPSGSAGTRPARAGLTVGSTGFAVMVAVLLVAIVFAANANDLIGWLVVAIAAGWLV
+FAVVVFLQMRKGVREAGRKVDTAMQNARADVAALRAPQQPAPAAAVPAAAGDPMRDTKLE
+HSFKICQVQARVITQQLDAEGPLDREMVDRALETITITAQNARDMIKESARDAEGPVSGT
+VVS*
+>NZ_CP097650.1_408
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVQAAGRKVDTAMQNARADVAALRGRDADAAAPAVAPSAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGESMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VIG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000458.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8614570f78676e2bd94dab1bb68f1e4ee8c9c62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000458.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_406
+MTALPEKDPVTGKYPEPAEGEPVVHANAGAPKADGAVRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV
+RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQVDKYRFLDEMVRR
+LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR
+ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA
+PLVVDYQF*
+>NZ_CP033200.1_136
+MTALPEKDPVTGKYPEPAEGEPVVHANAGAPKADGAVRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV
+RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQEDKYRFLDEMVRR
+LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR
+ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA
+PLVVDYQF*
+>NZ_CP040019.1_2483
+MTVLPEKDPVTGKYPEPAEGEPVVHANAGAPKEDGALRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADITAKLVREVVGEDWDEVHLADAEAAAKGRAGVAIASRFPIEAV
+RTGISDADAYFDDAGRWIEADLRLPDGSALTVVSAYVHSGEADTPKQVDKYRFLDEMVRR
+LGELSAGPDHALVTGDLNVGHTELDIKNWKGNQKKAGFLPEERAYFDRFFGELGFTDVHR
+SLAGQVPGPYTWWSMRGKAFDNDAGWRIDYQMATAALAEKASSAVVDRAPSWGTRFSDHA
+PLVVDYRF*
+>NZ_CP083691.1_2349
+MTVPQKDPVTGKHPGPAAGEPVVHANAGAPKPEGALRVATVNVNGIRASHRKGMGGWFAG
+RGVDVLTLQEVRAPQEIAHALVRDVVGDAWDEVHVADVEAASKGRAGVAVASRFPFEDVR
+TGIGGAEDHAADAGRWIEADVRLPDGSLLTVVSAYVHTGGVDTPKQVDKYRLLDEMVRRL
+PELAADGRHVLVTGDLNVGHTERDIKNWRGNVKKAGFLPEERAYFDRFFGELGYVDVHRT
+LAGDVPGPYTWWSMRGQAFDNDAGWRIDYQMATPELAARATSAVVDRAPSWGTRFSDHAP
+LVVDYQF*
+>NZ_CP097650.1_409
+MTALPEKDPVTGKYPEPAEGEPVVHAHAGAPKADGAVRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV
+RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQVDKYRFLDEMVRR
+LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR
+ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA
+PLVVDYQF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000459.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000459.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3e33e59f987d094431eed596964701a78ca3882
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000459.fa
@@ -0,0 +1,39 @@
+>NZ_CP042169.1_407
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLAPVRERALALLDDPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR
+*
+>NZ_CP033200.1_137
+MTMKKNSVQDVLAQDAAATAHLPGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILAAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLAPVRERALELLADPAELDRILASGAEKARAVATPVLEDVYAKVGFLPPLR
+*
+>NZ_CP040019.1_2482
+MKKNSVQDVLAQDVSATAHLAGASDRHRVLSGMQPSADSLHLGNYLGALTNWVRTQDDFE
+AFFFIPDLHAITVPQDPAALAQRTRVAAAQFIAAGIDPERSTLFVQSQVPEHAQLAWVLT
+CMTGMGEAMRMTQFKDKSAKQGAEAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQHVE
+LTRDLAQRFNHRHGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINVMDDPKR
+TAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAMTDVPVAELEGRYVGRMYGHLKVDV
+ADAVVERLAPVKARTEELLADPAELDRILAAGAAKARAVATPVLEDVYAKVGFLPPLR*
+>NZ_CP083691.1_2348
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSDRPIPELEAEFEGKMYGHLKV
+AVADAVVERLAPVRERALGLLDDPAELDRILAAGAAKAREVATPVLEDVYARVGFLRPLR
+*
+>NZ_CP097650.1_410
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLVPVRERALALLADPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000460.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000460.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a239894e99477534cd0846e10a705776310f71d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000460.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_408
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAERARRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA
+DERVGTERDGARA*
+>NZ_CP033200.1_138
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA
+DERVGTERDGARA*
+>NZ_CP040019.1_2481
+MHTVQQAAGAHAPAGREPVLETENLVKVYGRGESRFDALKGVTLQIQAGESVAIVGKSGS
+GKSTLMHLLALLDRPSAGVVAMDGRPVQDVSPAEVARLRNETFGFVFQQFFLNPAQTVLE
+NTVLPLKISGVPRAERRERGMAVLERLELADKAGNKATDLSGGQKQRVCIARALVNRPTV
+LFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAARCDRRLVMQDGMIVDE
+TTTAGAQA*
+>NZ_CP083691.1_2347
+MSTVHTHPPETQASRGEEPVLETENLVKVYGRGASRFDALKGVTLQIHRGESVAVVGKSG
+SGKSTLMHLLALLDVPTSGVVAMDGRPVSQLKAAEVAHLRNERFGFVFQQFFLNADQTVL
+ENVVLPLKIAGVPRHEREARGREVLERLEIADKAKNRANDLSGGQKQRVCIARALINRPT
+VLFADEPTGNLDSATSRSVEEILFGLHRDEGITLVVVTHDDDLAAQCDRRLVMQDGVIVA
+AEGAGRAVAAGTGARA*
+>NZ_CP097650.1_411
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDDGITLVVVTHDDDLAAKCDRRVELQDGVVID
+DERVGTEQDGARA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000477.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000477.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b7bbbd1490734d54db1b3c3fc054422efd49ffa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000477.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_426
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQAGLDEAVEADAAAGHAIRVGQLVTAMRHADRAQEIAELAVRHRAA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD*
+>NZ_CP033200.1_156
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQAGLDEAVEAADAAGHVIRVGQLVTAMRHADRAQEIAELAVRHREA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGIVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD*
+>NZ_CP040019.1_2463
+MTATQLPDTASPSPLEVDLAALPKVSLHDHLDGGLRVGTVLELATEAGVDVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQEGLDEAVDAAEAQGRLIRVGQLVTAMRHADRAQEIAELAVRHRER
+GVVGFDIAGAEAGFPPSRFAETFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEFGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+EAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLAELLDLQLNAAE
+AAFLAVDEREDLAEILVAGWGEVISGDDAGPVLEELDEDDEDEDA*
+>NZ_CP083691.1_2330
+MTISSQTPADAAPSPLTIDLGALPKVSLHDHLDGGLRVATVLELAREAGVEVPADTVDGL
+ADWFAEHANGESLEKYLETFALTTSVMQTHEQLRRVAREFVEDLVADGVVYGEIRWAPEQ
+HLASGLTLDEAVEAVQEGLDEAVDAADEAGHVIRVGQLVTAMRHADRAQEIAELAVRHRD
+RGVVGFDIAGAEIGFPPSRFADTFTWLAQQHLPVTVHAGEAEGLSSIQDALVSGRALRLG
+HGVRIADDIQVEFGGLDEDGVPVDADTGIVDLGETAAWVRDRQIALEICPSSNLQTGAVD
+AAAGIAGHPIDLLVQLGFRVTVNTDNRLVSNVSLTDELYLLAETFGYSLSELLDLQLNAA
+EAAFLAVDEREDLAEILVSGWGEVISGAGGTVALEELEADTDDEADA*
+>NZ_CP097650.1_429
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLTLDEAVEAVQAGLDEAVEAADAAGHVIRVGQLVTAMRHADRAQEIAELAVRHREA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000482.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000482.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16a8ace0819c2371c7ef866e8ec98ffab3c80656
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000482.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_435
+MANPVMNSQNFQQQMQGGGQAQPGWYQGGQQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA
+HQQSMEDAFRAPSAGPEQTGRMTYNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL
+VLGLVNSFKREPSPVLIMLYALAEGLFLGGISAVFEAAYPGIVVQAVLGTFSVFAVMLAL
+YTSGKFRPTPRMTKIVMTAMLGYLVFMLINLVLTWTGIANLRTGGLGLIIGAIAVLLAAY
+SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYVEILRIVAILRGND*
+>NZ_CP033200.1_162
+MANPVMNSQNFQQQMQGGGQAQPGWYQGGQQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA
+HQQSMEDAFRAPSAGPEQTGRMTFNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL
+VLGLVNAFKREPSPVLIMAYAVAQGLFLGGISAFFEGAYPGIVVQAVLGTFSVFAVMLAL
+YTSGKFRPTPRMTKIVMGAMIGYLVFMLVNLVLTWTGIGNMREGGLGLIIGAIAVLLAAY
+SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYIEILRIVAILRGND*
+>NZ_CP040019.1_2444
+MANPVMNSQNFQQQMQGGGQAQPGWYQGGTQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA
+HQQSMEDAFRAPSAGPEQTGRMTFNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL
+VLGLVNAFKREPSPVLIMAYAVAQGLFLGGISAFFEGAYPGIVVQAVLGTFSVFAVMLAL
+YTSGKFRPTPRMTKIVMGAMIGYLVFMLVNMVLTWTGIGNMREGGLGLIIGAIAVLLAAY
+SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYIEILRIVAILRGND*
+>NZ_CP083691.1_2324
+MANPVMNSNNFQQQMHAGQQQPGWYQNAAPQAPSGQQQSPYGQSQAYGAQQAAQQAAFQQ
+NMEQAFRAPAAGAAETGRMTYNDIVGKTALMLTLVVIGGAIGWTMPALMLIGAIVGLVLG
+LVNSFKREPSPVLIMGYALAEGLFLGGISASFEAAYGGIVLQAVLGTVSVFAVMLALYTS
+GKFRPTPRMTKIVMAAMIGYMLFMLLNLVLTFTGIANLRLGAMGLIVGAVAVLLAAYSLT
+MDFEMGAQGVKNGVPQKYSWTVAFGLTVTLIWLYVEILRILSILRSDD*
+>NZ_CP097650.1_435
+MANPVMNSQNFQQQMQGGGQAQPGWYQGGQQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA
+HQQSMEDAFRAPSAGPEQTGRMTFNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL
+VLGLVNAFKREPSPVLIMAYAVAQGLFLGGISAFFEGAYPGIVVQAVLGTFSVFAVMLAL
+YTSGKFRPTPRMTKIVMGAMIGYLVFMLVNLVLTWTGIGNMREGGLGLIIGAIAVLLAAY
+SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYIEILRIVAILRGND*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000485.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000485.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb004ebbfbb991ca37dabc55d142f6784c22d02b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000485.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_438
+MGAAQATDTPDRTVPTPSPRWVRPAGGPPAPTALPVTLEEIERARETLRGIAELSPLQHS
+RALSRAVGTDVHLKCENLQRAGSFKVRGAYVRMAQLSEEERGRGVVAASAGNHAQGVALA
+AAKLGIRARIFMPHGVALPKLQATRDHGAEVVLHGSTVDESLAEAQRWATETGAVFIPPF
+DDPAVIAGQGTVGLEILDVLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTVRVIGVQ
+AATAAAFPGSLEEGRVQVLESVSTIADGIAVGRPGALPLRIAAELVDAVVTVTDDEIAAA
+LVHLLERSKLVVEPAGAVGVAALLAGRTADLGFELGTTAVILSGGNIDPMLMLKSIQAGL
+SAAGRYMTVRIPLRDRPGELATISRIIADTDANVVRVDHTRVGPDLSMGGVHITIDMETR
+GTEHSAQVLEALRAAGYSPAPLP*
+>NZ_CP033200.1_165
+MGAAQATDTPDRTVPTPSPRWVRPAGGPPAPAELPVTLEEIERARATLRGIAELSPLQHS
+RALSRAVGTDVHLKCENLQRAGSFKVRGAYVRMAQLSEEERGRGVVAASAGNHAQGVALA
+AAKLGIRARIFMPHGVALPKLQATRDHGAEVVLHGSTVDESLAEAQRWATETGAVFIPPF
+DDPAVIAGQGTVGLEILDVLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTVRVIGVQ
+AATAAAFPGSLEEGRVQVLESVSTIADGIAVGRPGALPLRIAAELVDAVVTVTDDEIAAA
+LVHLLERSKLVVEPAGAVGVAALLAGRTADLGFELGTTAVILSGGNIDPMLMLKSIQAGL
+SAAGRYMTVRIPLRDRPGELATISRIIADTDANVVRVDHTRVGPELSMGGVHITIDMETR
+GAEHSAQVLEALRAAGYSPAPLP*
+>NZ_CP040019.1_2441
+MTAGEVAQEQESVQTAADAAPVAGPRWVRPADAEPAWEGLPVSYEDVEAARETLRGVSEV
+SPLQLSRSLSRAVGTDVHLKCENLQRAGSFKIRGAYVRMAGLSEAERVRGVVAASAGNHA
+QGVALAAAKLGISARIYMPRGVALPKLQATKDHGAEVVLHGSTVDESLAEAQRWAAETGA
+VFIPPFDDPAIIAGQGTVGLEILDTLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTV
+RVIGVQAATAAAFPGSLEEGRVQVLESVSTIADGIAVGKPGNLPLQITAELVDAVVTVTD
+DEIAAALVHLLERAKLVVEPAGAVGVAALLAGRTADLGFELGSTVAVLSGGNIDPMLLLK
+SVQSGLSAAGRYMTVRIPLRDRPGELATISRIIADSDANVVRVDHTRVGPELSMGGVHIT
+IDMETRGPEHSAAVLEALREAGYSPVPIH*
+>NZ_CP083691.1_2321
+MTAGGAAPAPWLRPADAQEPTGDRLPVRLEDVEAARGVLEDVAEHTPVMLSRALTDQLGT
+PVHLKCENLQRAGSFKVRGAYVRMARLSAEERAAGVVAASAGNHAQGVALAAAKLGIHAR
+IVMPRGVALPKLQATQDHGAEVQLYGSTVDEALAEAQRYAAATGAVFIPPFDDPAIVAGQ
+GTVGLEIMDDLPRVDTVLVGIGGGGLIAGLAIAVKERARREGRTVRVVGVQAATAAAYPV
+SLREGRVQVLESVSTIADGIAVGRPGALPFDIVSGLVDAVVTVTDDEIAGAMVHLVERSK
+LVVEPAGAVGVAALLSGRARDLGFDLGTTAVVLSGGNIDPMLMLKSIQSGLSAAGRYMTV
+RIPLRDRPGELATISRVIAETEANVVRVDHTRVGPELSMGSVHITLDMETKGWDHCEAVL
+TALRESGYSPLRLT*
+>NZ_CP097650.1_438
+MGAAQATDTPDRTVPTPSPRWVRPAGGPPAPTALPVTLEEIERARETLRGIAELSPLQHS
+RALSRAVGTDVHLKCENLQRAGSFKVRGAYVRMAQLSEEERGRGVVAASAGNHAQGVALA
+AAKLGIRARIFMPHGVALPKLQATRDHGAEVVLHGSTVDESLAEAQRWATETGAVFIPPF
+DDPAVIAGQGTVGLEILDVLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTVRVIGVQ
+AATAAAFPGSLEEGRVQVLESVSTIADGIAVGRPGALPLRIAAELVDAVVTVTDDEIAAA
+LVHLLERSKLVVEPAGAVGVAALLAGRTADLGFELGTTAVILSGGNIDPMLMLKSIQAGL
+SAAGRYMTVRIPLRDRPGELATISRIIADTDANVVRVDHTRVGPELSMGGVHITIDMETR
+GAEHSAQVLEALRAAGYSPAPLP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000492.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000492.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cf4bf8bf66a44fd5f9023cdf24e336fa5b781ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000492.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_445
+MGRPEAFYRLYERRLTRGLDPERLPRHIGVLVDGNRRWARAFGASTQQGHQAGAERILDF
+IGWCDEAGIPVVTLYMLSTENLRRPAEELAPLLEIIQTTAERLAQPAEGRAPVCVQPVGA
+VDLLPEPMARRLAEVAEQTKGHDGVHVNVAVGYGGRQEILDAVRELLRDEHALGHSAAEV
+AESVTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD
+FLRALRDYGSRQRRFGT*
+>NZ_CP033200.1_172
+MGRPEAFYRLYERRLTRGLDPERLPRHIGVLVDGNRRWARAFGASTQQGHQAGAERILDF
+IGWCDEAGIPVVTLYMLSTENLRRPAEELAPLLEIIQTTAERLAQPAEGRAPVCVQPVGA
+VDLLPEPMARRLAEVAEQTKGHDGVHVNVAVGYGGRQEILDAVRELLRDEHALGHSAAEV
+AESVTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD
+FLRALRDYGSRQRRFGT*
+>NZ_CP040019.1_2434
+MQRPEAFYRLYERRLARGLDPERLPRHVGVLVDGNRRWARAFGATTQEGHQAGAERILEF
+IDWCDETGIPVVTLYMLSTENLGRPPEELEALLGIILATAERLAEPREGRRPVRVQTVGA
+VDMLPEEMARRLRAVEERTRDNDGVHVNVAVGYGGRQEILDAVRELLRDEHGRGRTAAEI
+ADAMTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD
+FLRALRDYGSRQRRFGA*
+>NZ_CP083691.1_2314
+MRRPEVFYRLYERRLAGELDPERLPHHVGVLVDGNRRWARAFGATTQEGHQAGADRIIDF
+IGWCDEVGVPVVTLYMLSTENLARPAAELTPLLEIITTTTQRLAEPREDRAPVRVQPVGA
+VDLLPPRMAQQLRDVAERTRDNTGVHVNVAVGYGGRLEIVDAVRELLEEAAAEGRSAADV
+AAELTVDAISDRLYTRGQPDPDLVIRTSGEQRLSGFMTWQSAYSEFYFCEAMWPAFRRTD
+FLRALRDYGRRQRRFGS*
+>NZ_CP097650.1_445
+MGRPEAFYRLYERRLTRGLDPERLPRHIGVLVDGNRRWARAFGASTQQGHQAGAERILDF
+IGWCDEAGIPVVTLYMLSTENLRRPAEELAPLLEIIQTTAERLAQPAEGRAPVCVQPVGA
+VDLLPEPMARRLAEVAEQTKGHDGVHVNVAVGYGGRQEILDAVRELLRDEHALGHSAAEV
+AESVTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD
+FLRALRDYGSRQRRFGT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000495.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000495.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a22bfdd0574d1f0f006ddf71ab8972f7b171b459
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000495.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_448
+MSGVGWAWTHGAPATAVLWSLGLVWFAVCAGVLVRTDLREHRLPNRWTLRLALGGLTMMT
+GGALLAGRGDLTLCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA*
+>NZ_CP033200.1_175
+MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT
+GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA*
+>NZ_CP040019.1_2431
+MDGVGWAWAQGLPATAVLWSAGLAWFAVCAAVLVRVDLREHRLPNRWTLRLALGGLAAMA
+GGAALAGRADLVLSSVLGGLGYAAAMLVLHVLSRGSLGMGDVKLAAGLGAYTGVLGGSAV
+VAAGLGAILLGGAVAAVLVAARRASRSTALPFGPPMILAAAAVLAFAPAGG*
+>NZ_CP083691.1_2311
+MTWWTGAWEAGERLTAMLWAAGLVWFLLCSVVLARTDLREHRLPNRWTGRLALGGVVAMG
+GGAVLGGLWSVVASCLLGGLGYALAMLALHVLTRGGLGLGDVKLAAGLGLYCGVAGLAAV
+LAAAVLAVLLGGVVAVVLVLARRADRHTALPFGPAMVAGALGVLLLA*
+>NZ_CP097650.1_448
+MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT
+GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000499.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000499.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a832fca5c78aee6af9a921d256249613595c003
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000499.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_452
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR*
+>NZ_CP033200.1_179
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR*
+>NZ_CP040019.1_2427
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVSMAGTVVIGEGEKDEAPMLFNGEEVGDGSGAPVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDLRLPVKQNVALVAKALDKPASQVTVCVLDR
+PRHEGLVKEIREAGARVKFILDGDVAAAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGVIQGRLAPTDETEKQKALDAGLDLDAVLSTNDLVTSDHCYFAATGITDGDLLRGVRFV
+DGRVVTQSIVMRSWSGTVRTVDAEHDVRKWSKWLEDRGTRTGR*
+>NZ_CP083691.1_2307
+MTSASSENTGYENHVPDRNLAMELVRVTEAAAIAASPWVGGGDKNRADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGERVGDGKGASVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRAAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGVIQGRLAPTDDAEKQKALDAGLDLDAVLTTDELVTSDHCYFAATGITDGDLLRGVRFA
+GGRVHTQSIVMRSKSGTVRTVDAEHHVDKWSQWLKNRG*
+>NZ_CP097650.1_452
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDADHDVKKWSKWLEDRDAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000501.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000501.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f0155e70ee2fbc88317d44a74885dec6fe7f644
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000501.fa
@@ -0,0 +1,52 @@
+>NZ_CP042169.1_454
+MSSATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLI
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGQQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESVTAGSEPTGVSATPLLTVLAVVAQE
+TQTPDVDEDDPATWPAPPTRTDGEPFTAEDLMTAEDLGQEDVLNHASSTNGLCVPAP*
+>NZ_CP033200.1_181
+MSPATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLM
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGEQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESATAGSEPTGVSATPLLTVLAVVAQE
+TEAPDVDEDDPATWPAPPTRSDGEPFTAEDLMTAEDLGQEGVLNHASSTNGLCVPAP*
+>NZ_CP040019.1_2424
+MSPATGSVPAGHAQPDPLRDPRVASPTERTRRALILTLLTLFVPGGAQVVAGSRPLGRAA
+LRVTVAVWGVLLAGLLWWLVHRASLISLLARDGVLLVLAIALGLLAVGWAVLWIDTLRLI
+RLHLLAPGARKATAVATVLALVLTSGALLYGGWATNAGRGALGSVFGDGPAVARTEGRYN
+ILVMGGDAGEGREGLRPDSIHVASVDARSGAVVMFSLPRNLQNAPFTEGSPLWGVYPDGF
+SCGDECILNALYTDVETNHPDLYPDAENPGAEAMMDAAGGILGLEISGYALMDMGGFAQL
+IDAMGGVDLVTGGYVVHRGVRPDGEWGNIWWEPGEHHFDGKDALAFARSRHWSTDYARIR
+RQQCMQAAMLAQFSPGTVLTRFEQILDAGQQIVTTSLPQSQLGTFVDLAERSRGQKMRRL
+TIGPPDFGDTRDQFTTFPDYDLVHERVDEMLAEEPGQAGGATGGEAGHAAGVGSGASALP
+LLTVLAVAAQEAVPDEVDEDDPATWPAPPTRPDGGAYTAEDLMLAEDLGQEDLLNHASST
+NGLCAPGR*
+>NZ_CP083691.1_2305
+MPASAASSPVLTRDPVRDPRQATGPERRRRAGILLLLTLLVPGGAQAVAGSRRWGRIALR
+VTLAVWAAVLLALVLALTARAALVSVLANPVVLVLLGVVLVTLAIGWGLLWVDTFRLIRV
+HLLGPRARAATAAATVVALVVTSGGLGYTAWMTQSGRGALGSIFGSGPAIEAADGRYNIL
+VMGGDAGEDRVGLRPDSMHVASVDAETGAVTLFSLPRNLQNAPFTPDSPLWQAYPNGFDC
+GDDCILNALYMDVEEKHKDLYPDAEHPGAEAMMDAAGGVLGLEITGYAMMDMAGFAQLVD
+AMGGVDVVSGGYVTHRGARPDGTWGDIWWEPGTHHFGGDDALAFARSRKFATDYARIRRQ
+QCMQAAMLQQFTPATVLTRFEGIVSAGTQIVTTNVPQSQLGTFVDLADRSRGYRMARLTI
+GAPDFGTANDRFTTRPDYDLVHRRVAELLDEEPTKAGSASTAAPAASPGATPLLALTAAI
+PAPLLVAEASPAATGTGGTTRPGVDPDDPSTWPSAPTGPNGEPYSAMELMRIQDAGDEAQ
+LVRIASTNDLCAPGG*
+>NZ_CP097650.1_454
+MSSATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLI
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGQQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESVTAGSEPTGVSATPLLTVLAVVAQE
+TQTPDVDEDDPATWPAPPTRTDGEPFTAEDLMTAEDLGQEDVLNHASSTNGLCVPAP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000504.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000504.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8899223ff7253fe075138cf1fe959ccf3057926
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000504.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_458
+MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDEPGAVDQRIELSGRVTVNWAAKFAGLL
+GAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEGDSPAAVLTDRPEAWPDPSVAV
+FAVALPRGLEPEFDGPAVDPAVVDVAAEIRAQPDALPGPVDHVRPASIPAGADVAPDDDG
+PRPRLTWAGVRAALEAWDAGRAVTVRP*
+>NZ_CP033200.1_185
+MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDEPGAVDQRIELSGRVTVNWAAKFTGLL
+GAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEGDSPAAVLTDRPEAWPDPSVAV
+FAVALPRGLEPEFDGPATDPAVVDVAAEIRAQPDALPGPVDHVRPASIPAGTDVAPDDDG
+PRPRLTWAGVRAALEAWDAGRAVTVRP*
+>NZ_CP040019.1_2421
+MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPGEHGAVDQRIELSGRVTVNWAAKTAGLL
+ADEGLGPGDPVALDLPAHWLSHALALGVLCAGAEPADDGAAPAAVLTDRPERWTDPATAV
+FAVALPRGLELPTGGAVADPSVVDVAAEILGQPDALPGPVDHVRPEALPAADVAAADGDA
+RTDEDQDDDGPRPRLTWAGMRAVLQAWDAGRAVQVRP*
+>NZ_CP083691.1_2301
+MVSLSAPRPDGPLVTRLASSPRPALVQEPAPAGEAAGAAHGAVDQRIELSGSVTVNWAAK
+AAGLLLDEGVAPGDAVLLDLPDHWLSRALALGVLCAGARPAFVAGPADRAQEAPDDAAAV
+LTDRPEHWDDPVLTVVAVRLPRGIEPDFGDDDAGDPSVVDLAAEIRAQPDALPGRVDHVT
+VDAVPADPADAAGPLTEGGVGVGRARLDAPALRASLEAWDAGRAAHVPA*
+>NZ_CP097650.1_458
+MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDEPGAVDQRIELSGRVTVNWAAKFAGLL
+GAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEGDSPAAVLTDRPEAWPDPSVAV
+FAVALPRGLEPEFDGPAVDPAVVDVAAEIRAQPDALPGPVDHVRPASIPAGADVAPDDDG
+PRPRLTWAGVRAALEAWDAGRAVTVRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000505.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000505.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48a106aea89f664758d7ad0a57eef4aee00bfb02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000505.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_459
+MEQTQRVEDAHHADPAPAPRPRSVPSDWFLDPADPQAGVSGASLEDQATAFLTAHDLDGE
+TGTPAATVTALFPGDARPVEAAPVSADWAAIPGVTTEPVEGELAWQADALCAQTDPEAFF
+PEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA*
+>NZ_CP033200.1_186
+MEQTQRVEDTHRADPAPAPRPRSVPSDWFLDPADPQAGVSGASLEDQATAFLTAHDLDGE
+TGTPAATVTALFPGDARPVEAVPVSQDWAAIPGVTTEPVEGELAWQADALCAQTDPEAFF
+PEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA*
+>NZ_CP040019.1_2420
+MEHTQRVEDTHRAESAQAAAPRPRGVPSDWFLDPADPLAGADAATLEDQATALLSAHDLE
+DEAGTPSATVTALFPGDAGQPVEAAPVADDWAAIPGLVTEPVEGELAWQVDALCAQTDPE
+AFFPEKGGSTRDAKRVCEACVVKDQCLEYAMENDERFGIWGGLSERERRRLRRARA*
+>NZ_CP083691.1_2300
+MQNTQRVEDVARAERAPAASRSRGVPTDWFLDPADPTAGGRATAGLAAESLEDQATAFLA
+AHDLDDAGTPAATVTALVPRPAEAPAVDDALVPDAWQPVPGVVMEPAEGELAWQVDALCA
+QTDPEAFFPEKGGSTRDAKKVCAACDVRRECLDYAMANDERFGIWGGLSERERRRLRRER
+G*
+>NZ_CP097650.1_459
+MEQTQRVEDTHRADPAQAPAPRPRSVPSDWFLDPADPQADVSGVSLEDQATAFLTAHDLD
+GETGTPAATVTALFPGDARPVEAVPVSADWAAIPGVTTEPVEGELAWQADALCAQTDPEA
+FFPEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000509.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000509.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abdaa38cffff6fac7d3f311f29f5c1af0f8f2abe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000509.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_463
+MASHQAGRGRDERAGAEDFDSGLDYGAFVEDDAADDPNRTQALPAMGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDAGRPAADADRDIVASRAVPEGGRRPLPGADELGPLSAAVG
+ARAAGSSAAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAILAPLA
+LVLATVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIAAAALVVLLVVCALLIASLLRTSPGGVRRALFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVRDALIRLYPQQFWVDAAVVVGL
+VTLLASLVTLVLTWPTRRRRELSADRREQLLRTRLRWAREDDAVVR*
+>NZ_CP033200.1_190
+MASHQAGRGRDERAGAEDFESGLDYGAFVQDDAADDPNRTQALPATGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDADRPAPDADRDIVASRAVPESDRRPLPGADELGPLSAAVG
+ARAAGSSAAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAILAPLA
+LLLAAVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIATAALVVLVVVCALLIASLLRTSPGGVRRALFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVQDALIRLYPSQFWIDAAAAVGL
+ISLLTALLTLVFTWPTRRRRERTADQRSAFESTRLRWAREEDAQLR*
+>NZ_CP040019.1_2416
+MASHQAGRGREERAGAEDFESGLDYGAFAEDDAAEDPNRTQALPASGRDDAGVQHTSALS
+PEDLAALRGGDAAAADGRAERSAERGMPDARERDIVASRAVPSSDRRPLPGADELGPLSA
+AVGARSASGSSAADPADRYPQDASAAYAASSSAALQGPTPEERARLPKAGPRVAQVLLAI
+LAPLALLLAAVRFVASPAFLWLEYHRPGFPADRFGFDTGDRMHYGSAGLDYVTNLAGSRY
+LSSLTHQGEPLFTEAEVSHMTDVKVVLWIALAVLVALVVVCALLIAHLLRTSPGGVRRAL
+FAGALWLPLALIALAVLAVLGWEIFFAGFHSLFFADGTWTFSVRDALIRLYPEQFWVDAA
+LVVAAIAVIASLVTLVFTWPTRRRREMSADRRGQLLDTRLRWAREEDSPVR*
+>NZ_CP083691.1_2296
+MASHTPGRSDGAGSGSSDFESGLDYGAFVEDDDAQPTQALPRTTEEHGAQRTLAFDRDEL
+AAAAAGAGTGAGRSGAGSRAAGAAHGVAGEDITASRPAPAPAPSPASPWGADRYPSDATV
+PASAPAAADTRTPEERARLPKAGPRLAQVLLAVLAPLVLLLGAVRLVATPLFLWLEYHRP
+GFPADPYGFSTADRMTYGSAGLDYLHNLAGPRYLSELTFQGKPLLSEAAVSHMTDVKTVM
+WIATAVLVLLGLACLLLALYLRRTSPGGVRRALFAGALGLLVVIVVLAAMAATGWQGFFA
+GFHSLFFAEGTWTFSVSDPLIRLYPAQFWVDAAVAVAVLALIGIIAALVAGAPTRRRREM
+SQDRRAQLEATRLRWAREDAHGVR*
+>NZ_CP097650.1_463
+MASHQAGRGRDERAGAEDFESGLDYGAFVQDDAADDPNRTQALPAMGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDAGRPAADADRDIVASRAVPEGDRRPLPGADELGPLSAAVG
+ARTAGSSTAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAVLAPLA
+LLLAAVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIATAALVVLVVVCALLIASLLRTSPGGVRRGLFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVRDALIRLYPQQFWVDAAVVVGL
+VTLLASLVTLVLTWPTRRRRELSADHREQLLRTRLRWAREDDAVVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000516.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000516.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6745f7a873bf36d7f52c07578397e9905d363808
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000516.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_472
+MTTEDLGLDPTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD
+GRITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRHTLGLDPDSHGVHLEVAKQVPVAG
+GMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGVELTP
+VAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPPRPEVNEAVLRALTAADPLE
+LATAMDNDLQTPAVVLFPELSDVLDLGLDEGALRGMVSGSGPTLLFVAQDEASALRLASA
+IEERTGVRALPVHGPVPGAHVL*
+>NZ_CP033200.1_202
+MTTEDLGLDPTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD
+GRITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRRTLGLDPDTHGVHLEVAKQVPVAG
+GMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGAELTP
+VAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPTRPEVNEAVLRALTAADPLE
+LATAMDNDLQTPAVVLFPELSDVLDLGMDEGALRGMVSGSGPTLLFVAQDEASALRLASA
+IEERTGVRALPVHGPVPGAHVL*
+>NZ_CP040019.1_2407
+MSEARAGLSGTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD
+GRVTVGPCPRQVSLVDSHDVPWDERNLAHRAAVHLRTALGLDEATHGVHLDVAKQVPVAG
+GMGGGSADAAAALLACSVLWETGHTRSELAELAAPLGADVPFAVLGGAAVGLGTGAELTP
+VAARTPVHLVLVPADAGLSTPVVFGTLDELRRDGHVPEGAAHPEVNQEVVRALTAADPLA
+LATVMDNDLQTPAVALFPDLGDVLDLGLDEGALRGMVSGSGPTLLFVVPDEHSALSLATA
+VEERTGVRALPVHGPVAGAHVL*
+>NZ_CP083691.1_2287
+MSGLPGPSARHVTVRAPGKVNLSLRVGPPRPDGYHPVASVYLAVSLAETVTAVARPDGDA
+RITLAESTRQPSSVDTRDVPWDERNLAHRAALHLRQSLGLAPETHGVHLEVSKQVPVAGG
+MGGGSADAAAALLACSVLWDTGLTRSELAELAAPLGADVPFAVTGGAAVGRGTGSELTPV
+AARRPVHLVLVPADAGLSTPIVFRTLDELRSLGRAPEGQGEPAVDADVVRALAQADPLAL
+ALAMENDLQTPAVTLFPELSDVMDVGLDEGALRAMVSGSGPTLLLLAHSEQDAARLATAV
+QERTGVAALAVHGPVPGAHVL*
+>NZ_CP097650.1_471
+MTTEDLGLDPTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD
+GRITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRRTLGLDPDTHGVHLEVAKQVPVAG
+GMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGAELTP
+VAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPTRPEVNEAVLRALTAADPLE
+LATAMDNDLQTPAVVLFPELSDVLDLGMDEGALRGMVSGSGPTLLFVAQDEASALRLASA
+IEERTGVRALPVHGPVPGAHVL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000519.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000519.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ed7b944643ce8ac4d6fa2454930846972a87cb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000519.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_478
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA*
+>NZ_CP033200.1_208
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHAVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA*
+>NZ_CP040019.1_2403
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRTRVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKEAGAKDVIIAATHAVFSEPAAQRLGECGAREVVVTNTLPILEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGDA*
+>NZ_CP083691.1_2283
+MTELSRSEDKRLVLAAGRAHPGLAQEIAEALGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFVIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRGQVEGEKVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVRILKEAGAKDVIIAATHAVFSDPAAQRLGESGAREVVVTNTLPIPEEKRFDNLTVLS
+IAPLIARAIREVFEDGSVTSLFDGDA*
+>NZ_CP097650.1_477
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000521.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000521.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4e2ad4955a4433c8649eb8f343c31171afda209
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000521.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_481
+MPGAQGEDEAMSETTALRIRTGLDAVTVSGLTGDERAEVIASWARCGVEAVEPPARADAH
+RDADTARPWLQWHEDLVFLATSRTIESARGTHLLFHAACLAAPDTGAAMVLVAASGTGKT
+TATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPTLP
+DARLARIAVLDRVRDPAGPVTPRAEAIELVAALEALVPQTSSLSLLPRGLVTLCRVLDTV
+GGAQRLVYAEAEDLRDVVDGLLAAPPTSVTPAWEALTEEELRASVGAAAPGAVSRCAVDD
+GILTDSGRLVLLASDRLVVLEGLGPSVWLLLDESRTAADVVACLRAEGPVPEDAEARVRK
+AMDALVSAGLATAG*
+>NZ_CP033200.1_210
+MPGAQGEDEAMSETTALRIGTGLDAVTVSGLTGDERAEVIASWARCGVEAVEPPARADAH
+RDADTARPWLQWHEDLVFLATSRTIESARGTHLMFHAACLAAPDTGAAIVLVAASGTGKT
+TATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPTLP
+DARLARIAVLDRVRDPAGPVTPRAEAIELVAALAALVPQTSSLSLLPRGLVTLCRVLDAV
+GGAQRLVYAEAEDLRGVVDGLLAAPPTPVTPAWEALTEEELSASVGVATPGAVSRCAVDD
+GILTDSGRLVLLASDRLVVLEGLGPSVWLLLDEPRTAADVVARLRAEGPVPEDAEARVRE
+AMDALVTAQLATTG*
+>NZ_CP040019.1_2401
+MPAAPPDPSAAPVREALRIGAGLDAVTVSGLTGAERDELLRSWARCGVETVELTEDADAH
+RGPEHPRSWLDWHENLVFLATSRAIESARGTHLMFHAACLAAPDTGAAIVLAAASGTGKT
+TATRRLGPHYAYLTDETAMVDPADLSVTPYPKPLSLLEPGGSRPKTQRGPDELGLGLTRA
+DAVLARIAVLDRVREAAAPVPARAEPMDVVTALQHLVPQTSSLSLLPRGLVALCTLLDAL
+GGVQRLVYAEADDLRPVIDGLLAAAPQPVDPAWEPLDAAELAASEGAAEPGAVRRAAAAD
+GILTADGRLVLLAGTTLTVLDGIGPAVWFALESPLTPERIVARLAEDGPVPADAAERVAE
+AVAALESAGLLVTTPQGAGPEADALRS*
+>NZ_CP083691.1_2281
+MTDPRRGGRAVRIPAGDGSTTAAGLDETGVRTLLDAWRRCGAEEVAAPAEGAAAYWEATG
+WDWFHENLVHSATTAAITAGVGRRLLFHGACLADPGTGSAVALVAASGTGKTTATRRLGP
+HYAYLTDETVIVAPDTLEVTPFPKPLSLLGPSGVRPKTQVSPDELGLGDAVPARLARLAV
+LDRVRDVDGPVTARAETMGLGDALIAVVPQTSSLARLPRGLRELCRVIDRLGGVQRLVYA
+EADGLRPVVDELLAAAPEPLEPAWEPLTPAELAASRETGDAAAGAARREAVDDGIVTDDG
+RLILLAGPQLAALEGLGPVVWLMLEEPLTNAQIVERLAAEGPVPDDAADRVADAVTALAE
+SGLVRI*
+>NZ_CP097650.1_480
+MPGAQGEDEAMSETTALRIGTGLDAVTVSGLTGDERAEVIASWARCGVEVVQPPTHTDAH
+RGAHTASPWLQWHEDLVFLATSRAIESARGTHLLFHAACLAAPDTGAAMVLVAASGTGKT
+TATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPTLP
+DARLARIAVLDRVRDPAGPVTPRAEAIELVAALEALVPQTSSLSLLPRGLVTLCRVLDTV
+GGAQRLVYAEAEDLRDVVDGLLAAPPTPVTPAWEALTEEELRASVGAAVPGAVSRCAVDD
+GILTDSGRLVLLASDRLVVLEGLGPSVWLLLDESRTAADVVARLRAEGPVPEDAEARVHE
+AMDALVTAELARTG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000526.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000526.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e4f155a8d79aae71a6cdacca5d0be70dea3f902
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000526.fa
@@ -0,0 +1,70 @@
+>NZ_CP042169.1_486
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLLAQPE
+ASLDVAAADVAHRDPATAPLGATPAEMREALPAGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAEDMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIREAAALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLRVGATITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFEFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFSEPMPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPHEEEPIMVITMGGFTLDRHIRPEERLPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL*
+>NZ_CP033200.1_215
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLLAHPE
+ASLDVAAADVAHRDPATASLGASPDEMREALPAGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAADMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIRESVALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLQAGVTITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFQFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFREPLPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIVEVQRTIDITRDLKRWFPNEEEPIMVITMGGFTLDRHIRPEERRPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL*
+>NZ_CP040019.1_2396
+MITERHLTPYLVFPEDSLLVALQKMTDNRERIVFVVDSHGFLAGSLTDGDFRRWLLANPG
+ASLEVAAVEAANRTPATGPVGASPAEVLAALPAGALHLPLLDERGRLAALAINRESELRI
+GEHRIGPGRPAFLIAEIGNNHQGSVDLARELVDLAVEAGADAVKFQLRDMDALYRQSGAG
+TAGEDLGAQRTLDELAKFSLPAEDMVRVFDHVRDAGVALMCTPWDAPSMRVLAQYPVDGV
+KIASADLTNHGLLRDAAAARLPMVLSTGMSREDEIKEAVELVRSSGVPFAVLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVPLAAVARGASIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTREIEESIGVAAERVVSTGEAMNRINLAKSLVAARPLAAGETVTED
+AVTVKSPGRGLQPNELPRLVGRTLHRDMAEGDFFFAGDLTDTVPTGRQFEFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFTEPLPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPKEEAPIMVITMGGFTLDRHIAPAERQAKYDRIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL*
+>NZ_CP083691.1_2276
+MIIERHLTPYLVFPEDSLTVALQKMTDNRERIVFVVDTHGFLQGSLTDGDVRRWLLAHPG
+AALDSPAVAAANPSPATGLVGDAPSSVLAALPEGALHLPLLDERGHLTALAINRESELRI
+GSHRVGEGRPAFLIAEIGNNHQGSVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSVDDMVKVFDHTRAAGVALMCTPWDAPSMQVLADYPVDGV
+KIASADLTNHGLLRDAASRGIPMVLSTGMSREEEIQESAALVRSYGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQAPVGYSGHERGFHVALAAVVRGASIIEKHFTIDRSLEGNDHK
+VSLLPDEFAQMVRQTREIEESIGVAGERVVSTGEAMNRINLAKSLVAARSLTAGDVVAEA
+DVTVKSPGRGLQPNQLPQLVGRTLHRDLEEGDFFFAGDLTDSVPTGRQFEFRRPWGLPVR
+YHDYAALTKDCTPDFLEFHFSYKDLEIDIDTVFREPMPGGFTTHLPDIFAGDFLVDLASM
+DEQVWERSIAEVQRTIDITRDLKRWFPSEEAPIMVITMGGFTLDRHIRPEERQPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL*
+>NZ_CP097650.1_485
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLVAHPE
+ASLDVAAADVAHRDPVTAPLGASPAEMREALPTGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAEDMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIRESVALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLQAGATITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFQFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFTEPMPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPNEEEPIMVITMGGFTLDRHIRPEERLPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000537.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000537.fa
new file mode 100644
index 0000000000000000000000000000000000000000..654e18b1554c3b286b3d2e14a8841109c948991e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000537.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_510
+MTVETTEGWTLAPNIAWARTAGGQAAVMTLEAGQPLLLGASGDVIWDVLVGGRTPEDDLV
+ADPPASLSTTDVTVQVAEAFGLAPADVAADVHAFLEMLEAHGVLVRVRTA*
+>NZ_CP033200.1_240
+MTVETTEGWALAPDIAWARTAGGQTAVMTLEAGQPLLLSASGDVIWDVLVGGRTPADDLV
+ADPPAPLSTTDVTVQVAKAFGLYPADVAADVHAFLEMLEAHGVLVRVRTA*
+>NZ_CP040019.1_2374
+MAADRLPAPFGMTSERGSAWAVAPGVAWALTDGGDAAVMHLEHGVPLLLSPTGHAVWDVL
+VGGRTPEDDLTAAPPIPLPEEAVAAETAAAFGLAPEDVAADVGAFLAMLEQHGVVVRVGG
+VLPRP*
+>NZ_CP083691.1_2252
+MSDAEHPPFAQAPAARAWRVAPTTAWVRSGEHQVTVMDLDEGNPQVLSPTGSAVWELLLD
+GRTPEDDLAADPPKPVEEEALCGAVAEAFGVDVEVVAADTRAFLGMLAGHRLVVPAVLP*
+>NZ_CP097650.1_510
+MTVETTEGWALAPDIAWARTAGGQAAVMTLEAGQPLLLSASGDVIWDVLVGGRTPEDDLI
+ADPPVPLSTTDVTVQVAEAFGLDPADVAADVHAFLEMLEAHGILVRVRTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000538.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000538.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf42b54fbbda891a12e8280ebda96f812b452e86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000538.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_511
+MGERATRQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDHRRSS
+DVDLLVHPADATAVIELLRSHGWEPVATFSEGSIFQHAATLWHDQLGYVDVHRLFPGLGA
+SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE
+SWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRSAATA
+RERAVLVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR*
+>NZ_CP033200.1_241
+MGEHATGQRPAAPPSLDLEVRVRLAHARITHLLERAGIRGLHLKGYATEPGVYPDHRRSS
+DVDLLVPPADAAAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFPGLGA
+SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE
+SWAALREEARRLDAGAAWHVATGEAADGVDTRQLTLFAALHESQSGLELFRTRWRSAATV
+RERAALVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR*
+>NZ_CP040019.1_2373
+MTETGTTDQRAAAQPALDLAVRVRLGHARIAYVMEEAELRGLHVKGYAAEPGVYRGRRSS
+SDVDLLVHPSDAAAAVELLASHGWAPVADFSEGSIFEHAATLWHDHLGYVDVHRLFPGLG
+TDAARTFDALWAERTTRVIAGRPVPVPGPVHQRLVVIVHAARDSHRGALDVRHIRDTSSP
+AEWDALRQEARRLHATAAWHVATGEDADGMDAHDLALFEALQDDESGLDLFRTRWRTAHS
+ARERARLVLHTLPVNRPHLQMRLGHAPTRADLWREQRSRATALARWAWTRGVRRGR*
+>NZ_CP083691.1_2251
+MTAAPAPLETRVRLAHARITHLMAAAGVRSLHIKGYAMGPGVYAGGRTSSDVDLLVHPAD
+LSHALDALTSHGWRRIADFAEGSVFEHAATLWHDQLGYVDVHRRLPGLGRSPVDAFEALW
+GERTTTVVAGHAVPVPSLRHQRLVVLVHGARDAGRGRFDVDHLRHTLDAGQWAELRVQAQ
+ILGAGAAWSIATGETDVAGVDEREALLLSAVRGDESGIRLLATRWHAARGWRERLHLLVR
+TVPVNRAHLQMRLGRPPTTADVLREQASRGAALTRWAAGKAVPRVGR*
+>NZ_CP097650.1_511
+MLAAMGERATGQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDH
+RRSSDVDLLVPPADADAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFP
+GLGASPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRES
+LPAESWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRS
+AATVRERAALVARTIPVNRPHLQMRLGRPVTRADLWREQGARLGALAGWAWTKAVRRDR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000542.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..838565fe40eb22e94fb095ec30ace823cf53ff84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000542.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_515
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELAGS
+DVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD*
+>NZ_CP033200.1_248
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELADS
+DVLTCTVIGFPLGANTSEVKAFEARQAIDAGADEVDMVLDIAAARAGDRARLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGEDIGVKASGGVRTREDALAMIEAGATRIGASSALAILGSD*
+>NZ_CP040019.1_2366
+MTRTLSTAELAQYIDATALKTETSEADVRRLVAEARQAGVKSVCVNPRWVPLVSAELAGS
+DVLTCTVIGFPLGANASEVKTFEARQAIEAGAHEVDMVIDVAAARAGDRARLVEDVRAVA
+EAAHAAGPAGQGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGEHVGVKASGGVRTREDALAMIEAGATRIGASSALAILGTD*
+>NZ_CP083691.1_2244
+MSETPQLTTAELAKHIDHTLLKPEASREDILRVVAEAREAGVKSVCVNPRWVREVRAGLE
+GSDVLTCTVIGFPLGASSSAVKAFETTQAIADGADEVDMVIDIAAARAGDRARLEEDVRA
+VVAAAHASGPAGRAGTLVKVIIETALLDDAAKVLACEAAVAAGADFVKTSTGFSTGGATV
+EDVALMRRTVGPEIGVKASGGVRSREDALAMITAGATRIGASSALAILGDD*
+>NZ_CP097650.1_518
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELAGS
+DVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000550.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000550.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3d37f816c16bc11996b5d6121dbfc53ec42baff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000550.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_524
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL*
+>NZ_CP033200.1_258
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLAVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL*
+>NZ_CP040019.1_2355
+MSDPDLTTTAGRLADLHRRLEATAAPGGEGAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPETTDEDLALDEIVPDSANQPYDMLEVIGAIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPQQLAGTLDIAASEKAARFVRFCDAF
+NIPILTLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATQDAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGALIRALRATLHKREARPAKKHGNMPL*
+>NZ_CP083691.1_2234
+MSAPELSTTAGRLADLHRRLEATAAPGGEAAVERQHSRGKHTARERIDLLLDEGSFVELD
+ALATHRTTAFGMDAKHPAGDGVVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVMASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTTGTAHYMATSEE
+DAIAYVQDLLEYLPSNNLAEAPVFEAESLEETEQDLALDTIVPDSANQPYDMLEVIAALV
+DDGHLLQLQEMYAPNVITGLARLDGMSVGVVANQPQQLAGTLDIAASEKASRFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGPQGAVNILYRRELAAAEAAGEDVEARRAQIVADYEAELLN
+PYQAADLGYVDAVVPPRQTRAHLVRALRATFHKREARPAKKHGNMPL*
+>NZ_CP097650.1_527
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000555.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000555.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82ee10a6d06e75db929960e4cd6771b97cb5dbd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000555.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_530
+MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR
+RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA
+VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR
+DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV
+ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAM
+TGERA*
+>NZ_CP033200.1_264
+MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR
+RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA
+VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR
+DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV
+ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAM
+TGERA*
+>NZ_CP040019.1_2347
+MSSPTRVAHVPSQPPGISGLLVVAKAAARAGADVLARRWTGHHPAVPLGREEIGAETKTS
+GSDWVTDYDRRAEQAVREVLVAYRPQDEITGEEYGATVPAEPSGLRWSIDPLDGTTNFVR
+GLPQFCTSVAVTGPVDEETAALLGVPAGTRRWLAGVVAAPALGRTWFASAGRGAFSTADA
+TTAGVDVPDRDAAPVRITGPAPGRSGRLLATGFGYDPARRAMQVRALAALLPAFGDVRRI
+GSAALDLCMVADGTLDAYAEFGTQEYDWAAGALIAEEAGVRVRRPASGDGTAHPDWMVAG
+DVDEAALAAAQEETA*
+>NZ_CP083691.1_2228
+MSAAPARPASPAGLLVIAKAAARAGADVLAERWAGHHPAVPLTSDELGADTKSSGSDWVT
+DYDRRAEDAVRAVLTGYRPHDEITGEEHGSTAPVEPSGYRWSIDPLDGTTNFIRGLPQFG
+TSVAVEGPVDEETAALLGVLPGSRRWLAGVVAAPALGRTWFASAGRGAFSTADATTAGVA
+VPDRDAAPVRLTGPVPGRSGRLLATGFGYHPGRRAMQLRALAALLPAFGDVRRIGSAALD
+LCMVADGTLDAYAEFGTQEWDWAAGALIADEAGVPVDRPASGDGTGHPDWMTAGDVDAAA
+LAAAKEATA*
+>NZ_CP097650.1_533
+MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR
+RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA
+VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR
+DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV
+ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAV
+TGERA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000563.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..883bd1c58a51f787a80a42fb04a11ba72ae66741
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000563.fa
@@ -0,0 +1,43 @@
+>NZ_CP042169.1_539
+MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL
+DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG
+GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTTAFFGETLGNPRGDVLDVRAVAD
+AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ
+HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV
+NLGLETLSLRMERQVANAAAVAGWLEGRDDVEHVVYAGLESSPWHERAQRYLPKGAGAFV
+SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQRAAGVTPGLV
+RLSLGVEDVEDILADLERGFAAAARRGDDDAGERA*
+>NZ_CP033200.1_273
+MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL
+DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG
+GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTTAFFGETLGNPRGDVLDVRAVAD
+AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ
+HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV
+NLGLETLSLRMERQVANAAAVARWLEGRDDVEHVVYAGLESSPWHERAQRYLPKGAGAFV
+SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLADDEQRAAGVTPGLV
+RLSLGVEDIEDILADLERGFAAAARRGDDDAGERA*
+>NZ_CP040019.1_2336
+MVASASLYGGTQNLFKHTLAKVGIETTFVQDPDDVAAWTAAVRPNTKAFFGETLGNPRGD
+VLDVAAVADAAHAAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIV
+DAGTFDFAQHAERFPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSA
+ISPFNAFLVNLGLETLSLRMERQVANAAAVARWLEGRDDVEHVVYAGLESSPWHERAQRY
+LPKGAGAFVSFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQR
+AAGVTPGLVRLSLGVEDLEDILADLERGFAAAASAGERE*
+>NZ_CP083691.1_2216
+MSTQPTPRRGFSTTQIHAGTDAPHAFGATALPIYQTTSYDFPSAQVAADRFALADLGPIY
+TRIGNPTQSAVEEKIAALEGGVGALLLASGQSATTFAILNVAGAGDHVVASASLYGGTQN
+LFKHTLARVGVEVTFVQDPDDLDAWRAAARPETKAFFAEALGNPRGDVLDVAGVAAAAHD
+AGVPLIVDNTLTTPYLLRPFEHGADVVVHSATKYLGGHAAAMAGVIVDSGRFDFARDPER
+FPGFNEPDESYHGLVYARDLGVGSPLGANLAFVLKARVQLLRDYGSAISPFNAFLVNLGL
+ETLSLRMDRAVASALAVARHLEGHPQVESVSHPGLESSPWHARAQELLPRGAGAFVSFEI
+AGGAAAGAAFVDGLELHHHVANIGDVRSLVVHPASTTHAQLAEDEQRAAGVTPGLVRLSL
+GLEDVEDILADLDKGFAAAAAALDAADAAEQD*
+>NZ_CP097650.1_542
+MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL
+DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG
+GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTKAFFGETLGNPRGDVLDVRAVAD
+AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ
+HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV
+NLGLETLSLRMERQVANAAAVARWLEGRDDVERVVYAGLESSPWHERAQRYLPKGAGAFV
+SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQRAAGVTPGLV
+RLSLGVEDIEDILADLERGFAAAARRGDDDAGERA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000569.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000569.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94c05b1921a4b6f5f72e0dcee48256e6c8f5cb12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000569.fa
@@ -0,0 +1,38 @@
+>NZ_CP042169.1_545
+MDLPAGVTLRPWAEGDDLRLLEVWGDPADVQQHQDRAMLAPDADTPWRHTLVAEDDGVPV
+GAGTVVAQALHPRRLWLYLEVAPTARRRGIGSALLGALRDAVEQAHAAGQVTTTHLKTRF
+AVASRVAVATGRSADAAEATAPAAGEEAGEAHAAQVAGTEAFLVAAAFSPVQRSRRVAVA
+PGSIALPPLRDEDHPEGAVLEDAATGSVELTRAVAAFYDAVHGWDPAQMSVGAAQQLILG
+PATGASGAVVLRDAPREEGGAVQAFAVSYTAERQDAPADVFLGWDPELPLDQAQLAAGQL
+LAMLVAQHPVQVEVDEAMTALEPILDGLIAQRAAATLVDTRIWATDPA*
+>NZ_CP033200.1_279
+MTGAAGAAGHDDGGALFDSAAVAGGEIVLRPWRPGDDLALLEVWGDPANAQQHQDRAMLA
+EDAERPWRRALVAEAAGVPVAAGVVYASSVHPRRLWLYVETAAAERRRGIGRALVAALRG
+LAAEAHAAGAIPTTALKARFAKDALVPGVSGADPQTDAEGPAGQPPVDTEAVRSQTAALA
+AGTEAFLVAEGFTPVQRSRRVAIAPGAIGLPDVRGEEHPDGVVLEEASTGSVELTQAVTA
+FYDAVHAWDPSTLSVGAAQQLLLGPATGAAGAVVLRDAPKAEGGRIRAFAVSYTPERQDA
+PADVLVGWDPELGEEDALQAVADLLALLVAQYPVQIEVDEAMAPLERIVDGLIGGNAART
+LVDTYVFVDDAPGA*
+>NZ_CP040019.1_2330
+MSGAYDDDAGALFDSAAVSGGEVVLRPWRAGDDLALLQVWGDPANVQQHQDRAMLAEDAE
+RPWRRALVAEDAGVPVAAGVVYASSLHPQRLWLYVETAAPERRRGIGRALVAALRGLAAE
+AHAAGTVPTAALKARFAKDALVPGTAVEEGVDTEAVRAQTAALAAGTEAFLAAEGFTPVQ
+RSRRVAVAPGAIGLPDVRDEDRPDGVVLEEASTGSVELTQAVAAFYDAVHAWDPSTMSVG
+AAQQLLLGPATGASGAVVLRDAPKAEGGRIRAFAVSYTPERQEAPADVLVGWDPELSEED
+ALQSVADLLALLVAQHPVQVEVDEAMAPLERIVDGLIGGNAARTLVDTYVFVDDAA*
+>NZ_CP083691.1_2210
+MSPRHDDDAPALTAAVSGGEVVLRPWAEGDDLRLLEVWGDPADVQQHQDRAMLAADADSP
+WRRTLVAEEDGVPVGAAVAFAQPLHPGRLWVYGEVARTVRGRGVGRALLEALRGLVAAAH
+EAGAVPTTELKARFAVASRVPVGGGEVVEAAPGEAPEAGAAGAEAHAAQVAATERFLVAA
+GFTPVQRSRRIAVAPGVIALPALRDEEHPEGRVLEEISTGSVELTRAVAAFYDAAHAWDP
+SQMSVGAAQQLILGPQTGAAGAVVLRDAPREEGGTIQAFAVSYTAERQDAPADVLLGWDP
+SLGLEEAQLAVGDLLALLVAQHPVQVEADEAMTALEPILDALLAKRAAGTLVDTRVWATD
+PS*
+>NZ_CP097650.1_548
+MTGAAGAAGHDDGGALFDSAAVGGGEIVLRPWRPGDDLALLEVWGDPANAQQHQDRAMLA
+EDAERPWRRALVAEAAGVPVAAGVVYASSVHPRRLWLYVETAAAERRRGIGRALVAALRG
+LAAEAHAAGAIPTTALKARFAKDALVPGVTGADPQTEADGATGRPPVDTDAVRSQTAALA
+AGTEAFLVAEGFTPVQRSRRVAIAPGAIGLPDVRGEEHPDGVVLEEASTGSVELTQAVTA
+FYDAVHAWDPSTLSVGAAQQLLLGPATGAAGAVVLRDAPKAEGGRIRAFAVSYTPERQDA
+PADVLVGWDPELGEKDALQAVADLLALLVAQYPVQIEVDEAMAPLERIVDGLIGGNAART
+LVDTYVFVDDATGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000570.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000570.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a8c86bc30a5732654558f613344fc2906e71915
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000570.fa
@@ -0,0 +1,33 @@
+>NZ_CP042169.1_550
+MTRKHLGFLNFGHWIHRPGAEPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQRMFSSP
+FPILAAMAARTERISLGTGVIDLRYENPLYMAEAAATTDLISGGRLELGVSRGSPEAALD
+GQAQFGYALDEGQTWADVTRERGRRFLSAVRGEGIATPDLTSGWAHSSQPLRIEPHSPGL
+ADRIWWGSGSVGSVAGAATDGYNMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHAG
+PGRTAVTRSAFVIQDREDELYFGRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAAD
+DAVAAADWVLFANPNQLGVEYNAKIFAGWAEVWRLLGWDA*
+>NZ_CP033200.1_283
+MRYENPLYMAEAAATTDLISGGRLELGVSRGSPEAALDGQAQFGYALDEGQTWADVTRER
+GRRFLSAVRGEGIATPDLTSGWAHSSQPLRIGPHSPGLADRIWWGSGSTPSAVEAGRDGY
+NMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHTGPGRTAVTRSAFVIQDREDELYF
+GRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAADDAVAAADWVLFANPNQLGVEYN
+AKIFAGWAEVWRLLGWDA*
+>NZ_CP040019.1_2327
+MNECCNRDIRYENPLYMAEAAATADLLAGGRLELGVSRGSPEAAKDGQAQFGYELADGQT
+WAGVTRKRGRRFLAAVRGEGIATPDLASGWAHSSAPLRIEPHSPGLADRIWWGSGSAGSA
+VEAAKDGYDMLSSTLLLQDDGRPFHVQQADQIAGYLEAYEAAGHAGTGRTAVTRSAFVIQ
+DHEDELYFGRDRNSRESAGMLDGGRARSGPTYAGSAEEVAEKLAADDAVQAADWVLFANP
+NQLGPEYNAKIFAGWAEVWRLLGWDR*
+>NZ_CP083691.1_2203
+MTTKNLGFLNFGHWIHRPRVGRRPVEPDAKQAIDDVVQMAVDAEAAGLDGAWIRIHHFQR
+MFSSPFPILTAMAAHTERIHLGTGVIDLRYENPLYMAEAAATTDLLAGGRLELGVSRGSP
+EAARDGQAQFGYELADGQTWSDVARERGRRLLAGVRGEGIATPDLSSGWAHSSAPLRIEP
+HSPGLADRIWWGSGTVGSAVEAAKDGYGMLSSTLLLQDDGRPFHVQQADQIARYLEAYEA
+GGHTTPARTAVTRSAFVIQDHEDELYFGRDRHSRDSSGHLDGGAARSGPTYAGSAEEVAE
+LLAADDAVQAADWVLFANPNQLGAEYNAKLFAGWAEVWRLLGWDS*
+>NZ_CP097650.1_551
+MTRKHLGFLNFGHWIHRPGTAPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQRMFSSP
+FPILAAMAARTERISLGTGVIDLRYENPLYMAEAAATTDLLSGGRLELGVSRGSPEAALD
+GQAQFGYALAEGQTWADVTRERGRRFLSAVRGEGIATPDLTSGWAHSSQPLRIEPHSPGL
+ADRIWWGSGSVGSVAGAAADGYNMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHAG
+PGRTAVTRSAFVIQDREDELYFGRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAAD
+DAVAAADWVLFANPNQLGVEYNAKIFAGWAEVWRLLGWDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000571.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000571.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc25fcd7e0a88f78de12c022089d29c0a5552456
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000571.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_551
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHAGDSFLTLAAYHEHPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDGGGAAPPSEA*
+>NZ_CP033200.1_292
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHTGDSFLTLAAYHEHPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDGGDAAPASEA*
+>NZ_CP040019.1_2314
+MTEQPQDPRQDQTAAEPAPEPAEALAAETTDAVAPEAAPGEAGQPSPEMLELAGRMFDAA
+RSGDAETLEAYIVAGLNPDLQNGKGDTFLTLAAYHDQPGVVEMLIRVGADVEKANDRGQR
+PLTCATFKGDVASMRLLLAAGADPDAGTPSARQTAQMFGGEEITAVLDEPR*
+>NZ_CP083691.1_2201
+MTEHQDTQGQHAPATPPAEPAVESAGPSPEMLELAGRMFDAARTGDVDTLEAYIVAGLNP
+DLQNGKGDTFLTLAAYHDQPAVVEMLIRVGADVEKANDRGQRPLTCATFKGDVASMCLLL
+AAGADPDAGTPSARQTAQMFGGERVAAVLDEAR*
+>NZ_CP097650.1_552
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHAGDSFLTLAAYHERPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDREDAAPSSEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000572.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000572.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43a6253706f97b034a32158afd01f084d9d81a5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000572.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_552
+MTSSHTLPAAAVTDADDVAHYAKSAGAGRRITDDDQLHEARHPAPTTDRLTLPPLRLGPL
+TIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHDPDEVP
+RSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKAELFASIV
+KAAVTEAAKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAV
+WDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGDLQAAF
+EGRQDRFQPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYLKGYPVGSEIRTA
+LSTVPDLATMREILARVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNAEQQAM
+IQAAELDVSGG*
+>NZ_CP033200.1_293
+MTSSHTLPAAAMTDADDVADPHAAHYAKSAGAGRRITDDDQLHEGRHPAPTTDRLTLPPL
+RLGPLTIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHD
+PDEVPRSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSEL
+FASIVKAAVTEAAKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFY
+SGTAVWDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGD
+LQAAFEGRQDRFQPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYFKGYPVGS
+EIRTALSTVPDLATMREILTRVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNA
+EQQAMIQAAELDVSGG*
+>NZ_CP040019.1_2313
+MTVSSSTTTPERGAATDGLSAADPAAGAPAAVDPHASHYAKSAGAGRRIADDEQLHEGRH
+AAPTTDRLSLPALTLGPITVDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALV
+ERKPESMRIIKHDPDEVPRSVQLYSVDPVTTGAAVRMLVEEDRADHIDLNFGCPVPKVTR
+RGGGSALPWKSELFASIVKAAVTEAGRKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVA
+AVALHGRTTRQFYSGTAVWEDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVI
+GRGCQGRPWLFGDLQAAFEGRHDRFRPTLGMVADTLYRHAELLVDTFEGDELKALRDIRK
+HVAWYFKGYPVGSEIRTALSTVPDLATMAEILSRVDRDQPYPGLDAEGPRGRSGAPKRPH
+LPDGWLDSRELNAEQKAMIAAAELDVSGG*
+>NZ_CP083691.1_2200
+MTASHTLPDAAVDPHYAKSAGAGRRIADDDQLHEGGHAAPRSDRLNLPPLKLGPITVDVP
+VVLAPMAGITNTAFRRLCREYGGGLYVNEMVTSRALVERKPESMRIIQHDPDEVPRSVQL
+YSVDPVTTAAAVRMLVEEDRADHIDMNFGCPVPKVTRRGGGSALPWKSELFASIVKAAVT
+EASKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAVWEDIA
+RLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWMFGDIQNAFEGRPE
+RFHPTLGMVADTLYRHAELLVDTFGGDEVKALRDIRKHVAWYFKGYPVGSEVRTGLSTVP
+NLATLRELLDRLDRDMPYPGAPAEGPRGRAGAPKRPHLPDGWLDSRELNEEQRAMIHAAE
+LDVSGG*
+>NZ_CP097650.1_553
+MTSSHTLPAAAVTDADDVADPHAAHYAKSAGAGRRIADDDQLHEARHPAPTTDRLTLPPL
+RLGPLTIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHD
+PDEVPRSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSEL
+FASIVKAAVTEASKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFY
+SGTAVWDDIARLREALPDIPVLGNGDIWSAEDAIAMVERTGVDGVVIGRGCQGRPWLFGD
+LQAAFEGRQDRFRPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYFKGYPVGS
+EIRTALSTVPDLATLREILARVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNA
+EQKAMIQAAELDVSGG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000575.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000575.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbfec89cfcbf42c70aff2eab4f0a307bb6ea9689
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000575.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_558
+MPTAPAPSEAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP
+DPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHDDPADPDRAWAGLAAAAAPRPVVGGE
+GLPLRGGLVGWLGYELGLADLGVTPPSRRAEDPAPLPAQFWVRPSRYVVADHAAGVLHCC
+VVSLDPTTAEAGADRWAADVRRALAAARRALETAAGDAVVPPPQDAVPGPRADEEAPGTW
+REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVDPLVLFHELAAHQPAPYAAL
+LEHGTGSRRWAVVSASPERFLSGREGRYSTKPIKGTAARLADPAGDAEAARALAADPKTR
+AENLMIVDLLRNDLSRVCEPGSVQVPSLMAVESYASVHQLVSTVTGTARAGIEPVDVVRS
+LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS
+VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGLPTTAPDIA*
+>NZ_CP033200.1_300
+MPTAPAPSVAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP
+DPAEARWSVAGDGLDVLGEEQGRTPSPGPRLVRHDDPADPDRAWADLAAAAAPRPVVGGE
+GLPLRGGLVGWLGYELGLADLGVTPPSPRPGDPASLPAQFWVRPSRYVVADHAAGVLHCC
+VVSLAPTAAETGADRWAADVRRALAAARRALETASGDVVVPPPRDAGPGPQADEEAPGTW
+REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVDPLVLFHELAAHQPAPYAAL
+LEHGTGARRWAVVSASPERFLAGRAGRYSTKPIKGTAARLADPVADAEAARALAADPKTR
+AENLMIVDLLRNDLSRVCEPGSVEVPSLMAVESYASVHQLVSTVTGTARAGVEPVDVVRS
+LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS
+VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGVPTTAPDVA*
+>NZ_CP040019.1_2307
+MAAVYAHAVQRGAGSFWLDSALPDPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHADP
+ADPERAWSDLAAAAAPRRVVGGEGLPLRGGLVGWLGYELGLADLGVRPPSRRAGDPAALP
+AQFWVRPSRYAVADHAAGTLSCCVVALDAAAAEAAADRWAADVRRALDAARRATQAAADD
+AAASEVRADVAPEAGTGEAAGAWREDRAAYDEHIARCHAALHAGDSYELCLTTRFDADPA
+LRVDPLALFLELAAHQPAPYAALMEHGTGPRGWAVVSASPERFLAGRDGRYSTKPIKGTA
+ARLPDPAADAEAARALAADPKTRAENLMIVDLLRNDLSRVCEPGSVQVPSLMAVESYATV
+HQLVSTVTGTARAGVAPVDVVRSLFPGGSMTGAPKRRSVELLAQWEDSPRGVYSGALGLL
+GADGAVSLSIVIRTAVLAAGRWGIGAGGAIVADSTAEAEHEEVLLKARGLRRALARADGT
+ARTTTAPPRSR*
+>NZ_CP083691.1_2197
+MPTAPGRPDASPAPLHVAVRTLDIATLAAVGHTAATAAGAVYAHAVQRGTASFWLDSALP
+DGGEARWSMVGDGVDVLGEEEGRIPSPGLRLIRHGDPADPDRAWADLAAAAAPREVHGGE
+GLPLRGGLVGWLGYELGLADLGVTPPPPRPGDPAALPAQFWVRPSRYAVADHVAGALSCC
+VVSLDADAAEAAADRWEADVRRALEAARTSTEEVEVDVDAPEAPGVWREDGAAYAEQIAR
+CRAALHAGDSYELCLTTRFDADPALRVDPLALFRDLAAHQPAPYAALMEHGTGAERWAVV
+SASPERFLSGRDGRYSTKPIKGTAARLPDPTEDAAAAAALAADPKTRAENLMIVDLLRND
+LSRVCEPGTVQVPALMAVESYATVHQLVSTVTGVARAGVAPVDVVRSLFPGGSMTGAPKR
+RTVELLAAWEGSPRGVYSGALGMLGADGTVELSIVIRTAVLSPTTPDAPARWSVGAGGAI
+VADSDAHAEHEEVLLKARGLRRALTRAAGTA*
+>NZ_CP097650.1_559
+MPTAPAPSEAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP
+DPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHDDPADPDRAWADLGAAAAPRSVVGGE
+GLPLRGGLVGWLGYELGMADLGVSPPSRRPEDPAPLPAQFWVRPSRYAVADHAAGVLHCC
+VVSLDPTAAEAGADRWAADVRRALAAARRDLETAAGDAVVPPPEDAGPEPRADEEAPGTW
+REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVNPLVLFHELAAHQPAPYAAL
+LEHGTGARRWAVVSASPERFLAGREGRYSTKPIKGTAARLPDPAADAAAARALADDPKTR
+AENLMIVDLLRNDLSRVCEPGSVEVPSLMAVESYASVHQLVSTVTGTARAGVEPVEVVRS
+LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS
+VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGVPTTAPDIA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000577.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000577.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02c810c0a2880d19076d75011bb74bb658f5ad26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000577.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_562
+MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPEVDASSSLASTPATDDASGS
+ATSSSASSASASSTAAAAGSDSATGQADDPAYAVIDAVLEKYGDGIIVAVDADDDDTTWE
+VDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDGVTLDE
+MDLDDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDEH*
+>NZ_CP033200.1_304
+MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSVSPEVDASSAVASTPATDDASTT
+SASASSSASSTSASSTAAAASSGSGTGQADDPAYAVIDAVLEKHGDGIIVEVDANDDDTT
+WEVDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDGVTL
+DEMDLEDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDER*
+>NZ_CP040019.1_2304
+MNATSLARKTALTGTGLLAALALAACGTADDDTAANPQETAVQQSPTQAATTAPASASGS
+ASASASGSASASASGSASPAAASGSVERQGDDPAYAAIDAILGLHDDGVIVEMDLDDDDA
+KWEVDVVVGDDVKEYDVTTGGQVSEGVRPQIDDDVRRAGEAQVTAETAISTALQGRTDQT
+VDEVDLDEEGGTLVWKVELDRENGEDGAEVKIDAKTGDVIEVEEG*
+>NZ_CP083691.1_2195
+MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSASLEVDASSAVASTPATEDASTT
+SASASSASSAPASSTAAAAGRDSATGQADDPASAVIDAVLEKYGDGIIVGVDANDDDTTW
+EVDVVVDKEVKELDVTADGDITETDRESDPEDVQKAKDAEVTAQQALDTARKGRDGVTLD
+EMDLDDDNGTLQWEVEFDREDGSDGPEVEIDATSGEVLTVDEH*
+>NZ_CP097650.1_563
+MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPGVDASSAVASTPTTDDASGS
+ASSSASSASASSTAAAAGSGSATGQADEPAYAVIDAVLEKYADGIIVAVDANDDDTTWEV
+DVVVGEGAKELDVTADGDITETDRESDPEDVQKAKEAEVTAQQALDTAREGRDGVTLDEM
+DLEDDNGTLQWEVRFDREDGSDGPEVEIDATSGEVLTVDER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000578.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000578.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f413a2145aa4952b17fa49b7912428456d0e011
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000578.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_586
+MSSACGCEAPTPGAPEEPEEHRPWWRDAAILLPVLSGVAFIAGLVLEWSGAGLVATVVFW
+VGLVLGAWTFVPGALRGLFTRGRLGIGLLMTISAIGAVILGYIEEAAALAFLYSIAEALE
+DKAMDRARAGLRALLKLVPETATIRQGGATVQVEAKDLHPGQVLVVRPGERIATDGIVRT
+GRSSLDTSAITGESIPVEVGPGDTVSAGSINTSGALEIDATAAGTDNSLTTIVHLVEQAQ
+TEKGARARLADRIAKPLVPGVLVLAVLVAALGSLFGDPELWITRALVVLVAASPCALAIA
+VPVTVVSAIGAASRFGVVIKSGAAFERLGGIRHLAVDKTGTLTRNQPTVTAVLTTPGLTE
+DQVLGWAAALEQHSTHPLAAAIIAAAPDAPGAKAVTETAGHGITGRIDGATITVGSPRWL
+DPGPLAAQVQQLEDQGMTVVIIHRDGTVAGAIGVRDELRPEVPAVVTTLTGQGIGLTMLT
+GDNARTARAIAAQAGIGDVRAELRPEDKAAAVGQLTGTRPTAMIGDGINDAPALAAAEVG
+IAMGATGSDAAIESADVAFTGHDLRLIPQALAHARRGRAIMNQNIVLSLLIIGVLLPLAI
+TGMLGLAAVVLVHEVAEVIVIGNGLRAATTRRTALASLTDRQAQRSTVG*
+>NZ_CP033200.1_1724
+MSAACGCEAPTPTPGAPEEHEEHRPWWRDAAILLPALSGLAFLTGLVLEWSGAGLVATVV
+FWVGLVLGAWTFVPGALRGLFTRGRLGIGLLMTISAIGAVILGYIEEAAALAFLYSIAEA
+LEDKAMDRARAGLRALLKLVPETATIRAGGATVEVEAKDLRPGQVLVVRPGERVATDGIV
+RTGRSSLDTSAITGESIPVEVGPGDTVSAGSINTAGALEIDATAAGTDNSLTTIVHLVEQ
+AQAEKGDRARLADRIAKPLVPGVLILAVLVAALGSLLGDPELWITRALVVLVAASPCALA
+IAVPVTVVSAIGAASRFGVVIKSGAAFERLGGIRHLAVDKTGTLTRNQPTVTAVLAAPGI
+TEDQVLGWAAALEQHSTHPLAAAITAATPDTPAAEGVTETAGHGITGRLDGATVTVGSPR
+WLAPGPLAAQVQGLEDQGMTVVIIHRDGAVAGAIGVRDELRPEVPTVVTTLTGQGIDLTM
+LTGDNARTARAIADQAGIDDVRAELRPEDKATAVHQLTGTRPTAMIGDGINDSPALAAAE
+VGIAMGATGSDAAIESADVAFTGHDLRLIPQALAHARRGRAIINQNIILSLLIIAVLLPL
+AITGVLGLAAVVLVHEVAEVIVIGNGLRAATTRRTALEPLTDRQAQPATTG*
+>NZ_CP040019.1_712
+MRATTHTPVEELETDDEHETPWWADRAVLIPIASGVAFVAGLACEWSGAQSAALVLFWVG
+LLLGASTFVPGALRKLATGKLGIALLMTMSATGAVILGHVEEAAALAFLYSIAEALEDRA
+MDRARAGLRALLKLVPQSATVLTDGHSASVPARDLAAGQVMLIRPGERIATDGIVRSGHS
+SVDTSAITGESIPVEVGPGDEVSAGAINAAGALQVEATAPGTDNSLTTIVSLVERAQAEK
+GQRARLADRIARPLVPGVLVLAVLVALIGSLAGDPQTWITRALVVLVAASPCALAIAVPI
+TVVSAVGSASKFGVIIKSGAIFERFGDIGHVAFDKTGTLTRNQPTVTAVVPAADVTEQQV
+LAWAAALEQHSTHPLATAITHAAPHNPRRPGHHRGSRPRNPRHRRRRRSAGRQPPLGRPR
+RPHLPGP*
+>NZ_CP040019.1_713
+MLVGSPRWVDPGDLTYRVRDLEAQGMTVVVVHRDGAVAGAIGVRDELRPEVPEVITTLAG
+QGIDVTMLTGDNERTARALAAQAGISDVRAELRPEGKSAAVGELSVRRPTAMIGDGINDA
+PALAAADVGIAMGATGSDAAIESADIAFTGQDLRLLPQAIAHARRGRRIVNQNIVLSLLI
+IAALPPLAITGVLGLAAVVLIHEVAEVLVILNGLRAARTHQPTRGH*
+>NZ_CP040019.1_2319
+MVPVFSGVAFLTGLVLEWAGLEVPALVLFWIGLLLGASTFTPGAIRKLFKGKLGIGLLMT
+ISAVGAVILGYVEEAAALAFLYSIAEALEDKAMDRARGGLRALLKLVPETATIRRDGASV
+EVPAKDLAVGQLMLVRPGERIATDGIVRTGRSSLDTSAITGESIPVEVEPGDTVSAGAIN
+TAGALEVETTAAGTDNSLTTIVDLVEKAQADKGDRARLADRIARPLVPGVLILAALVAII
+GSLLGDPELWITRALVVLVAASPCALAISVPLTVVAAIGSASKFGVIIKSGAVFERFGVI
+RHVAVDKTGTLTRNEPAVTAVLTAEGVTEKQALAWAAALEQHSTHPLAAAITAAAPGAPA
+ADGVTEQAGHGIEGTLDGARITVGSPRWLDAGTLGEQVAGLEEQGMTVVIVHRDGTPVAA
+IGVRDELRPEVPEVVRTLAAQGIGVTMLTGDNARTARALAAQAGIGDVRAELRPEDKAAA
+IAELGEKGAVAMIGDGINDAPALAAADIGIAMGATGSDAAIESADVAFTGHDLRLLPRAF
+DHARRGRHIINQNLILSLLIITALLPLALFGVLGLAAVVLVHEIAEVVVILNGLRAARTR
+KSAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000590.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000590.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90910fb96a843821341e288af604da6339d26e72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000590.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_629
+MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET
+VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI
+DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL
+GIPVVAILDTNCDPDEVAYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE
+PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAPAERAEAPAAEAAPQGE*
+>NZ_CP033200.1_375
+MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET
+VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI
+DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL
+GIPVVAILDTNCDPDEVPYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE
+PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAAPQGE*
+>NZ_CP040019.1_2267
+MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET
+VAHGGTILFVGTKKQGQEVIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI
+DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMSKTPSAVWVVDTKKEHLAVDEAKKL
+GIPVVAILDTNCDPDEVTYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQSAAE
+PMAEWERELLEQHNAQQAEQAEAPAEAQAQAEEASAEAPAQAEEASAGAPAQAE*
+>NZ_CP083691.1_2120
+MSVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLTYIDRAYEFVKQT
+VAHGGTILFVGTKKQAQEAIAEQATRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEAI
+DFEDVAGSTHTKKELLLLNRELEKLQGNLGGIRDMARTPSAVWIVDTKKEHLAVDEAQKL
+NIPVVAILDTNCDPDEVAYPIPGNDDAIRSVTLLTRIVADAVAEGLIARQGGKSGDSSAE
+PMAEWERELLEQHNAEQAAQAEAPAAEAAESEAPAAE*
+>NZ_CP097650.1_598
+MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET
+VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI
+DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL
+GIPVVAILDTNCDPDEVAYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE
+PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAPAEQAEAPAAEAAPQGE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000598.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000598.fa
new file mode 100644
index 0000000000000000000000000000000000000000..980a9919723ba9d2f2168b0997f67fe4685b9e84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000598.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_638
+MAGTRDGDAVEPRPERSTAVLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFD
+YHWAHLLGDEDTVVRTIEHEGRAVGALVCTQQDGVGELSFWTAQDYWGLGLTTAAVDRFL
+EEHTARPLRAHVPEDNVGSVKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD*
+>NZ_CP033200.1_384
+MLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFDYHWAHLLGDEDTVVRTIEH
+EGRAVGALVCIQQDGVGELSFWTAQDYWGLGLTTAAVDRFLEEHTARPLRAHVPEDNVGS
+VKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD*
+>NZ_CP040019.1_2258
+MLLRDVRPEDLDEFFLHQQDEQASLMSAFAPRNPRDRGVFDYHWSSLLAAETAVVRTIEH
+EGRAVGAIVCTEHDGVGELSFWTAQDYWGLGLTTAAVDAFLREHTRRPLRAHVPEDNAGS
+VKVLSRRGFETVGQEKVFSNARAEVITELVMELPAGAE*
+>NZ_CP083691.1_2110
+MPLRDVRPDDLDAFFLHQQDERANLMSAFAPRNPSDRGVFDYHWAHLLGDDATEVRTIEH
+EGRPVGALVCTRVDGVDELSFWVAREFWGQGLTTSAVDEFLSTHRERPVRAHVPEDNLGS
+VKVLTRRGFREVGREKVFSNARAEVVEELVLELPGA*
+>NZ_CP097650.1_607
+MLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFDYHWAHLLGDEDTVVRTIEH
+EGRAVGALVCTQQDGVGELSFWTAQDYWGLGLTTAAVDRFLEEHTARPLRAHVPEDNVGS
+VKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000601.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000601.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ce83a97fa175293505a010d151aec6310625c4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000601.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_645
+MSSSEPTAPVPTAAQFRAAQQSEEFTELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF
+MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAHENP
+EATR*
+>NZ_CP033200.1_391
+MSSSEPTAPVPTAAQFRAAQQSEEFIELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF
+MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAHENP
+EATR*
+>NZ_CP040019.1_2250
+MSSSEPTAPAPTAAQFRAAQQSEEFTELRSTYRSFAFPMTVAFFVWYLVFVIAGAFFPEF
+MSIRLGGNITLGLVLGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGGAPET
+PEATR*
+>NZ_CP083691.1_2108
+MSTGPHTPPAPTPAQFRAAQDSPEFRELRRTQRSFAFPMTVTFFVWYLLFVILGAFFPQV
+MAVRLGGNITLGLVLGLLQFVTTFAITFAYVRFSNRVLDPRAAALRERLEREAAGAAPET
+PEVAL*
+>NZ_CP097650.1_614
+MSSSEPTAPVPTAAQFRAAQQSEEFIELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF
+MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAPENP
+EATR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000604.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000604.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b56986bbfd40c83b4fddd4f89629f7f12491743c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000604.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_648
+MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE
+TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE
+HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ
+QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI
+EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD
+AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA
+TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF
+DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF*
+>NZ_CP033200.1_394
+MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE
+TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE
+HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ
+QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI
+EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD
+AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA
+TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF
+DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF*
+>NZ_CP040019.1_2247
+MSAVEVLWYVLGVVAVALGLAVSIALHEVGHLMPAKLFGVRVTQYMIGFGPTIASWRRGE
+TEYGFKAVPLGGYVAMVGMLPPPRPGQEPRTASTGFVQQLGRMADDARTQAAAELTAADE
+GRQFIQLPVWKRVVIMLGGPFMNLLIALGVTALLVTTVGTSQPSTTAAEVYRCVVTTDEQ
+QARAAEGGGQDCRPGDPVAPAHEAGLRPGDTVTSFDGRPVDDWDALSGLIRERAGQPTAI
+EWERDGEPHSATITPRLTQRPVTDAVGRPERAPDGTALTEEVGFIGMGSQIETVQQSPLA
+AGPVVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALQEA
+ELADKAALLLSLVAGVNVALMVFNLIPLLPLDGGHVAGALWEALRRGWARLRGRPDPGPF
+DLARMLPLTYAVAGLMLVMGVVLIVADIVEPIRLF*
+>NZ_CP083691.1_2105
+MSAVEALWFVGGVVVVALGLALSIALHEVGHLVPAKLFGVRVTQYMVGFGPTVASWRRGE
+TEYGIKAFPLGGYVAMVGMLPPPKGGTVARTGSTGFRARAGRMADDARAQAAEEITAADE
+GRQFIQLPVWKRVVIMLGGPFVNLLIALALTAVLVSTLGVARPSTTADEVFQCVVSQSEQ
+QSRAADGGAAQDCRPGDPAAPAYEAGLRPGDRVVSFDGRDVGSWAELSTAIRARAGQATA
+IAWERDGTRTESTLTPLLTERPVTDALGVPERGADGGVKTEPVGFIGLASRQETVTLAPW
+EAVPLVGRQAQGVVGVILALPQRLWDTAVAVVTPAPRDPNGPMSVVGVGRIAGEAAALDT
+ASPADKAALLLSLVAGVNVALLVFNLIPLLPLDGGHVAGALWEGLRRGWARLRGRPDPGP
+FDLAVMMPLTYVVGAAMLAMGVLLIVADIVKPVQLF*
+>NZ_CP097650.1_617
+MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE
+TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE
+HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ
+QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI
+EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD
+AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA
+TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF
+DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000610.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000610.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e42fba553c82be307184f5dbdbc3392a7adbee9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000610.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_654
+MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE
+DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN
+RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK
+LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN
+DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR
+LAAKLTGWRIDIVGDGVTTSAPGR*
+>NZ_CP033200.1_400
+MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE
+DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN
+RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK
+LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN
+DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR
+LAAKLTGWRIDIVGDGVTTSAPGR*
+>NZ_CP040019.1_2241
+MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRVSGHVTVWATELDE
+DGTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGLIQQGVN
+RHMIQVNLGTLEAVLPPPEQVPGEDYSHGRRLRAYVVSATRGNKGPSVTVSRSHPGLVRK
+LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN
+DEKIDIVEHAEDPAQMIANALSPAKTVSVEVLDADQHSARAVVPEHQLSLAIGKEGQNAR
+LAAKLTGWRIDIVGDGSDASAPAR*
+>NZ_CP083691.1_2099
+MSALRMLVAERDIPLDRLVPAIEQALLIAYHRTPGAIKGSRVELDRSTGHVTVWAPEVED
+DGTCVGEFDDTPNGFGRIAASTARQVIFQRLRDADDAKVLGEFKDREGELVSGVIQQGSH
+RHMVQVDLGSLEAVLPPPEQVPGEDYRHGRRIRAVIVSATRGPKGPSVTLSRSHPNLVRR
+LFALEVPEIADGTVEITALAREAGHRTKMAVKATRPGVNPKGAAIGEMGSRVRAVMTELG
+GEKIDIVEHADDPAEMIKHALSPAQALSVEILDADQHSARAVVPQHQLSLAIGKEGQNAR
+LAARLTGWRIDIVGDAAQQPGADAAQQPGADAASEMAPATEAGAEA*
+>NZ_CP097650.1_623
+MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE
+DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN
+RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK
+LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN
+DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR
+LAAKLTGWRIDIVGDGVTTSAPGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000622.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000622.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81c9366c51defcc100eb2cb5665abd4b24776c6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000622.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_667
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG*
+>NZ_CP033200.1_413
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG*
+>NZ_CP040019.1_2221
+MTDAPAPSAVPADDAVPRVAILGAGGKMGRHAVPAVREAAALELVAELGSADPLEAILDA
+GATHVLDLTVPDVSPRNAAFAVEHGLHTVIGTSGWGPERREALAAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAKAARFFESVELIEMHHPAKLDAPSGTAVRTAELIGQARREAGVPPSP
+DATERDPDGSRGAVVDGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGIV
+LGLRTVASRPGLTYGLDGYLDLG*
+>NZ_CP083691.1_2085
+MTETTPRTPVPGDATPRVAILGASGKMGRHAVPAVRAAQGLELVAELGSGDPLQAVLDAG
+ATHVLDLTVPDASPENVAFAVEHGLHVVVGTSGWGAERRAALEERLAARPGVGVLIAPNF
+SVGSVLASAFAARAARWFESVEVVELHHPAKLDAPSGTAVRTAEMIAASRAEAGVGPSPD
+ATERDPDGARGAVVDGVHVHAVRLRGLEAHQEVLLGGPGEQLTVRHDAFDRQAYMPGVVL
+ALREVAGRPGLTYGLDAVLGLD*
+>NZ_CP097650.1_636
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000623.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000623.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b727c5c442fc46b237d24a63974abd3b0347617
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000623.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_668
+MDWTDTWTLAEPSRTPDDGAVGPPAPAVRARRSTVMSKVWVGFVCLLVLLFAGFALNASV
+ALVRAPQPLAKAIGAGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSP
+GGRIDREAADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG
+*
+>NZ_CP033200.1_414
+MAEPSRTPDDGAVGPTEHAARARRSTVMSKVWVGFVSLLVLLFAGFALNASVALVRAPQP
+LAKAIGAGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSPGGRIDREA
+ADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG*
+>NZ_CP040019.1_2220
+MADRAPRPAEQTVADPAEHAARARRSTLMSKLWVGFVSLLVLFFASFAVYVAVAFIRAPQ
+LLAKGIGVGVIFVVLVTVAVLAREVWFGQQTERLADLLEAEGGLPEDDLPRSPGGRIDRA
+AADAQFEVYRVEAEAAPRDWRTRYRLALAYDASGDRRRAREAAREAVRLHRQG*
+>NZ_CP083691.1_2084
+MASTDPRPGVDREQAPRAGSSTGAKLWVLFVAALTLFFAFFVVRAAVVFIAAGGVLPAVI
+GVAVILVVLVGLGLLGREMLFGLQTERLARTLEAEGGLPADDLPRSPGGRIDRDAADAAF
+ADAADEVRAAPEDWRARYRLSLAYDAAGDRRRAREAARQAISLASRRG*
+>NZ_CP097650.1_637
+MAEPSRTPDDGAVGPTEHAARARRSTVMSKVWVGFVSLLVLLFAGFALNASVALVRAPQP
+LAKAIGVGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSPGGRIDREA
+ADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000624.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000624.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19e804ccbaa08e42b87ff56affdcd2be248bbada
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000624.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_670
+MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDRGADGLVVTGTTGE
+TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY
+NKPNQAGIRAHFETVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL
+QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGA
+RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATRDELSVIRADLAE
+AGITF*
+>NZ_CP033200.1_416
+MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDRGADGLVVTGTTGE
+TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY
+NKPNQAGIRAHFETVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL
+QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGS
+RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATPDELSVIRADLAE
+AGITF*
+>NZ_CP040019.1_2217
+MSAVRSASAPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDGGADGLVVTGTTGE
+TSTLTDEENLAMFRTVVEAVGDRAKVVAGTGTNDTAHTLELSRRAKETGVDGLLLVTPYY
+NKPNQAGIRAHFEAVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL
+QSTTTVLAHSDLDLYSGDDGATLPLMALGAVGVVSVAAHVAPGLYRKLVDAVHAGDLAAA
+REHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQASADELSDIRADLAE
+AGITF*
+>NZ_CP083691.1_2083
+MTDARRTVNPSELPFGTVVPAMVTPMDQDGAVDLQAAAVLATHLVDQGADALVITGTTGE
+TSTLTDEENLAMFRTVVEAVGERARVIAGTGTNDTHHSLELSRRAAEIGVHGLLLVTPYY
+NKPNQAGIRRHFETIADGVDLPIMLYDIPGRSVMPIQPETLVALAAHPNITALKDAKGDL
+QSTTTVLAHTDLHVYSGDDGATLPLMAMGAVGVVSVAAHVAVPGYRALVDAVHAGDLRAA
+RDAHFALDPVQRGIMSHVQGAVAAKTVLAGQGIIPTAAVRLPLVAADDAELAAIRADLAE
+AGISF*
+>NZ_CP097650.1_639
+MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAVLAEHLVDRGADGLVVTGTTGE
+TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY
+NKPNQAGIRAHFEAVADGVDLPIMLYDIPGRSVMPIEPETIIALAQHPNIRALKDAKGDL
+QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGA
+RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATPDELSVIRADLAE
+AGITF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000628.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000628.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d42dc8c42b29421d68fa7e659a2a1738306061b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000628.fa
@@ -0,0 +1,22 @@
+>NZ_CP042169.1_674
+MAGAQDVVHALAHAGRTVATGESLTAGLLAARLADVPGASAVLHGGVVAYQNAVKTGLLG
+VPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLAVP
+DADANALDVLGGERDGAATAILLRLDGDRAAIREATVAAALQALTRLLAVRGH*
+>NZ_CP033200.1_420
+MAAARDVVHALADAGLTVATGESLTAGLVAARLADVPGASAVLHGGVVAYQNAVKTGLLG
+VPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLAVP
+DADASALDVFGGERDGAATAILLRLDGDRAAIREATVAAALQALTRLLAGRGH*
+>NZ_CP040019.1_2213
+MAAQETVRALAGAGLTVATAESLTAGLVAARLADVPGASAVLQGGVVAYQNSVKAGLLGV
+PADLLERVGAVDPEVARRMAEGARAGLGADVGVATTGVAGPEPHQGRPVGTVWLGVAVPE
+RLTAALDGLGGERRGAATAIPLALDGDRRAIREATVAAALAALTRLGAPVGERATGEGAA
+GEPCAGA*
+>NZ_CP083691.1_2080
+MSTGVGAVAAEGEAADPARAAVRALTTAGLTVATAESLTAGLVAARLADVPGASAALQGG
+VVAYQNHVKAGLLGVDAGLLTARGAVDPEVARQMACGARRAAGADVGVATTGVAGPEPHQ
+GKPVGTVFVGVAVPAELAPALAGLDGEPGAGEAAPGEAGSGGSEAGVAAAAFALTLPGNR
+AEIRAATVETVLDLLAALGTTGRGMPDEAPALS*
+>NZ_CP097650.1_643
+MTTAAARDVVHALADAGLTVATGESLTAGLVAARLADVPGASAVLHGGVVAYQNAVKTGL
+LGVPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLA
+VPDADASALDVLGGERDGAATAILLRLDGDRAAIREATVAAALQALTHLLAGPGH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000631.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..124b64bcbc1c04b58f58f103f76479df04a8921a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000631.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_681
+MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG
+RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP
+DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT
+GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG
+NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG
+QGKENARRFLKDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG*
+>NZ_CP033200.1_424
+MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG
+RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP
+DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT
+GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG
+NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG
+QGKENARRFLKDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG*
+>NZ_CP040019.1_2209
+MSKTPDREKALEAALAQIDKQFGKGSVMRLGDQTQTPVEVIPTGSVAMDVALGIGGLPRG
+RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARKLGVDTDALLVSQP
+DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKIT
+GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG
+NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG
+QGKENARRFLKDNPDLAQEIEERILTKLGIGVDPEAEADEAPALTAVPGDTAAG*
+>NZ_CP083691.1_2077
+MSKASATEKVATEREKALEAALAQIDKQFGKGSVMRLGERSQAPVEVIPTGSVAMDVALG
+IGGLPRGRVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARKLGVDTD
+ALLVSQPDTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMS
+QALRKVTGRLHQTNTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLK
+EAGSPVGNRTRVKIVKNKMAPPFKQAEFDILYGEGISKEGSLIDMGVEEGIVKKSGAWFT
+YDGDQLGQGKENARRFLKDNPDLADEIEHRIFTKLGIGADPQAEDDAEGETPALQAVAGD
+VAAG*
+>NZ_CP097650.1_647
+MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG
+RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP
+DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT
+GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG
+NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG
+QGKENARRFLRDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000641.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000641.fa
new file mode 100644
index 0000000000000000000000000000000000000000..777ce927729add073f62dbe2c3d3e432e8af9e4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000641.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_694
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR*
+>NZ_CP033200.1_434
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR*
+>NZ_CP040019.1_2197
+MTLMTAQFAGSPAAARRRPAAIRLTRRGRLLLRGIPVMAAAAAATLAVAFLLGVLLSPAA
+VSADTAAPATQTVTVMPGDSLWTIATTIAPEEDVYEVIAAIDELNGLEGRAPALGEELFI
+PATR*
+>NZ_CP083691.1_2065
+MTAVTAVLSRTHQLTSVRARPTRAVAASTRAAARTSGVRLTRRGRLLFRGLPVILSVAAA
+TVAAAFFAGVLFSPPAVSADTPAEELQTVTVMPGDSLWTIARDVAPEADRRDTMRRIDEL
+NGLEGRDPELGQELYVPPTR*
+>NZ_CP097650.1_657
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000647.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000647.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a750826ac5dc8c193070313de4e966ce2f40245e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000647.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_700
+MTGSHDDGGLARDDGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP
+WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMSALTDGSAGEREVTEVLARIRVFA
+AVVPTLAGDEDDVHDHADHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALT
+AWNPVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQREWTPAYRD
+QEIADEIAEVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADAA
+GVRLMTATLKTLLADLPLLAERADSVEITVRRP*
+>NZ_CP033200.1_440
+MTGSHDDGGLARDEGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP
+WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMAALTDGSAGEREVTEVLARIRVFA
+AVVPTLAVDEDDVHDHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALTAWN
+PVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQKEWTPAYRDQEI
+ADEIAQVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADATGVR
+LMTATLKTLLADLPVLAERADSVEITVRRP*
+>NZ_CP040019.1_2191
+MTHGHDDGAPAGVAGAGPIEETVAVPRPDSRELPGHIRAALDRMREKTAGPNTADTAGVP
+WEGRDLSGPGVDGSANPLHVFDEDDGTSPEEWTRVMAALTTGAAGEAEVTDVLSRIRVFA
+AVVPTLAVDEDDVHDHADHSGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTSVPALT
+AWNPIARPVAVWMPRACLSAVDEGCELVVVDAGAEHTYAVRRPAVWALAQQKPWTPSYRD
+QEIADEIAQVADLVPHLLNLGLAPGSGVATHTGSGAVMSGGGAGPELQIVAMPARDADAA
+GVRLMAATLKTLLADLPLLAERADSVEVTVRRP*
+>NZ_CP083691.1_2059
+MSSASSSEPAHDAEATVPVPAPGGRELPGHIRAAMERMRQKTARENTADTAGVPWAGRDL
+SGPGLEGSANPLHIFDEDDGTAPAEWARVMDALTEGTAGEAEVVDVLGRIRVFAAVVPTL
+AVDEADVHDHAAHSVHEHAQHEDAAHGDKAADVALVTMRAPDGRQALPVFTSVPALTAWN
+PLARPVAVWAPRACLSAVDEGCELVVVDAGAEHTYAVRRPAVWALAQQKPWTPSYLDQEI
+AEEIAGVADLVPNLLNLGLAPGPGVATETASGEVMNGGGSGTELTVLAMPARDADAAGIR
+LMTTTLAMLLGDLPLLAERADSVEITVRRP*
+>NZ_CP097650.1_663
+MTGSHDDGGLARDDGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP
+WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMSALTDGSADEREVTEVLARIRVFA
+AVVPTLAVDEDDVHDHADHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALT
+AWNPVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQREWTPAYRD
+QEIADEIAEVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADAA
+GVRLMTATLKTLLADLPLLAERADSVEITVRRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000649.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000649.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14b0981819be6a47c2dd5ffad0739e46b3b2bc05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000649.fa
@@ -0,0 +1,23 @@
+>NZ_CP042169.1_702
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR
+LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL
+C*
+>NZ_CP033200.1_442
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR
+LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL
+C*
+>NZ_CP040019.1_2189
+MNSSSTPTPEPSETARHAWRAYFEATQMLSEMLERGLKKDSGMSLADYNLLLLLYEAPEG
+RLRMGELASGMVFSPSRITYQVKTLVARGLIERRAAECDRRGFEAVLTDEGRTAFRRAAA
+GHARQVDELFLSHLEPGEAETLERIFTRLGGRLEGLC*
+>NZ_CP083691.1_2057
+MTSSSTPAAEPTGPRAARHAWRAYFESTQMLQDQLERGLKAECGITLADYNLLLLLVESD
+GGRLRLGELASRMVFSPSRVTYQVKSLVARGLIERRRVECDRRGFEAVLTDAGRTAFRRA
+AVVHARQVDELFLDLLQPGEAEVLGRVFTRVGTALESRCAGRAAPSEPCGAQASNSADA*
+>NZ_CP097650.1_665
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVLERR
+LKQDCGMSLADYNLLLLLYESPEDRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLVDLAPGEAESLTRIFSRLGRRLEGL
+C*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000653.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000653.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b71a71104d79e304f848f7a60b7b9c8bd35f95a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000653.fa
@@ -0,0 +1,46 @@
+>NZ_CP042169.1_706
+MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL
+GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS
+VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG
+GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL
+PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRTHFSWVGPEVLGVLVVSMA
+AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA
+VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVVEERRGEAMGFYGSAMTAG
+AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVMRGRRPA*
+>NZ_CP033200.1_446
+MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL
+GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS
+VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG
+GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL
+PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRSHFSWVGSEVLGVLVVSMA
+AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA
+VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVEEERRGEAMGFYGSAMTAG
+AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVARGRRSA*
+>NZ_CP040019.1_2182
+MGFIARFPHTAAGVILTLHVALTLDLGYGQAGLAAAAMTLGIAVGSPWRGRVVDAKGLRR
+ALLPSVIAEALIWPLVPWLPFWLMLVAVFFGGVFALPIFSVVRQGLGVLTHGRDRQTAFA
+LDSIITETIFMVGPALGAVVAATWSSALGLTIVGLSSALGGVLLMWFNPPTRSSQLAVVG
+PETEDPYTEDEDREEAVAQTVHGAPMHVEMTAPSLATGALPVVTEAIPLVTGALPVIAAD
+GSGPATPTPGLTRAERLRLWRARHFAWVGPEALGVLVVSMAAGLVMVGTEVTMVAELEHA
+GMAGSVGVVYAFWCGASAVGGLFYGAWGRQVHPYLLMGLLALLTLPMAFVDGLWALALAA
+IPSGLFTAPTLASASSRLSTLVPEERRGEAMGFYGSAMTAGAAMGAPLSGVFIDAIHPAA
+GYVFAGLAGAVLVLAAALVTLARRRRVGGTSA*
+>NZ_CP083691.1_2052
+MDFRAYGRLLQDPRIRNLLAVGFIARFPHTAAGVILTLHVAVTLGLGYGQAGLAAAAMTL
+GIACGSPWRGRAIDRDGLRRALLPSVVAEAVIWPVVPWLPFGFLLVAVFFGGLFAVPIFS
+VVRQGLGVLTHGADRQTAFTLDSIITELVFMVGPALGAVIAATGSTALGLTVVGLSGALS
+GALLMWFNPPTRSTQLAADGPSAGDPFTEEEDREQALSQAVHTAPVRATVAAADLATGAL
+PVVTEAVPIVTGSLPVIAADGSGPVSPAPRAGRHDDGRAADGLTRDERWRLWRVRHFGWV
+TPEVLGVLVVAMAAGIALVGTEVTMVAELEHAGQEASVGVVYAFWCGASALGGLFYGAWG
+RQVHPYLLGALFALAVAPMAFVDGLWALAWASVPSGLLTAPTLAAASSRISLLVSEERRG
+EAMGYYGSAMTAGSALGAPVVGLVIDGVGPGAGYVGAAGAAVVMIGAAAILTAARRRRSP
+ARG*
+>NZ_CP097650.1_669
+MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL
+GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS
+VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG
+GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL
+PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRTHFSWVGPEVLGVLVVSMA
+AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA
+VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVVEERRGEAMGFYGSAMTAG
+AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVMRGRRPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000669.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000669.fa
new file mode 100644
index 0000000000000000000000000000000000000000..228935c33d8fd2d3ee3fb99072af1ca1489cf063
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000669.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_727
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEVGMVTTVDRGRYAVVLPERLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGEEGTLARIVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGVPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED*
+>NZ_CP033200.1_466
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAQVGMVTTVDRGRYAVVLPDRLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIIRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED*
+>NZ_CP040019.1_2136
+MGRRVDPGAWDESDVRVRPSKRGTRPRTKERPKHEDAVVGMVTTVDRGRYTVVLPERLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARVVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALMAHYESL
+DLEVMTSGAAVFEAETGDTALDGALVARVAERLQGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTDDDGVPLADTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCAHTADSPGCGLDGWVAAGHAGPSGAARLASLRRLLGNRLGPAGAED
+SASSED*
+>NZ_CP083691.1_2027
+MGRSLDPSAWDESHVRVRPSKRGTRPRTKQRPQHEDAQTGLVTTVDRGRYTVVLPGRAHA
+PVTAMRARELRRTPIATGDRVDVVGDLSGDEGSLARIVRVQERDTVLRRSADDSDAVERV
+VVANADTLMVMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAELVAHYEAL
+DLEVMTSGASRFEAESGDTDLDDGLVERVAERLAGHTAAFVGPSGVGKSTLLNALTGAGR
+ATGHVNAVTGRGRHTSSSALAMSLPGPDGEPVPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+EDLAGGLEGCPRGCTHLADSPGCGLDAWVAEGHAGEAGPARLASLRRLLGNRTTAEAGGS
+ASSED*
+>NZ_CP097650.1_690
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEIGMVTTVDRGRYAVVLPDRLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000672.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000672.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a41d19b5cf611af9b296a97ce79b6cfdc151f3bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000672.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_730
+MTADQHGHECRVAQDASLERLYQYLDGALTPEDIEQVRAHVAECPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQISTTTVTWG*
+>NZ_CP033200.1_469
+MTVDQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG*
+>NZ_CP040019.1_2133
+MTADQHGRECRDAQEDTLERLYQYLDGALTPEEIDQVRAHVEDCEDCRHQQELEQFIRTA
+VRRSCQEKAPEQLRTTILTRITQLSTTRVTWR*
+>NZ_CP083691.1_2024
+MSQDGDCRGCNDGEDRLEQLYQYLDGALTPEDIDQVRAHVDQCPDCHHQQELELIIRSAL
+RRSCQEKAPAQLRATIMTRITQVSTTTVRRAG*
+>NZ_CP097650.1_693
+MTADQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000674.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000674.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0abd0bd3c2d7340b4ed20bd78c2d4bf376324d47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000674.fa
@@ -0,0 +1,110 @@
+>NZ_CP042169.1_732
+MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAEAEPKAAA
+KTEPKTAAKAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADT
+ATTTADEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKVLIDNRVVINSHLART
+RGGKVSFTHFIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA
+LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH
+GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYSMAYHPDLDIREHGLTLWDLDRKWPTGGFGGAGSLTLRKILGVLRDAYCRTIGV
+EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP
+DSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVVVNNQVGFTTPPTQARSA
+VYSTDVAKTIQAPIFHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETHEDAP
+ASGGEGLRPAEDRDAAPEAPASTAISAETLRAIGQAHIDVPEGFTVHPKLAALLERRAKM
+AVDGGIDWGFAELAAFGSLLMERVPVRLAGQDSQRGTFTQRHSVFHDRITGDTWAPLRHL
+SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD
+QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREHA
+YARPRRPLIVFTPKQLLRLKAAANSVEDFTEGGFQPVIPDAGVDAKDVTRVLLVSGRLYY
+DLLARRQKSGDTSTAIVRVEQLYPLPLDEIRKALRAYPVADVTWVQDEPANQGPWPFMAL
+NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR*
+>NZ_CP033200.1_471
+MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAEAEPKAAA
+KTEPKTAAKAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADT
+ATTTADEKQEKATVLKGMAKAVATNMDASLSVPTATTVRDLPAKVLIDNRVVINSHLART
+RGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA
+LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH
+GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYSMAYHPDLDIREHGLTLWDLDRQWPTGGFGGASSLTLRKILGVLRDAYCRTIGV
+EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP
+DSFSVLPILVHGDAAFAGQGVVAEVLQLSQLPGYRTGGTIHVIVNNQVGFTTPPTQARSA
+VYSTDVAKTIQAPILHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETHEDAP
+ASGGEGLRPAEDRDAAPEAPASTAISAETLRAIGQAHIDVPEGFTVHPKLAALLERRAKM
+AVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITDETWAPLKHL
+SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD
+QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREQA
+YARPRRPLVVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDAKDVTRVLLVSGRLYY
+DLLARREKSGDTSTAIVRVEQLYPLPLEEIRKALRAYPDADVAWVQDEPANQGPWPFMAL
+NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR*
+>NZ_CP040019.1_2131
+MLRKRRYTVPELTSDRLAQEFPGNERLVAEIYRKYRADSGSVDRQWAQIFARLEASAPAP
+AEKAPAQAAAKAAPKAEPQAEAKVTEPKAKPAPARGAQPKETSTSTGPKVKKTPAAQAVP
+SEPADPSKDAAKEEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDVPAKVLIDNRVVI
+NSHLARTRGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLP
+RPDGSRSLVVPNVKAAETLDFRGFWQAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGT
+VHSVPRLSKGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSG
+EFLKIVHGLLLGEDGFYDEVFHSLRIPYEPVRWAQDLQVNPEEQVGKVARVQQLIHAYRD
+RGHLMANVDPLEYSMPYHPDLDIREHGLTLWDLDRQWPTGGFGGASTLTLRKILGVLRDA
+YCRTIGVEYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIG
+QKRFSLEGGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYGQVFREFE
+GATPGGTSGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRL
+DLGGQRPDSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVIVNNQVGFTTP
+PTQARSAVYSTDVAKTIQAPILHVNGDEPESVMHVAELAFEYRQRFNKDVVIDLVCYRRR
+GHNEGDDPSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFA
+ETHEGSASSGGEGIRPAEDRDQAPEAPETTAISAETLRAIGQAHIDVPEGFTVHPKLAAL
+LERRAKMAVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITGDE
+WAPLKNLSEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFINGAQTIID
+EFISSAEQKWAQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPTTGANHF
+HLLREQAYARPRRPLVVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDPKKVTRVQL
+VSGRLYYDLLARRNKDGDETTAIVRVEQLYPLPLDELRAALEAYPQAEVVWVQDEPANQG
+PWPFMALNLLPQLDREVRLVSRPASASTSAGTKGRHDQELSTLLDAGFAR*
+>NZ_CP083691.1_2022
+MPELTSDRLSQEFPGNEDLVAQIYRKYREDQGAVDRQWAQIFARLEASQPQPEPAAAAPK
+ATSSATAEPAPAVKPAVKRGAATPADPQAAAKKSGPTDVSAPAQRKRSVSEAVPSEPARD
+AAAGASEKQDKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKLLIDNRTVINSHLART
+RGGKVSFTHLIGYAVVRALKAMPSMNTLYEERDGKPTMVEPAHVNFGLAIDLPKPDGTRA
+LVVPNIKAAETLSFRQFWEAYDDLVKRGRANKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SKGQAAIIGVGALTYPAAFQGAAESTLNSLAISKTITLTSTYDHRVIQGAGSGEFLKLIH
+GYLLGEDGFYDDVFHDLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYRMPTHPDLDIREHGLTLWDLDREWPTGGFGGADTLTLRRILGVLRDAYCRTVGV
+EYMHIQNPAERAWFQDKLERPYEKPSREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDSILGDAADEGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVARAKQDRLEAAGESG
+AAFPVLPILVHGDAAFAGQGVVTEVLNLSQLPGYRTGGTIHVVVNNQVGFTTSPAEGRSS
+VYATDVAKTIQAPILHVNGDEPESVLRVARLAYEYRQRFHKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYTLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFAETHAAET
+GQAVATTGLEPARDRDAARPAPSTTAISPDTLRRIGDVHLEVPEDFTVHPKLSQLLEKRA
+KMAVDGGIDWGFAELAAFGSLLMEGVPVRLSGQDSQRGTFTQRHSVFHDRVTDETWTPLN
+HLSESEAPFWVYNSLLSEYAVLGFEYGYSVERSDALVLWEAQFGDFINGAQTMIDEFISS
+AEQKWSQNSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSHGANHFHLLRE
+QAYSRPRRPLVVFTPKQLLRLKAAADPVEAFTQGGFRKVIGDASVDAAQVERVILVSGRL
+YYDLLARREKSGDTSTAIVRVEQLYPLPAEEIRAELAKYPGAQVRWVQDEPANQGPWPFM
+ALNLLPQLDREVTLVSRPALAATSAGTKGRHDEELSTLLDTAFGA*
+>NZ_CP097650.1_695
+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_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000676.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000676.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5558e6c51a59fb20f27d3b134c26c2902a37970
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000676.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_734
+MEWLLLILGLALIVGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE
+LIPKNMSIAEPMAIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVREDQALPEVLD
+LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF
+PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR
+RIERVRFDPAAEDEETRA*
+>NZ_CP033200.1_473
+MEWLLLILGLALIVGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE
+LIPKNMSIAEPMAIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVREDQALPEVLD
+LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF
+PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR
+RIERVRFDPAAEDEETRA*
+>NZ_CP040019.1_2129
+MEWLLLILGFALVLGTGFFVAVEFSMIAIDVPTVQRMVDEGDKGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPVLLDVGVPESVVGTVSLVVAMVVATLLSMLIGE
+LIPKNMAIAEPMTIGRALARPQLLFSTVFKPAILVLNGFSNGVLARFGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDEQTATFLDRTLRFADRTAADVMTPRIRVETVGEDQPLPEVVD
+LARRTGFSRFPVIGESSDDIRGVVHVKKVVAVPRERRADLEAGSLMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDKVTPGVLQTAAGRWYF
+PAELRPDEAQAQITSLSVPEDGAYETIGGFIMARLGRLAAVGDVVSVDGGTLSVERMDGR
+RVERVRFDPAAAADKEARA*
+>NZ_CP083691.1_2020
+MEWILLILGLLLVLGTGFFVMVEFSLIAIDAPTVQRMVDDGDRSWEPLLTCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLVDPLILAVGLPQSVAGPVSLVVAMAAATLLSMLLGE
+LVPKNMAIAEPLRLGRALARPQLVFAAVFKPAILVLNGFSNGVLHRMGLEAKEEISGARS
+PEELSSLVRRSAQLGTLDEQTATFLDRTLRFAERTAADVMTPRIRMETVGEDDGLLDVVE
+LARRSGYSRFPVIGESPDDVLGVVHVKKAVAVPMDRRADLTAGALMTDVIRVPETVHLDQ
+LLAELREASLQLAIVVDEYGGTAGVVTLEDVVEEIVGEVSDEHDRVTPGVLQTASGRWYL
+PAELRPDEAHAQIKALDVPEDGAYETIGGFVMARLGRIPAVGDVVPLDVGTLTVERMDGR
+RVDRVRFDPRPVTEEARA*
+>NZ_CP097650.1_697
+MEWLLLILGLLLIAGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE
+LIPKNMSIAEPMTIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVGEDQALPEVLD
+LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF
+PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR
+RIERVRFDPAAEDEETRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000678.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000678.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33a2fbde7fa6e79a272b6cc9985d96eef6482687
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000678.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_736
+MLRRRRLPALTGALAALTLSLAACGGTSGDSAGAQAAGASADSGSGSAAGAPVAVATTTQ
+LGSVLDRVVACADARSATVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDERFAECGATVRGELEQTDAQVREILAGVPEDRRTLVTDHDAYGYFSDAYD
+FTVSGVVVPGGSTDGEPSSQEIAELARSIRDGGADAVITSVGARNSLVDTVAEEAGNLPV
+IEVYESGVGPKDTPEADYAEAMLANARTLADALEG*
+>NZ_CP033200.1_475
+MLRRRRLPALTGALTALTLSLAACGGTSGDSAGEQAAGASAAAGSGSAAGAPVAVATTTQ
+LGSVLDRVVACADARSVTVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDERFAECGATVRGELEQTDTQVREILAGVPEDRRTLVTDHDAYGYFSEAYD
+FTVSGVVVPGGSTDGEPSSQEIAELARSIRDGGADAVITSVGARNSLVDTVAEEAGDLPV
+IEVYEGGVGPKDTPEADYAEAMLLNARTLADALEG*
+>NZ_CP040019.1_2127
+MHRTPRRRAAAALTLASALALAGCGADSGGDGQAGSGEPAAVATTTQLGSVLGDVARCAG
+ATTATVMGPGDDPHDFAPSSQQVAQMARAGLVFANGFGLEAGMASALENAAQDGAQVLEV
+APRLDPLPFGAGEGAADGHAGETADEHAAHAEEGSAGAHDGHDHGSQDPHVWMDVARMAR
+AAEVMGDALAEHTGEDRFADCGRQVRGELEATDAEVREILAAVPEDRRRLIADHDAYGYF
+AAAYGFEVAGVVVPGGSTDGEPSSQRIAELTQAVAEAGADALVTSAGGGAPTVETIAADG
+GGSTPVVELYEGGVGPADGEPAGYAEAMLHNARVLADALGE*
+>NZ_CP083691.1_2018
+MSRSSPTPRLAAPAVVAALGVALAGCSVADSSSPSAAEEGAVTASSSAAGPVVAVATTTQ
+LASVADRVARCGGGSVVSVMGPGDDPHDVAASSDQVAQMVHSGLVFTNGLGLEGGMDSAL
+DNARQDGAVVVEVAPRLDPLPFGEHDADHAGHEGADAHAGHEHGSQDPHVWMDVARMAAA
+ARVVGDELAAETGEQKYAECGATVEGELEETDRQVREILAAVPQERRTLVTDHDAYGYFS
+AAYGFTIEGVVVPGGSTDAEPSSRELAALTQQVKDHGAAALLTSTGTPNGLVETVAREAG
+GLPVVQLYEGGVGPVGTPEADYAQAMLHNARTLADALKG*
+>NZ_CP097650.1_699
+MLRRRRLPALTGALTALTLSLAACGGTSGDSSGAQAAGASADAGSGSAVGEPVAVATTTQ
+LGSVLDRVVACAGARSATVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDEQFAECGATVRGELEQTDTQVREILAGVPEDRRTLVTDHDAYGYFSEAYD
+FTVSGVVVPGGSTDGEPSSQELAELARSIRDGGADAVITSVGARNSLVDTVAEEAGDLPV
+IEVYEGGVGPKDTPEADYAEAMLVNARTLADALEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000682.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000682.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73119c22d519f17bb51d00905c155a6c1e68ff4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000682.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_741
+MATVFSRIIAGELPARFVWQDQTCVAFLSAAPLQPGHALVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD*
+>NZ_CP033200.1_480
+MATVFSRIIAGELPARFVWQDQTCVAFLSAAPLQPGHALVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD*
+>NZ_CP040019.1_2121
+MASVFSRIIAGELPARFVWQDETCVAFLSTGPLNPGHALVVPREEVDAWVDADPALVMHL
+MTVAQQLGKAQVRAFSAQRAGLMVAGYEILHLHVHVWPSNSLADFDLNRVDNSPDPAEMD
+DAAARLRAALRELGHGEVVPQD*
+>NZ_CP083691.1_2013
+MATVFSRIIAGELPARFVWQDEQCVAFLSLGPLAQGHTLVVPREEVDQWVDADPDLLAHL
+TRVAQAIGRVQVRAFGAQRAGLMVAGYEIPHLHVHVWPSNSMNDYDMARVDNAPEPESLD
+EAAAAIRAGLREDGHGDVVPQD*
+>NZ_CP097650.1_704
+MATVFSRIVAGELPARFVWQDQTCVAFLSAAPLQPGHTLVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000683.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000683.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df9b10994864377b676da53455e270439b58723f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000683.fa
@@ -0,0 +1,121 @@
+>NZ_CP042169.1_742
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT
+TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKA
+TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII
+TSATIDPERFARHFGRPLAEGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELASEPPGDILVFLPGEREIREAADHLTGVV
+AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT
+GTARISRYSHRTKVQRLPIERVSQASANQRSGRSGRTSDGIAIRLYSEEDYLSRPEFTDP
+EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA
+GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE
+LHRRFADENSDFSAILNLWAYLRERQQELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ
+LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLAQIGAYDERRREYAGARGTRFAVFPGSA
+LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRAYNEPHWSRRAGSVVAR
+EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL
+ETRLRRRDLRIGDEDLFAFYDARIPANVVSERHFDAWWKKARQEQPDLLDLDVAALLTAD
+AEDLDTDAFPTTFSYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW
+LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPEALSAAVRR
+VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA
+GTDDPASARPGPRGTGRGGRAQADARAGAEGRRRPEGPGRSGATPAFEERHRLTSWSIGT
+VPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLAT
+LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD
+RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGSVSLALAPALSDVKAHLEQLVFPGFVA
+ATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG
+TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA*
+>NZ_CP033200.1_481
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT
+TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKA
+TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII
+TSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPVPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVV
+AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT
+GTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDGIAIRLYSEEDYLSRPEFTDP
+EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA
+GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE
+LHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ
+LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLSQIGAYDERRREYAGARGTRFAVFPGSA
+LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRAYNEPHWSRRAGSVVAR
+EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL
+ETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTAD
+AEDLDTDAFPTTFAYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW
+LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPDALSAAVRR
+VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA
+GTDDPASARPGPRGTGRGGRAPADARAGAEGHRRPEGPGRSGATPVFEERHGLTSWSIGT
+VPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLAT
+LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD
+RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKDSVSLALAPALSDVKAHLEQLVFPGFVA
+ATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG
+TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA*
+>NZ_CP040019.1_2120
+MTETPTPPAAASSAPAIVFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKTTQLPKMC
+LALGLGEAGVIGHTQPRRIAARSVAERIAEELGEDIGRTVGYQVRFTAQTSKATRVKVMT
+DGILLAEIPHDPQLRRYSVVIVDEAHERSLNIDFLLGYLRTLLPQRPDLKVIITSATIDP
+ERFARHFGRALAEGEEHEDAVPADDGGLVVPAPVIEVSGRTYPVEVRYRPLTGEPSPDDP
+EDDSDDAAETRDPLDAIGEAVLELAAEPPGDILVFLPGEREIRDAADHLSGVVASSKRLA
+GTEVLPLFGRLSMAEQHRVFGRAAAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISR
+YSHRTKVQRLPIERVSQASANQRAGRSGRTSPGIAIRLYSEEDYLSRPEFTDPEILRTSL
+ASVILQMLSLGVAATPADVQGFPFVQPPDGRQVSDGATTLTELGALHPPRPSGAKDGHDG
+GRGRGGRAPEPGTITPIGRRLARLPVDPRLGRMILESGERGCVREVMVLAAALTIQDPRE
+RPVEQREAADELHRRFADENSDFSAILNLWAYLQEQQKELSGSQFRKLCRREHINWLRVH
+EWQDLVRQLRQLAKDVGVAVHAGPVDPVGQHEAVHRSLLTGLLSQIGSYDERRREYAGAR
+GTRFAVFPGSALFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEAAGGLVKRTYNEPH
+WSRRAGAVVAREKVTLFGVTLIPDRSVKYGRIDPELSRELFIRHALVEGDWRTRHRFFAR
+NRAALEEVDALETRLRRRDLRIGDEDLFAFYDARVPANVVSERHFDAWWKKARQERPDLL
+DLDVAALLTADAEDLDTDAFPTVFPYPLSGGDVDLDLEYTFDPTGASGTDGVTVSVPVLL
+LNQVSPGPFAWLVPGLRVELVTALIKALPKAVRKQLVPAPDVARQLVADLDAHADPLADE
+LTEALSAAVRRVRGIVVEPGLWAPDAVPAHLRMDYRVVDARGAVMGAGQDLAALQARLAK
+ANRSAIAARLAGTDDPANARPGPGRQGGRRDGGGNDGGAGRRGSGRGVRGRGRDGTGRPE
+AGAQGAGGAAAAFAERHGLTSWSIGTVPRRITTDPGARGPAITGYPALVPETTAEGGPAA
+GLTVARSAEDQAAWHRAGVIRLLLATLPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVAD
+CSQAAVDRLVGDELPFDEAAFRALFDRVRADLIDTVFAVTRLVEQVLSRAAEVRRRLKGS
+VSLAMAPALSDVKAHLEQLVFPGFVAATGWERLQHLPRYLQGILVRLDRLDAGGHLQRDG
+QHMAVVQRLEDEFDAAVQAHRARFSGVPVPADLERVRWLIEELRVSFFAQELGTAVSVSE
+KRVRQALAQAARA*
+>NZ_CP083691.1_2012
+MTDFPQPPAAAPVITFPAHLPVAERREEIMDAVRENQVVIVAGETGSGKTTQLPKMLLAL
+GLGGAGVVGHTQPRRIAARSVAERIAEELGEDVGRTVGYQVRFTAQTSTRTRVKVMTDGI
+LLAEIPHDPDLRKYSAIIVDEAHERSLNIDFLLGYLKRLLPRRPDLKVIITSATIDPERF
+ARHFGTEDEPAPIIEVSGRTYPVEIRYRPLTEEPSPDDPDDDADDHAETRDPIDAVGDAV
+LELAGEAPGDILVFFPGEREIREAADHLAGVVASTPRLAGTEVLPLYGRLSMAEQHRVFG
+RAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERISQASAN
+QRSGRSGRTSDGIAIRLYSEEDFLSRPEFTDPEILRTSLASVILQMLSLGVADTPREVMD
+FPFVQPPDSRQVTDGAATLTELGALHADAPTRGGGRGRGKGAGNRSAAGTITDIGRRLAR
+LPVDPRLGRMILESGRRDCTREVMVLAAALTIQDPRERPVEQRQAADELHARFADDRSDF
+SAYLNLWEYLREQQRELSGSQFRKLCRREHINWLRVHEWQDLVRQLRQLSKDVGVSVHPG
+PVDPVGKHDDVHKSLLTGLLSQIGAYDERRREYQGARNTRFAVFPGSALFKKRHPFVMAA
+ELVETSRLWARAVARIEPEWIEEVAGDLVLRSYAEPHWSRKAGAAVAMEKVTLFGVTIVP
+ERSVRYGRIDPVLSRELFLRHALVEGDWRTRHRFFARNRRLLEEVDELETRLRRRDLRVG
+DEELFAFYDARVPANVVSERHFDAWWKKARQETPDLLDLDLDALLTQDADELDTDAFPTA
+FRYPLPGGDADLALDYTYDPTGASGTDGVTVAVPILLLNEVAPGPFAWLVPGLRGELVTA
+LIKALPKAVRKNLVPAPDVARLLVEDLDAHADPLRDELPAALSSAVRRVRGAVVEPELWR
+LDAVPDHLRMDYRVVDARGAVMGAGQDLPALQARLAKANRSAIAARLAGTDDPRNARPGQ
+GAGRGRGKTEPKGGDGGARGPAADTGRPGPSRTADGAPAFRERHGLTSWTVGEVPRQITT
+APGDRGPAITGYPSLIPETTADGSPAAGLVVARSAQDQAAWHRAGVIALLLATLPSTHRY
+VLDHLDNKEKLTFTQNPHGSVESLVRDATHVAVDRLVGTDLPFTEVGFRALFDRVRADLI
+DTVFAVTALVEQVLSRAAEVRRRLKGGVSLAMAPAKSDVQAHLEQLVFPGFLAATGWQQL
+QHLPRYVQGMLARLDKLDAGGHLQRDGQHMAVVQGLEDEFDAAVTAHRSRFPGTPVPAEL
+ERVRWLLEELRVSYFAQELGTAVSVSEKRVRQALAQARQG*
+>NZ_CP097650.1_705
+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_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000684.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000684.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e86480d8084ce6f1d85a40b2fdb86a56081b0dab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000684.fa
@@ -0,0 +1,53 @@
+>NZ_CP042169.1_743
+MDTNTVFLLAAIGLYFLAMIAIGLYASRKNTDLDDYMLAGRDMKPSVAALSAGASDMSGW
+LLMGLPGAIYAAGLVEGWMAVGLTVGAWVNWRVVAPRLRSYTEVAGNSITIPSFLENRFK
+DRTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPESFYAQGISINYLTGMLVVAG
+ITVLYTLFGGFLGASLTDVAQGVLMFLSLLAVPIVVILTMGGWDAVVEGIRAADAAGGGV
+NHFSMFENATLIGVLSSLAWGLGYFGQPHIIVRFMALRTPHDAAVARRVGIGWMALSVFG
+AVMVALVGIAYFQANPGTTLEDPETVFLVLASIMFHPFVAGLVLAAVLAAIMSTLSSQLI
+VCSSALVEDLYMLRGRTGSPTFTLWLGRIGVLVVALVAGLLALDPDSSVLELVSFAWAGF
+GAAFGPVILLALYWPRFTSWGAMAAMVTGAAVAWVWSEASAETWEWFGLYELLPGFVAAF
+VVGVVVSLVTQRSRRVQRRIDAEFTGAIDIVAGREPDPDVAPAAMTRDAAGGSTAAAADP
+RAQA*
+>NZ_CP033200.1_482
+MDTNTVFLLAAIGLYFLAMIAIGLYASRKNTDLDDYMLAGRDMKPSVAALSAGASDMSGW
+LLMGLPGAIYAAGLVEGWMAVGLTVGAWVNWRVVAPRLRSYTEVAGNSITIPSFLENRFK
+DRTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPDSFYAQGISINYLTGMLVVAG
+ITVLYTLFGGFLGASLTDVAQGILMFLSLLAVPIVVILTMGGWDAVVEGIRAADAAGGGV
+NHFSMFENATLIGVLSSLAWGLGYFGQPHIIVRFMALRTPHDAAVARRVGIGWMALSVFG
+AVMVALVGIAYFQANPGTTLEDPETVFLVLASIMFHPFVAGLVLAAVLAAIMSTLSSQLI
+VCSSALVEDLYMLRGRTGSSTFTLWLGRIGVLVVALVAGLLALNPDSSVLELVSFAWAGF
+GAAFGPVILLALYWPRFTSWGAMAAMVTGAAVAWAWSEASAETWEWFGLYELLPGFVAAL
+VVGVVVSLVTQRSRRVQRRIDAEFTGAIDIVAGREPHPDVAPAAMTRDAAGGSTAAAADP
+RAQA*
+>NZ_CP040019.1_2119
+MDQNTFFLILAIGLYFAAMIAIGLWASRKNTDLDDYMLAGRDMKPGVAALSAGASDMSGW
+LLMGLPGAVYAAGLVEAWMAIGLTVGAWINWKVVAPRLRAYTQVAGNSITIPSFLENRFQ
+DRTHILRIVSGLIILVFFTFYVSSGMVAGGKFVESTFGPESLYAQGVSVNYLTGMLVVAG
+ITVLYTLFGGFLGASLTDVAQGTIMFLALIAVPIATIVAMGGWGAMVEGLRAADAASAAA
+GEAVDHLSLFHNATLIGVLSSLAWGLGYFGQPHIIVRFMALRTVQDASTARRIGIGWMAL
+SVFGAVMVALVGIAYFQANPGTTLADPETVFLVLASILFHPFIAGLVLAAVLAAIMSTLS
+SQLIVCSSALVEDLYKLTGRQGSPRAMVWLGRIGVLVVAVVAGLLALDPESSVLELVSFA
+WAGFGAAFGPVILLALYWQRFTSWGAMAAVVTGALVAWLWSEASAETWEWFGLYELLPGF
+IAALVVGVVVSLLTQRSRPVQTRIEREFTGAVDVVAGRAAPTA*
+>NZ_CP083691.1_2011
+MDSNTAFLLAAIGLYFVAMIAIGLYAARRNNDLDDYMLAGRDMKPGVAALSAGASDMSGW
+LLMGLPGAVYASGLIEGWMAIGLIVGAWVNWKVVAPRLRSYTEVAGDSITIPTFLENRFK
+DHTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPDSIYAQGVSVNYLTGMVVVAG
+ITVLYTLFGGFLGASLTDVAQGVLMFLALLVVPVAVIATMGGWDQVLEGIRAADAAVGPE
+ADRFSLFQNATRIGVLSSLAWGLGYFGQPHIIVRFMALRTPQDAAAARRIGIGWMVLSVF
+GAVMVGLVGLAYFQANPGTELNDPETVFLVLASILFHPFVAGLVLAAVLAAIMSTLSSQL
+IVCSSALVEDLYMLRGRRGSPRTMVWLGRIGVLVVALIAGLLALNPDASVLELVSFAWAG
+FGAAFGPVILLALYWERFTSWGAMAAMVVGAAVAWFWSTASADTWDWFGLYELLPGFVAA
+LAAGVVVSRLTRRPDHVQEHISGEFTGAADIVAGREPTALTGSTGAVGGSTAAPRA*
+>NZ_CP097650.1_706
+MDTNTVFLLAAIGLYFLAMIAIGLYASRKNTDLDDYMLAGRDMKPSVAALSAGASDMSGW
+LLMGLPGAIYAAGLVEGWMAVGLTVGAWVNWRVVAPRLRSYTEVAGNSITIPSFLENRFK
+DRTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPDSFYAQGISINYLTGMLVVAG
+ITVLYTLFGGFLGASLTDVAQGILMFLSLLAVPIVVILTMGGWDAVVEGIRAADAAGGGV
+NHFSMFENATLIGVLSSLAWGLGYFGQPHIIVRFMALRTPHDAAVARRVGIGWMALSVFG
+AVMVALVGIAYFQANPGTTLEDPETVFLVLASIMFHPFVAGLVLAAVLAAIMSTLSSQLI
+VCSSALVEDLYMLRGRTGSPTFTLWLGRIGVLVVALVAGLLALNPDSSVLELVSFAWAGF
+GAAFGPVILLALYWPRFTSWGAMAAMVTGAAVAWVWSEASAETWEWFGLYELLPGFVAAF
+VVGVVVSLVTQRSRRVQRRIDAEFTGAIDIVAGREPDPDVAPAAMTRDAAGGSTASAADP
+RAQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000691.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000691.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54c5af7e6d6570527cadab3cd4d6ada5ff9d7504
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000691.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_752
+MSTLTLTLNGEPAELAVATVRDVVAHVTGRAIGEDGAAADGRRLGVAVAVGGEVVPRSAW
+ATRELAAGDEVDVVTAVQGG*
+>NZ_CP033200.1_492
+MSTLTLTLNGEPAELAVATVRDVVAHVTGRAIGDDGAAADGRRLGVAVAVGGEVVPRSAW
+ATRALAAGDEVDVVTAVQGG*
+>NZ_CP040019.1_2111
+MSTLTLTLNGEPAELAAATVRDVVAHVTGRAIGDDGAAADARRLGVAVAVGGEVVPRSAW
+ATRELTAGDEVDVVTAVQGG*
+>NZ_CP083691.1_2002
+MSALPLTLNGEPAELDGPTVRDVVEHVTGRTVRDDGAAADGRRLGVAVAVDGEVVPRSAW
+AARTLAGGEAVEVVTAVQGG*
+>NZ_CP097650.1_718
+MSTLPLTLNGEPAELAVATVRDVVAHVTGRAIGDDGAAADGRRLGVAVAVGGEVVPRSAW
+ATRALAAGDEVDVVTAVQGG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000692.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000692.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff0a373193b67b85ebff8c29fdaff666871dd322
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000692.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_753
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER*
+>NZ_CP033200.1_493
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER*
+>NZ_CP040019.1_2110
+MAEHRTPPATPAIPPLRIGGYDLAARLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATELLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER*
+>NZ_CP083691.1_2001
+MAPHDTTERRRAREASTAVPPLRIGGYELSSRLIMGTGGITDLAALEGALVASETTLTTV
+ALRRWSTDARDGLIALLDRLGIDVLPNTAGCRTARDAVLTARLGREALETELVKVEVIAD
+DRTLLPDVVETLDATEQLAAAGFTVLAYTSDDPAMALRLEHAGAAAVMPLGSPIGSGLGI
+LNRTNLELIVSRAGVPVVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACR
+LALEAGYHAHRAGRIPRRLHALASSPMAGRIGGAEERA*
+>NZ_CP097650.1_719
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000694.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000694.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b023267b7a35d263fe7c94abd1ea14bbe4ef9d20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000694.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_755
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTDKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLREQGHVEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM*
+>NZ_CP033200.1_495
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTGKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLRAQGHIEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM*
+>NZ_CP040019.1_2108
+MKPEDLSALLSAVLTDAVDAGDLPAELREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTGKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPDYGRNA
+ALVGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPEGGYPGAYVQELADAVALEHPDVRELTDEAARPVVRQAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHESGAIEQAVERLREQGHIEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVDTLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM*
+>NZ_CP083691.1_1998
+MKPEELSALIHAQLLAAVDAGELPAELREQLSADRVKVERPRSREHGDWATNVALQFAKQ
+AGMNPREFASALASRVGEQPGVATVDVAGPGFLNITLDAAAAGELARQIVEAGEAYGRNE
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIVRLLRASGADVTAEYYINDAGNQMNV
+FADSVLARMAGRDVPEGGYPGAYVKDLADAVATDHPQVRELTDDAARPVVRQAAYELQMQ
+DIKDTLAAFDVHFDVFTSETRLHESGAIQAAVDRLREQGHVEDREGAVWLRTTDFGDDKD
+RVMIRANGEPTYFAADAAYYLDKRDRGFEEKVYLLGADHHGYVGRLKAIAAAAGDDPEEN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVQWLGKDALRYDLARYPADSPITIDPELLRS
+QTNDNPVYYVQYAHARACGAARTAAAHGVDRCAFDASLLTDPTESELLAQLAEFPAVVAS
+AARLREPHRVARHLEVIAGAYHSWYAAQRIVPVPLEDGTPAPVEDVNRTRLWLNDAAAQV
+LRNGLGLLGVSAPETM*
+>NZ_CP097650.1_721
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTDKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKNTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLRAQGHVEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVGA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVTAPEKM*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000697.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000697.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c73aa1db4d99cf4e6682b1f86c1b5286a7af223
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000697.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_758
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS*
+>NZ_CP033200.1_498
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS*
+>NZ_CP040019.1_2105
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVDQGAKAVVCASTGNTSASAAAYAAQAGLTCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDALGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDEELPAVSTKTPVMWGFQAAGAAPI
+VLGHPVTEPDTIATAIRIGNPASWEQAEAARDGSGGMIDSVTDEEILAAHRWLSAKEGVF
+VEPASAAGVAGLIKHHAAGNVPAGKSWVITVTGHGLKDPQWALRDADGEDVTPRTVPFDV
+VTVAQALGLA*
+>NZ_CP083691.1_1995
+MAHVWRGVIREYAGRLPVTEDTRVVSLGEGGTPLIRAPHLSELVEGEVYVKFEGMNPTGS
+FKDRGMTMAITAAVENGAKAVVCASTGNTSASAAAFAAQAGLTCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDNCLDIARKLSENYPVFLVNSVNPARIEGQKTAAFEVVDLLGDAP
+DYHLLPVGNAGNITAYWKGYQEYSRPYVNPHPGTSDEELPAVATKTPVMWGFQAAGAAPL
+VLGHPVTEPETIATAIRIGNPASWDQATAARDASGGMIDSVTDEEILAAHRWLSSKEGVF
+VEPASAAGVAGLIKHHAAGNVPAGKTWVITVTGHGLKDPQWALKGADGDDVTPRSVPFDV
+VTVAEALGLT*
+>NZ_CP097650.1_724
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000698.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d637b18997877396b7a842f8f18545ad90e8bfa5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000698.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_759
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA
+TLPRDGAHLILRLAREQLRGRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATVRLRLHERVVPVV
+AIPDTELSTHVARGVLPADVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA
+VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL
+VPCVAVDGVRVESLHHG*
+>NZ_CP033200.1_499
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA
+TLPRDGAHLILRLAREHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV
+AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLLAATRDWLHQEPRA
+VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL
+VPCVAVDGVRVESLHHG*
+>NZ_CP040019.1_2104
+MPAPRTLAAGTAVVVAVPATSANLGPGFDSMGLALELRDEVSLTVVDGPDVAEVTGEGAD
+VLPRDGSHLILRLAHEHLRARGVRAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAADRRPPEALLEAATDFEGHPDNVAPALVGGATVSWTRDDDARPATAPLRLHERIVPVV
+AIPDTELSTHAARGVLPESVPHAVAAAQAGRAALLVHALAERPELLMAGTRDWLHQGPRA
+AAMPASAALVAGLRVRGHAAVVSGAGPTVLALCDGAEAAEQAAAAARALTADDVLAWRVL
+VPAVAADGVRVEPLHHG*
+>NZ_CP083691.1_1994
+MRELRDLTPGTGARVLAPATSANLGPGFDALGLALELRDEVTLTVVDGPDTAVVTGEGAA
+ELPTDGEHLVLRLAHAHLTRRRFRAPGLALTAVNRIPHARGLGSSAAAVVTAVLAAEALL
+PADERLSAAELLDVTARREGHPDNVAPALSGGASVSWHRDGGPGWATAAVALHPQITPVI
+GIPDVTLSTHAARAALPESVPHAVAAEQAGRAALLTLALASRPDLLLPATRDWLHQDARA
+SAMPPSAALVRGLREQGHAAVVSGAGPTVLVLAPTPADAERAAEAMRALAPETGAAWRVL
+VPGVAAEGARVEPLHHG*
+>NZ_CP097650.1_725
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVVGEGEA
+TLPRDGAHLILRLAHEHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV
+AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA
+VTMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAAAWRVL
+VPCVAVDGVRVESLHHG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000702.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000702.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cfab9b429074ef25827c1c2d58fc37efcc032b13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000702.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_764
+MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE
+RRRADRNDAAAHPDERGDA*
+>NZ_CP033200.1_504
+MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE
+RRRADRNDAAAHPDERGDA*
+>NZ_CP040019.1_2100
+MRAYLVLVVVTALACGALTPLMRRIGLRARVFTPVRQRDMHRRPIPKLGGVAMAAAVLVG
+LAVGGTVPFLQGIYADDAAMVGLLVAVAVVFVVGIADDLWDLRWWVKMAGQVCAGLAVAL
+GGIRIEAMPVGWIPVGSEAMQIALTVFAVVLTMNALNFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACLGFLPFNRFPARIFMGEVGAMLLGLLMAAAAV
+AVTADVKALDGMRFRNVPAYMPILLPIAVLALPLLDLALAVVRRTARGASPFSADRGHLH
+HKLVDGGYTHAQAVWLLWLWAFLVAWGAVSLNFVDDMIVLPVLGLALLGAGYLTLRTPVR
+RRRAGAPAAGPALDPEEGA*
+>NZ_CP083691.1_1989
+MRAYLLVAAVTALTCLALTPWVRRVGVRARAYTPHRDRDVHRAPVPKLGGVAMVAAVLAG
+LAVAGTVPFLGGIFTDASAMRGLLAALGIILVLGVVDDLVDLRWWAKLGGQSLAALAVAL
+GGIRIAALPVGWIHVGSEAVQVALTVFVVVLTMNAINFIDGLDGLAAGVALIGGSAFFVY
+SYLLTRTIDQFDYSNLATLLMALLIGACAGFLPYNRHPARIFMGESGALLLGLLLSTAAV
+AVTADLDALEGFRFRNVPAYMPVLLPIAVLALPLADLTISVIRRAAHGESPFGADRGHLH
+HRLVDGGFTHAQAVRVLWLWSFIVAWGVLSLNFADDAVVLLLAAAGLAVATWLTVHPLRA
+RAARPASRPDAQPKDQP*
+>NZ_CP097650.1_730
+MRAYLVLVVVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVALLWLWAFLVAWGAVSLNFVDPMIVLPVLAVALAGAGYLTLHPIVE
+RRRAVRNDAAAHPDERGDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000707.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000707.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2ddef895caadc94e85666322f85696f07e58a64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000707.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_769
+MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAVHAAAAEAARGGHAGLAAL
+LGELLAFNRTVEDSHELQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG
+LKPSAAIRKAADAVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH
+VVGGVRVQVGDDVVDGSMASRLHDLQRRMAG*
+>NZ_CP033200.1_509
+MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAVHAAAAEAARGGHAGLAAL
+LGELLAFNRTVEDSHELQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG
+LKPSAAIRKAADVVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH
+VVGGVRVQVGDDVVDGSMASRLHDLQRRMAG*
+>NZ_CP040019.1_2095
+MMTGASRDSLTASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVIKDLAGRRWSAERDLGDALETVAAHAAAAEAGRGGHAGLAAL
+SGELLAFNRTVEDSHEVQRALTDQHAPVEARAALARRLLGESASPAGQLLVERAVAAPRG
+VKPAAAVRQAADVVAERQRQWIAEVTVARPLGAEQQERLALGLRRAFERDLVMDVTVDPH
+VVGGIRVQVGDDVVDGSMASRLNDLQRRMAG*
+>NZ_CP083691.1_1984
+MMTGASGDSLTASLESVRTVLDEGGVALARELFAALDVVDQQGALRRALTDPAWSTERRH
+GVLDSLFGGRVSPGALQVLKDLAGRRWSAERDFGDALEAVAADAAAGEAARGGHAGLAAL
+SGELLGFQRVFQDSHEVERALTDQRAPRESRSGLARRLLGAQASPAAVLLVERAVTDGRG
+VKPATALRSYADVVATRQRQWIAEVTVARPLEDGQRERLAAGLRRAFGRDLVLDVNVDPT
+VVGGIRVQVGDDVIDGSMASRLNDLQRRMAA*
+>NZ_CP097650.1_735
+MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAAHAAAAEAARGGHAGLAAL
+SGELLAFNRTVEDSHEVQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG
+LKPSAAVRKAADVVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH
+VVGGIRVQVGDDVVDGSMASRLHDLQRRMAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000712.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000712.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b16084c4a9eaf184c75d79c08ee4d6d7367a7644
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000712.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_774
+MQGPVLIASATVAAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL
+RLTGRWRLSRERWSADRSRLQIDRLPADEAGRTVLELSAGARPVRVVVDPDDAGALRAWS
+EAGPSAASSFWRR*
+>NZ_CP033200.1_514
+MLIASATVVAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRLRLTG
+GWRLSRERWSADRSRLQIDRLPADEAGRAVLELSAGARPVRVVVDPDDAGALRAWSEAGP
+SAASSFWRR*
+>NZ_CP040019.1_2090
+MLIALAGVLAVFALSASALAVRRRALLRTSAAFPAVLQGHGRPRERVIGVYDETRLLFTG
+RWMIRRERWSVGRCDLQIDRLPVAEDGRAVLELDGGRGSVTVVVDPDDAGALRAWSEAGP
+SAASSFWRR*
+>NZ_CP083691.1_1979
+MRGPVLLLSGALAVFALLALAGWARHRALVRGPGRFAGVLVTDGGRRCRVVGCFRSHELV
+LSHHLLPERRLWSAERWRLEVDRLPAAEAGHTRLRITDASGRSDDAVDLEVEDDVAGAVR
+AWTEAGPSQAGQSWWRPPGAA*
+>NZ_CP097650.1_740
+MEGPVLIASATVVAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL
+RLTGGWRLSRERWSADRSRLQIDRLPADEAGRAVLELSAGTRPVRVVVDPDDAGALRAWS
+EAGPSAASSFWRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000721.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000721.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0cbb7e39504398fca055338bfc2535ecfa50ec4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000721.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_784
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYAAVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVEAGAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS*
+>NZ_CP033200.1_525
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYASVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESGAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS*
+>NZ_CP040019.1_2079
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYAAVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDIEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESDAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAASQAALHEMEAAGADLELSEGR*
+>NZ_CP083691.1_1966
+MSEQNRALVIVDVQNDFCEGGALAVAGGADVAAAIADHVNEAREDYAAVVTTRDWHVDPV
+GHFAAASLEDRDAEPDYVRTWPVHCVAGTPGAELHPGLSAEDLEIDAEFLKGQHSDGYSG
+FDGHAGDPDAVRSGDEARAAAGPYGATQGAAHAADGGLGLDEWLREQDVDALTVVGLATD
+HCVRATVLDGLEAGYEVTVRTDLVAGVDDAAGEAALHEMEAAGALLRAGD*
+>NZ_CP097650.1_752
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYASVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESGAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000724.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6511719dc56af6cec4c97cdf303f8f4c3142989c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000724.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_787
+MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD
+TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL
+PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAPAFGRALNDV
+RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG
+ADESAPGAGDAEDEQ*
+>NZ_CP033200.1_528
+MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD
+TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL
+PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHNQAPAFGRALNDV
+RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG
+SDESAPGAGDAEGEQ*
+>NZ_CP040019.1_2076
+MAERFRWTRRGYTAQLEKPEVRLLRGLVKDVITLLEGRRRNVLSEADDLPADAPGAPEPS
+ADVAPVPQGPEAGAGPAAGLDEADAAFWELVSGLHLSQDRVPHRAAPADPAVARLLPEAM
+PQADAQERGAHRALTEDALSEGKLADARLALELLRSTRVEVPHHQAPAFGRALNDVRLVL
+AARLGVETEEDAERVHAVDDWRSAEDVESTMALLYNFTTWLLETLMTEMLSELPEGADED
+APGADEAGDDA*
+>NZ_CP083691.1_1963
+MAQRFRWTRRGYVAELEDAELRLLRGLVKDVVTLLENRQDEVAPPGSDAGTAEDAPEAGA
+EPVADARPGDAVGPGEETPHDAAFWALVGGLDLVADPVAERSAPEDPAVARLLPDAMPHA
+EPAERARQRALTEDALTAAKLADARRALEALRSVRVTVPHEHAVSFGRALNDVRLVLAAR
+LGIETEQDAARVHAVDDWRDAQDVEATMALLYNFTTWLQETLMAEMLSELPLEGAAGPDE
+EERA*
+>NZ_CP097650.1_755
+MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD
+TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL
+PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAPAFGRALNDV
+RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG
+SDESAPGAGDAEGEQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000728.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000728.fa
new file mode 100644
index 0000000000000000000000000000000000000000..591eb894c48b1cf427626f466c278195c12ac1a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000728.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_791
+MSAPASSSAGLPEGARVVLATHNAGKVRELRQLLAGAVPGLEVETAVVDAGAVGAPDVVE
+DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL
+LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG
+FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP*
+>NZ_CP033200.1_532
+MSAPASSSAGLPEGARVVLATHNAGKVRELRQLLAGAVPGLDVEAAVVDAGAVGAPDVVE
+DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL
+LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG
+FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP*
+>NZ_CP040019.1_2072
+MSGAATGVPEGARVVLATHNAGKVRELRQLLEGAVPGLDASVAVVDAGAVGAPDIVEDGV
+TFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLELLLA
+QLADVPDAHRGAEFVCAAALAVPSSADARGTHAIHVEHVEHGRLRGTLLRAPVGDGGFGY
+DPILRPDGRDESTAQLSAADKNAISHRGHAFRALLPYLVDALDARA*
+>NZ_CP083691.1_1959
+MSTPTAPVAPAGARVVLATHNAGKVRELRSLLAEALPALDVETAVVDAGAVGAPDVVEDG
+VTFEQNALKKARAVAAHTGLIAVADDSGLAVDVLGGAPGIFSARWAGRHGDDKANLELLL
+AQLGDVPDEHRGAAFVCAAALATPRGGDHVELGRMPGMLLREPVGDGGFGYDPILRPAGE
+DRSTAQLSSAEKNAISHRGQAFRALLPHLVAALSADS*
+>NZ_CP097650.1_759
+MSAPASSSAGLPEGARIVLATHNAGKVRELRQLLAGAVPGLDVEAAVVDAGAVGAPDVVE
+DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL
+LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG
+FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000732.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1991773cfe7c3943c74a194b0473ab6f8038a3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000732.fa
@@ -0,0 +1,91 @@
+>NZ_CP042169.1_795
+MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR
+SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS
+LRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLLPQGQFAQFLTAKSDERRALL
+RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP
+DTDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR
+DHDAEAETAAARRRAVDAHERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAA
+AWLAAARADGAADAPASRQALGEAERAAEAVARAVQDRARMGELEQEAAAAAERRAEIGR
+DRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEA
+ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT
+ADTAVTEADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERA
+EAERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR
+DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETDQALTAALAEQHF
+DDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQ
+TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL
+DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE
+LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA
+DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA*
+>NZ_CP033200.1_536
+MRIHRMRLEGLGPYAQAQDVDFDRLNAAGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR
+SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS
+LRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFIQVVLLPQGQFAQFLTAKSDERRVLL
+RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP
+DTDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR
+DHDAEAETAAARRRAVDAHERAGRVLAAAQRASAAADAAGTASEAVTEALAHVEDEPTAA
+AWLAAARADGAADAPASRQALGEAERAAEAVARAVRDRDRMRELEQEAAAAAERRAEIDR
+DRAALVESRPEREAAVAAHRAVVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEV
+ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT
+ADTAVTEADVRDAEQARTAADRAATDAETALRAAEQTLRSAGEAAAGLAPEAAREALERA
+ETERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR
+DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETGQALTATLAEQRF
+DDVDAARAARLEETEAADRTAAVQEWDAERARLAELEASEPVRRGRALAEAGVEPPTEEQ
+TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL
+DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE
+LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA
+DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA*
+>NZ_CP040019.1_2068
+MRIHRMRLQGIGPYAEAQDVDMDRLNDAGLFLLDGPTGAGKSTVLAALCYALYGSVPGGR
+SPESLVTTLRPPGAVVPEVLVEFTVQGRRFEVVRSPRHERLKKRRSASGKDTTPTPAAVS
+LREHVDGAWQEPLTRNDEVGVQVADVMHLDAAQFMQVVMLPQGRFAEFLTARSDERQRLL
+RRLFGTQRFDGVEEHLKAEAERLGSRAAADAKVAASAREQLREAVAAELGEDWHAPEPFP
+ATDEELVERTAERTREAVDAARAGRDAAAAEEAAARGTQAELRATGEALAAAAAWTERER
+AHREGAEAAAGDRTAVAAHERAGRVLGAADRSESARAAEDRAREADGTAQAAAAEDPLSA
+GWLEQARRDAAETPADDAAETSADAAALPRDAVALAERAVEEVVRAVRDRAAAERLEETE
+RTEAARRTQIVAEREAAEAERSGREEGLAAVREAVEAASARLGAQADVDRRVAEAEQGLA
+AAREAERHALAADAADRAREAARTGRDAAAQHRLGLLRSRYEQAAADLAADLEDGTPCAV
+CGSPEHPDPAPRVGTAVTEADVAAAEEGLAAAEAVLADAETARTAAHERVRASSAAAGGR
+TPAQAEEALAAARTEHAELAAVRKALAADRRRLRALETERDEAAAAETARTAEDARLQEA
+ARQRHERLLELRAGIERARGDAPDLDARGALVRAARGRLEALAGAVEVRERAVAVAADAD
+RALAAALREQEFEDVGAARAARLPAEDAAARTARVRAWDDEQARLAELAQSDAVRRGREL
+QDQQATAPTPEDLEAAAARLLEAERSRREQDEALGRRTAVAAAVERQAALLRGVLDRSAA
+LLAEHERVTGLLALVRGGGENRLKMPLASYVLAGRLEEVAAAATERLLAMTDGRYSIEYS
+DDSAGRGNKGLELVVRDHYVDETRHPSTLSGGETFMASLALALGLADTVQAEAGGVELDT
+LFVDEGFGSLDSDTLDDVLDVVDGLRSGGRTVGLVSHVERMKQEIPVRLAVTKEREGSSL
+AVHVDA*
+>NZ_CP083691.1_1955
+MRIHRMRLEGIGPYAEPQDLDLDPLNDAGLFLLDGPTGAGKSTVLAALCFALYGSVPGGR
+TPESLVTTLRPPGAVVPQVLVEFTVQGRRFEVLRSPRHARPKKRGGGTTATQASVSLRER
+VDGAWTAPLTRADEVGRQVAEVLRLDAAQFMQVVSLPQGRFAEFLTARSDDRQRLLRRLF
+GTQRFDGVEDRLKECAEALGTRVAADAAEAAGARAQLLEQARLELGEDWHAPDPAPEEGE
+DERLVELTRTRADAALAEARTAQQAADAAEAAARAAQDRLTADTEALRALAAWEGREREH
+RQAADHVAADRSAVALHERASHVLGAATRAEQTRAAHASTAERARAAAEAVAADALAAAW
+LDEAEDADAARRRADRETDALARAVRDRDALTRLEAEGTQADAERERLEDEARSAREKGK
+RRAAQIAELHDTVDAAAARLGAEDEVARRLAEATERAAAAGQAAERAVAQERARAARDER
+RDAQRGAAQARLDLLRSRFEQAAAELAAGLEDGSPCPVCGSAEHPDPAPRADGAVTEADV
+AAADRALEAADAALAEAEQALAAASEEHRAARERAGGQDVAAAEEALSAVRAEHEALAAA
+RTALATDRRALARRESEQRTADEAATARTAALARLSEAQARRTERAAELTAAVAAAQGDA
+ADLDARTAHVRTATRALSALVEAGDAAARAAAVAEDAAQALAGALAEQDFADVAAARAAA
+LPPDDAAARAARVRSWDVEEARLAEAAASEPLVRGRALREAGTSEPTAEEFAAAQETLRE
+ATAARTARAAVVGRREALVASLERQARRLRAVLERSSELLAEHERATGLLALVRGQGENR
+LKMPLASYVLAGRLEEVAAAATERLLAMTDRRYSIEYSDEATGRGNKGLELVIRDHYVDE
+TRHPSTLSGGETFMASLALALGLADTVQAEAGGVELDTLFVDEGFGSLDADTLDDVLDVV
+DGLRAGGRTVGLVSHVERMKQEIPVRLEVTKSRAGSTLAIHDGG*
+>NZ_CP097650.1_763
+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_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000733.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000733.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d3b54cf9d2f717fb84a4696b79361a818d5d32b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000733.fa
@@ -0,0 +1,98 @@
+>NZ_CP042169.1_796
+MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD
+ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR
+GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR
+DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV
+TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR
+TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI
+VPVLCWWFLRSPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA
+LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV
+QWTAGTAAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ
+GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA
+ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP
+VPLADLAEVSRVSVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA
+AVGGAAEQQAQTFRDLGLALLAAVATVYVVLVATFNSLRQPLVLLVSIPFAATGVFLALL
+ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMPLDEAIEVGALNRVRPVVM
+TALATVLAMTPMALGVTGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR
+LQEERRVAAAWEAQRVAAERAAKQERRAEQGSAAPSELDAGRLGRLRQRLRRRWRRA*
+>NZ_CP033200.1_537
+MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD
+ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR
+GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR
+DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV
+TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR
+TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI
+VPVLCWWFLRSPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA
+LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV
+QWTAGTAAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ
+GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA
+ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP
+VPLGDLAEVSRVPVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA
+AVGGAAEQQAQTFRDLGLALLAAVATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALL
+ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMTLDEAIEVGALNRVRPVVM
+TALATILAMTPMALGITGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR
+LQEERRVAAEREAQRVAAERAAEQARRAEERWAAPSELDAGRLGRLRQRLRRRWRRA*
+>NZ_CP040019.1_2067
+MGALARFSLRRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DSLVGEPLETALQAVEGLESSGSTSQASFNSIQLQFAYGTDLNRARSQVDRVVSNLASQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNELRRRAEAVLAPRLQKLEGVRGADVLGGTE
+EHVSVVPDPEALAAAGLSTQDITTALEENAGLFPVGQVTEGESTYPVQAGAAVEDLEGLR
+GIVVTPAEGGQGAAPQDRTADGGPVGGGGGPPADAEATPAAPAEPAGDGEPRTLGEVAEV
+SLQAAEPTSVTRTDGADTLSVSVTATPDADLVAVSEAVREALPELESVVGGGADLTVVFD
+QAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSLRSTLVTAVSIPLSLLAALIGVAVFGY
+SLNTLTLGALTISIGRVVDDAIVVVENIRRHLDLGADRRTAILIGTREVATAITASTLVS
+VAVFLPIAFVGGLAGELFRPFAVTATIALLASLVVALTIVPVLCWWFLRTPRRPAGDESP
+ADAAEGGAPAVPAGEHGHDAHPSAAGGWLARAYRPVLRWTQRHTVATLAGAVAVLAGTAA
+LVPLIPTNLIGDTGQNSFVVTADQEPGTSLEATAAAAGVIERTLLETEGVETVQWTAGTA
+GGPAGAFGGSSADRARFTVVTDENADQTALQDGVRADLAALEGVGEVSVSTQQGPGGGQD
+IEVSVSAPDPQALATAADEVAGALRGVEGAREVTTPAADVRPTFQVDVDTEAAARLGLTE
+EAVAGQAAAALQAVPVGDVRFGFEQFQVRLGDPDPVESLEALRQVAVQTGSGPVPLEELA
+SVERVDVPARVTSSNGERTAVVTVTPDDQDLGAVSRRVTEAVDGLALPEGVTATVGGAAE
+QQAATFRELGLALLAAIATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALLATGTALG
+LSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMGLDEAIEVGALNRVRPVVMTALATIL
+AMVPMALGLTGHSGFISQPLAVAVVGGLLSSTLLTLVLVPVLYRLTEARGERRIQAERAE
+QARRDEEARRRAAEAEQAAAEQAESARAGLLARRRTGGAPAASAAAGMADDGGRRPGPLG
+RLRARLGGLVGRARRA*
+>NZ_CP083691.1_1954
+MGALARFSLSRRALVALVTAFIAVFGVLSAGLLKRELIPSLELPVISVSTTYPGASPEVV
+DAEIGQPLEQALQAVEGLDSSASTSATSFNSVQLRFRYGTDLTRARSQVDRVISNLASQL
+PEEAQTTSFAGSVSDFPVVFLALSGDEDLNALKRRAEDVLVPRLQRIDGVRGAQVLGGTE
+EYVSVVPDAAKLAAAGLTTQDVTTALEENAGLFPIGQATSGTVTYPVQAGAPVGSVADLE
+QVTVTPGGGQSSTGAADQGAGAGAGGGPGAATGTPARLGDVAAVSMQAADPTSVTRTDGA
+PTLSLSVTATPDADLVAVSHAVADALPELESLAGSGAKLTVVFDQAPFIEQSIRTLFVEG
+LLGLAMAILVIAVFLLSARSTMVTAVSIPLSLLTALIGVAVFGYSLNTLTLGALTISIGR
+VVDDAIVVVENIRRHLGLGADKRTAILEGTREVATAITASTLVSVAVFLPIAFVDGLAGE
+LFRPFAVTTSIALLASLVVALTIVPVLCWWFLRAPRAAAAPGGAEGVSSPVEDAAQDTWL
+ARAYRPVLRWTQRHAVATLAGAAALLAGTVALAPLIPTNLLGDSGQNSFVVTAQQAPGTS
+LEATTAIAGRIEAALRDTPGVRTVQFTAGSAGGAMGAFGRGSADRATFTVVTDPDADQTA
+LQDEVRGRLAGLGDVGEVDVSAQQGPAGGQDITVSVTAPDPEALADGIDRVAEALRGLDG
+VLQASTPSSDVRPTFQVDVDTLAAAERGLTEKAVSGQVAAALQAVPAGTVRFGFQEFTVR
+LGDPDPVESLGALRAVPISTPSGPVPLSELADVRRADVPAQVTSSNGQRTAEVTVTPDPA
+DLGGVSRRVSDALEGVALPDGVEATVGGAATEQAKTFRDLGLALLAAIAAVYVVMVATFN
+SLRQPFVLLVSIPFAATGVVLALLASGTALGVATMIGLLMLVGIVVTNAIVLIDLINQYR
+RRHGMALDEAIERGALHRVRPVVMTALATVLAMTPMALGITGHAGFISQPLAVAVVGGLA
+SSTVLTLVLVPVLYRLTEARGERRIQAERAAREAEERELAEREARERELAEREAAARAVA
+GPAAAAHPAPAGRLSRRRGWRGWIRRATS*
+>NZ_CP097650.1_764
+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_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000737.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..64ec4c4ad9a9629fb1d932d9728989d552de32c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000737.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_800
+MTRADGSAYVGPMDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLE
+MLLCPFDPTSTPDDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQ
+VETVTGFRTWFDVPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPE
+TDATDVTPPDLHGV*
+>NZ_CP033200.1_541
+MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQVETVTGFRTWFD
+VPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPETDATDVTPPDLH
+GV*
+>NZ_CP040019.1_2055
+MDSPTLQRRLRGVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDAPADAPAADAPEEDPHGPVAEPSSHGTDVVGVALGNVATVADTGSGYQVETVTGFRTW
+FDVPEHARVPVGDLTEDGTAGLDQAEDAVDFHAFMTAFMDELDRLYAAPEAGGTDVTGPD
+LHAR*
+>NZ_CP083691.1_1950
+MDSPTLARRIRGAFDARVFNHGDYNLVYGQRSGGSLPLVIGYRHSPLEMLLCPLDPVEAV
+AAVPEEVALANVATVADTGSGYQVETVTGFRTWFEVVDRPRVPVGEASEDGLAELDQADD
+AADFHAFMTAFMDELDRLYAEPADPDLHPPQKSV*
+>NZ_CP097650.1_768
+MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQVETVTGFRTWFD
+VPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPETDATDVTPPDLR
+GV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000739.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000739.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2cced73a2977c9712ab4d2bf2d33cc1c152fed4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000739.fa
@@ -0,0 +1,41 @@
+>NZ_CP042169.1_803
+MPDPHPAPPRVEPATPPADVPPSVLRADRVHDGERLGGPGWIALAEGRVVAVGTGDPPRT
+HGPVHDLGDALLAPGCVDVHCHGGGGHAVESGAAAARAAAAAHARAGTTTVVASLVTDEV
+DALAAQLTALTALCAEGVLAGVHLEGPWLSPLHRGAHRAASLRAPEPEDVARLVEVGAGH
+LAMVTLAPELPGALDAVGRLAGAGVVVAIGHTDASYETTRAAIEAGARMATHLHNACRPT
+HHREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDSMAAAGCGDGE
+FPLGPLRVRVHDGVARVVGADGAAGAIAGSTATVTGSVRSAVAAGVDLDAALRAATAAPA
+DALGLPDVGRLRAGSRADAVVFGPELEVRGVLHHGTWVKAAAPAAAD*
+>NZ_CP033200.1_544
+MPDPHPAPPRVEPATPPADVPPSVLRADRVHDGERLGGPGWIALAEGRVTAVGAGDPPRT
+HGPVHELGDALLAPGCVDVHCHGGGGHAVESGPDAARAAAAAHARAGTTTVVASLVTDEV
+DALVAQLTALAPLRAEGVLAGVHLEGPWLSPLHRGAHRAASLRAPEPEDVARLVEAGAGS
+LAMVTLAPELPGALDAVGRLAEAGVLVAIGHTDASYEVTRAAIEAGARMATHLHNACRPA
+HHREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDAMAAAGCGDGD
+FSLGPLRARVHDGVARVVGADGAAGAIAGSTATVAGSVRSAVAAGVDLDAALRAATAAPA
+DALGLPDVGRLRAGSRADAVVFGPELEVRGVLRHGAWVEAAAPAAAD*
+>NZ_CP040019.1_2089
+MRPGGHARARRITPPLADHHVHGGAGVDLATSGAEDVRRWLAELRAAGASVVLGSLPALV
+PADLAAALERLRPLWEDGALAGVHLEGPFLSPARAGAQHPDALCAPDSAAGRRVRALLRA
+QPRGFVRTLTLAPELPGAREVAAELEAAGTVLCLGHTDAGPAEVAAALDWPRPRAAATPV
+ATHLFNGMRPFHHRDPGPVPTLLAAARRGRLRLELVADGAHVAPELMELILEDPDLAAQT
+CLVSDAIAATGAPCGTVHRLGPAVVHAAPDAPRLGEPAEDGQGSKATGPEDGGRAPLAGG
+RRTLVEAVTALLDADLDADAVLRAAVHVPRRSLPETPAPELEDGALVWDEGRPLVALPAA
+RA*
+>NZ_CP083691.1_1978
+MTASALLRTTAPWVGADPGATPVRVSAVWSAGPDGALLVWAGLAERVPQELWETAVDAPA
+LRLSPALTSHHVHGGAGVDLATSPAADVRSWLAAQRQAGVGAVVGSLPTLAEDALAAALD
+RLRPLWAEGLLAGVHLEGPFLSPARAGAHDPALLLTPPSPAGRRVRALIAAQPEGFVRTL
+TLAPELPGADALTRELTGTGVVVCPGHTDADGATTRAWLQTADDARAAATAAGLPAPTPV
+ATHLFNGMRGFHHRAPGPLPALLGAARAGRARLELIGDGVHVDDEVLTAILGDPGLAPAA
+CLVSDAVAATGATRGTAHRLGSLPIHAAQDGPRVGADEPTGPAEAALAGGAADLPEIVGR
+LLHSDLDPDAVLRAATHVPARTLGGSHAVPVGTPETTEHAAPGGDVLVWAPDGAVTVLRS
+QAAPGGRHHD*
+>NZ_CP097650.1_771
+MPASVPHRPRAEQAPQAAASPSVLRADRVHDGERLGGPGWIALAEGRVVAVGTGDPPRTH
+GPVHDLGDALLAPGCVDVHCHGGGGHAVESGAAAARAAAAAHARAGTTTVVASLVTDEVD
+ALAAQLTALTPLCAEGVLAGVHLEGPWLSPRHRGAHRAASLRAPEPEDVARLVEVGAGHL
+AMVTLAPELPGALDAVGRLAEAGVVVAIGHTDASYETTRAAIDAGARMATHLHNACRPTH
+HREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDAMAAAGCGDGEF
+PLGPLRVQVHDGVARVVGADGAAGAIAGSTATVAGSVRSAVAAGVDLDAALRAATAAPAD
+ALGLPDVGRLRVGSRADAVVFGPELEVRGVLRHGTWVKAAAPAVAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000747.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000747.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae22a59709f4a5809085eeabbc8d9a5183c610b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000747.fa
@@ -0,0 +1,70 @@
+>NZ_CP042169.1_823
+MSSHRSSAAAEGAPLPATTPEDLPPTEAAGRPRWTPAKIAVWVAVALLGGVAWTMLALHR
+GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL
+YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV
+YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR
+GIYFAMNAPAALTGGTPETAAAWVMSLGLAGVDVTPEQLTALANLVGEDTVVSRTGGAPT
+LAVGLSIIMGQLIGGEALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF
+KDTGWRVGAWVCTGIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLAI
+VAGRRHFRGLWIVALPLGFITVVTTVASFQKIFSSVPAVGYWAQHNAFKDALASGATSFG
+AAKSVPAMEAVVRNTFIQGTLSIVFLVLALVVITTSVLATVRAFRGTEVIDHQDPYVPSQ
+RFAPAGLFATAEEKELQAQWDALPAEKQPVRGH*
+>NZ_CP033200.1_554
+MSSHRSSAPAEGAPRPATTPEDLPPTEAADRPRWTPVKIAVWVAVALLGGVAWTMLALHR
+GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL
+YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV
+YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR
+GIYFAMNAPAALTGGTPETAADFVMGLGLAGVNLAPGDLTHLADLVGEETVVSRTGGAPT
+LAVGLAHIMGQLVGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF
+KDTSWRVGAWVCTAIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLTI
+VARRRDFRGLWIVALPLAFITVVTTVASFQKIFSSIPAVGYWAQHRAFQDALAAGKTSFG
+AAKSVPAMEAVVRNTFIQGTLSVVFLVLALIVITTSVLATVRAFRGTEVIDHQDPYVPSQ
+RFAPAGLFATAEEKELQRKWDALPADRQPVRGH*
+>NZ_CP040019.1_2045
+MSSHRSAAPAEGMAPRDPARDGGPDGLPPVEAAQRPRWTPLKIAVWVVVALVGGVAWTML
+ALHRGESINAIWFVFAAVATFAIGYRFYSKYVERMIVRPDDTRATPAEYRADGRDYVATD
+RRVLYGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGG
+RSLGQMARDELGRIGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVALTIPIAI
+FMGLYLRYLRPGRITEVSIIGFVLLMAAIIGGGWVAETDWGVALFTLDRVTIAWGIIIYG
+FVAAVLPVWLLLAPRDYLSTFMKIGVIAGLAVAIVIVQPQITAPAISEFASGQTGPVWPG
+SLFPFLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAV
+SIDRGIYFAMNAPAALTGGTPETAAAWVMSLGLAGVDVTPEQLTALANLVGEDTVVSRTG
+GAPTLAVGLSIIMGQLIGGEALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNV
+APRFKDTGWRVGAWVCTGIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAV
+VLAIVAGRRHFRGLWIVALPLGFITVVTTVASFQKIFSSVPAVGYWAQHNAFKDALASGA
+TSFGAAKSVPAMEAVVRNTFIQGTLSIVFLVLALVVITTSVLATIRAFRSTEVVDHADPY
+VPSRRFAPAGLIATAEEKELQRQWDALPADQRPERGH*
+>NZ_CP083691.1_1941
+MSSTRSVIPTGGSAPHDARPDGLPPVEAPHEQRWTPARVAVWAVIALLGAVAWTMLALHR
+GESINAIWFVFAAVSTFLIGYRFYSKYVERAIVRPDDTRATPAEYNADGRDFVATDRRVL
+FGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRIGGTAAIIATLLIMVIITAILALIVVNALGDSPWGVFSVGMTIPIALFMGL
+YLRYLRPGAITEVSIIGFVLLLAAIIGGGFIAETPWGAALFTLDRVTLAWAVIVYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLAIAIVIVQPRVQAPAFSEFAGGQAGPVWAGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAIMALVAAVTIDR
+GVYFAMNAPTALTGGAVDSAVAWVNGLGLANADLTPDQLTTLANQVGEETVVSRTGGAPT
+LAVGLAQIMGQLIGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDTLGNVFPKF
+KDHNWTPGAWLATAVMVAAWGAVLVMGVTDPLGGINTLFPLFGIANQLLASIALAVVMAI
+VAKRRTFKGLWIVALPLAFITVVTTVASLHKIFSPVPAVGYWAQHRAFQDALAAGKTSFG
+AATTVPAMEAVVRNTFVQGTLSVLFLALALIVITSSIVATVRAFRSTEVVDHQDPYVPSR
+RFAPAGLTATPAEKEIQAQWDALPADRQPVRGH*
+>NZ_CP097650.1_781
+MSSHRSSAPAEGAPRPATTPEDLPPTEAADRPRWTPVKIAVWVAVALLGGVAWTMLALHR
+GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL
+YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV
+YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR
+GIYFAMNAPAALTGGTPETAADFVMGLGLAGVNLAPGDLTHLADLVGEETVVSRTGGAPT
+LAVGLAHIMGQLVGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF
+KDTSWRVGAWVCTAIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLTI
+VARRRDFRGLWIVALPLAFITVVTTVASFQKIFSSIPAVGYWAQHRAFQDALAAGKTSFG
+AAKSVPAMEAVVRNTFIQGTLSVVFLVLALIVITTSVLATVRAFRGTEVIDHQDPYVPSQ
+RFAPAGLFATAEEKELQRKWDALPADRQPVRGH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000748.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000748.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1387d0f7499a15c426f31c0deea8248e1901f19
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000748.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_824
+MVAPRTTPGGAPAAEASPARRTWQAARWWVRQLSGEGKYDAYVAHHRAHHPERAPMTERE
+FWRAEYARQEANPGSRCC*
+>NZ_CP033200.1_555
+MRCRRTGSRCGVTDVADPRATPAGPSSAEGPAGPSRPSVWARARWWVRQLSGEGKYDAYV
+AHHRAHHPERAPMTEREFWRAEYARQEANPGSRCC*
+>NZ_CP040019.1_2044
+MAASGTCPTPTGGSAAEPAAARRAGDGTGPAAGSGLRAAWASARWWVRQLAGEGKYDAYL
+AHHRAQHPGVEPMSEREFWRDEYAKQEANPGSRCC*
+>NZ_CP083691.1_1940
+MAGIWASTRWWVRQLTGEGKYDAYLAHHRAHHPGEVPMTEREFWRDEYARQDANPGSRCC
+*
+>NZ_CP097650.1_782
+MRCRRTGSRCGVTDVADPRATPAGPSSAEGPAGPSRPSVWARARWWVRQLSGEGKYDAYV
+AHHRAHHPERAPMTEREFWRAEYARQEANPGSRCC*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000749.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000749.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70e4e41fc938c387e2b4542d7ce6c43f6e07fd5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000749.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_825
+MRIARFVDQAEPTYGIVEGPADADPAELTVTALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPAGGLRITSRLDGETRQDGTTTDMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG
+TVQEGQRVEAEVEGIGVLATVFRR*
+>NZ_CP033200.1_556
+MRIARFVDQAEPTYGIVEGPADADPAELSITALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPTGGLRITSRLDGETRQDGTTADMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG
+TVQEGQRVEAEVEGIGILATVFRR*
+>NZ_CP040019.1_2042
+MRIARFVDQAEPTYGVVEGPADADLSELTITALQGDPFFHGIQPTSTVHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNETPASPQFFLKPNTSVVGPGEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPAGGLRITSRLDGQTRQDGTTADMVFGVRELVAAASEAFTLLPGDVILTGTPAGVG
+TVAEGQRVEAEVEGIGVLATVFRR*
+>NZ_CP083691.1_1933
+MRIARFVDQAEPTYGVVEGPADADLSALTVTALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPSSPQFFLKPNTSVVGPDEPVTLPSWSEEVSYEAEL
+AVVIGTICKDVPLSRVDDVVFGYTVANDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEQAGGLRVTSRLAGETRQDGTTADMVFGVKELVAAASEMFTLLPGDVILTGTPAGVG
+TVEAGQRVEAEVEGIGVLGTHVRR*
+>NZ_CP097650.1_783
+MRIARFVDQAEPTYGIVEGPADADPAELSITALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPTGGLRITSRLDGETRQDGTTADMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG
+TVQEGQRVEAEVEGIGILATVFRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000750.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000750.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f3738ae06778c942b1b2068d9f65b117e3862b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000750.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_826
+MTDATAPVSENAPAPFADVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGYIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALHAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMQILTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEDEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQGRPTDA*
+>NZ_CP033200.1_557
+MTDATAPVSENAPAPFVDVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALYAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMEVLTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEEEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQDQPTDA*
+>NZ_CP040019.1_2041
+MDAETPVRVRFCPSPTGTPHVGLIRTALFNWGWARHTGGTLVFRIEDTDAKRDSEESYQQ
+LLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGEIYAEVIEKLKAGGHIYPSYSSPEETEAR
+HRAAGRDPKLGYDGFDRDLTDEQVAAFEAEGRAPVWRLRMPDTDITFTDLVRGEITFKAG
+TVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLLSSTPRQIALYRALHAVGVAAY
+MPVFGHLPYVMGEGNKKLSKRDPQANLFLHREHGFIREGLLNYLALLGWSLSADEDIFTP
+EQFVEHFDVHKVLANPARFDEKKAIAINGSHVRMLDADDFRERLVPYLHAAGLVDAEPTE
+REREILAAAAPLVQERVQLLGEAVEMLAFLFTADADVATSEGALKGMPADLGAAVAAARD
+ALAALPEDGFTTERIEEALRAALIDGLGLKPRQAFGPVRVAVTGRKVSPPLFESLEILGR
+DSALARLDRFAAEQGLDQGLPTDA*
+>NZ_CP083691.1_1932
+MTEPTTASDTAAENAPAVFADVPQVDADTPVRVRFCPSPTGTPHVGLIRTALFNWGWARH
+TGGTLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGEIYAE
+VIEKLKAGGHIYPSYSTPEETEARHRAAGRDPKLGYDGADRDLSAEQVEAYEAEGRRPVW
+RLRMPDADITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGE
+DLLSSTPRQIALYRALHAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQSNLFLHRDRGFI
+PEGLLNYLALLGWSLSADEDIFTPEQFVEHFDIHKVLANPARFDEKKATAINGTHVRMLE
+PADFRARLVPYLQAAGLVGERLTEREERILDAAAPLVHERVALLGEAVDMLAFLFTPDAE
+IATAEGALKGMPADLPTAVAAAREALAGIDEAEFTTAAVEEALRAALIDGLELKPRQAFG
+PVRVAVTGKKVSPPLFESLEILGKESALARLDRFAAEQAAA*
+>NZ_CP097650.1_784
+MTDATAPVSENAPAPFVDVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALYAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMEVLTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEEEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQDQPTDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000755.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000755.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a7148b3b2fc81ff073544ced905d543f8ec23ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000755.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_833
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA*
+>NZ_CP033200.1_564
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADPTSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFTDPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+LQEA*
+>NZ_CP040019.1_2034
+MTSETTRPRTLAEKVWDEHVVVRGEGEGSSRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLEIDKPIADPTSRTQIETLRANAAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAIT
+VDGTLRPGVTAKDVILAVIAKIGTGGGQGFVLEYRGEAIRSLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADELEPFVT
+WGTNPGQGVSLNGAVPAPEDFDDPVAQESARKALGYMDLTPGTPMKEVAVDTVFMGSCTN
+SRIEDLRAFAEVVKGRKKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA*
+>NZ_CP083691.1_1925
+MSTQTQTPRPRTLAEKVWDEHVVVRGEGEGARRTPDLLYIDLHLVHEVTSPQAFDGLRLA
+DRPVARPELTIATEDHNTPTLEIDRPIADETSRVQIETLRANAEEFGVRLHSLGDREQGI
+VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLRLKPFRTMA
+ITVDGTLRPGVTAKDVILAVIAKIGTGGGQGYVLEYRGEAIRSLSMEGRMTLCNMSIEAG
+ARAGMVAPDDTTFEYLKGRPHAPQGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF
+VTWGTNPGQGVSLNDAVPAPEDFSDPAAQEAARKALSYMDLTPGTPMKDVAVDTVFMGSC
+TNSRIEDLRAFAEVVKGRTKADGLRVMVVPGSARVRLQAMDEGLDKVFEDFGAEWRFAGC
+SMCLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPLVAAATAVLGRLASPSDLPA
+LENQEA*
+>NZ_CP097650.1_791
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000763.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000763.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87f53bbd1db09e97c872394e58f5009e2d85fc86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000763.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_841
+MGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACPAQDDAGAVLAHAGAAALDSA
+RGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRAARQALSDPREGTILTVLSAA
+ARSLARSSTQAPDTPAVAGDADPAVRLGPAVTLMLADCVQAVEETESLLAPLTRAHVVDA
+GAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGAHAAEAEPAAAAEAPAEGAVEVMGT
+LALTPLAAAELRRRLTEVGDAVILAPLGTARDGQGRVPWRVHVHVPRAEDAIGPLRAAGD
+VEGLTVTDLAGPSHGDDAAPDGCHGR*
+>NZ_CP033200.1_572
+MSTPSRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP
+AQDDAGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRA
+ARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTVMLADCVQ
+AVEETESLLAPLTGAQVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGVHAAE
+GEPAAAAEAPAEGAVEVMGTLTLTPLAAAELRRRLADVGDAVILAPLGTARDGQGRVPWR
+VHVHVPRAEDAIGPLRAAGDVEGLTVTDLAGPSHGDDAAPDGCHGR*
+>NZ_CP040019.1_2026
+MSTPPRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP
+AQDDAGAVLARAGAAALDLARGNSGTLLAVALAGMAEPLRGRARADAFALAAAFGAADRA
+ARQALSDPREGTILTVLSAASRSLARSATQAPDSPAVAADVDPAVRLGPAVTAMMADCLR
+AVEQTESQLAPLAQARVVDAGAVGLLWVLEALRAAVTDTAPDEELATALHGYVEGVRPGP
+EPAGEDAVEVMGTLALTPLAAADLRRRLAETGDSVILAPVGTERDEHGRVPWRVHVHVPR
+AADAVELMRAAGEVQGLAVTELSGDAAGPDADGCHGR*
+>NZ_CP083691.1_1917
+MIRARLRGALAWLRGAEAALAQAAPRLDALNLFPVPDADTGSNMLATVRAARQAAERSAG
+TDMSAVLRDAGAAALDSARGNSGTLLAVALVGLAAPLTPDAPLTTAELAAGARAADRAAR
+AALSDPREGTILTVLREAATVLEAAAAGGREPAEALGSVVEAARRAVEDTEGQLAPLTRA
+RVVDAGAVGLLLVLEALRAEVTRTPFDEGVVAALHGWADGPGAAGEDPQADGREAPGVEV
+MCSIDLTPVDAAGLRRGLEEAGDSVILAPLSRAVDGAGRLRWRVHVHVARAEDAVALLEA
+AGAPEEVAVTDLWDPAHRHPDDPAEGDAASPAPDGHGR*
+>NZ_CP097650.1_799
+MSTPSRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP
+AQDDVGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRA
+ARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTVMLADCVQ
+AVEETESLLAPLTRAHVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGVHAAE
+GEPAAAAETPAEGAVEVMGTLALTPLAAAELRRRLADVGDAVILAPVGTARDGQGRVPWR
+VHVHVPRAEDAIGPLRAAGDVEGLAVTDLAGPSHGDAAPDGCHGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000766.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000766.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f108309f75a60b3e1d5f7a0512095f6f8b50830
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000766.fa
@@ -0,0 +1,41 @@
+>NZ_CP042169.1_844
+MDGTQPTPGAAPHDVDVDAPWRRTAAAAGLLGDAGPVPTVFETMTGLAVEHGAVNLGQGF
+PDADGPDALLRLAADAVLAGPNQYAPGTGDPALRQAVAEHRRRHWGVTEDPATQVMITTG
+ATEGIAATVLAFVRPGDEVVTVEPFYDSHAATIALAGARHVSVPVEAPDFLPDPARVAAA
+MTDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLILSDEVYDHLVYEGEHVSLRS
+VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY
+LPTDGAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA
+VRWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAA*
+>NZ_CP033200.1_575
+MDGTQPTPGSARHDVDVDAPWRRTAAAAGLLGDTGPVPTVFETMTGLAVEHGAVNLGQGF
+PDADGPDALLRLAADAVLAGPNQYAPGTGDPVLRQAVAEHRRRHWGVTEDPATQAMITTG
+ATEGIASTVLAFVRPGDEVITVEPFYDSHAATIALAGGRHVSVPVEAPDFLPDPARVADA
+ITDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLMLSDEVYDHLVYEGEHVSLRS
+VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY
+LPTDDAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA
+VQWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAP*
+>NZ_CP040019.1_2023
+MNADASDRTRPPRTGPAPAPATGPAPADVAGTAFVAGPWRRTAAAAGLLDDGAPVPTVFE
+TMTGLAVEHGAVNLGQGFPDADGPDALLRLAAEAVLAGPNQYAPGTGDPVLRQAVAEHRR
+RHWGVTEDPATQVMITTGATEGIAATVLAFVRPGDEVITVEPFYDSHAATIALAGGRHVS
+VPVEAPDFLPDPARVADAITDRTRLLIVNTPHNPTGAVYPRELLEELVTLCRSRGVLILS
+DEVYDHLVYEGEHVSLRSVAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVK
+QFLTYSSGPAFQRALGAYLPTEDAKRHLAGQRERYRDARDRLVAGLRAADLDPVVPAAGY
+FVVVDLAPWGVTDAAEAAVRWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDE
+AMRRLAAAAPALDGRRPRP*
+>NZ_CP083691.1_1914
+MSHDSPSPTDAAAAPSDVRLAGPWRAASAAAGVLRDGAPVPTVFETMTALAVEHGAVNLG
+QGFPDADGPPELLALAAEAVTTGPNQYAPGTGRADLRAAVAAHRARHWGVAEDPDTQVLA
+TTGATEAIAATVLALVRPGDEVITVEPFYDSHAAVVALAGGRHVTVPVHAPDFLPDPARI
+AAAITPRTRLLIVNTPHNPTGAVYPRALLEELVALCRARDVLMLSDEVYDHLVHEGRHVT
+LRAIPGAERIALTASSAGKSLAVTGWKVGWLTGPADLVAAVRGVKQFLSYSSGPAFQQAV
+AAFLPRADDFLAGQLARHRRSRDLLVSGLRDIGLDPVVPAAGYFTVVDLAPWGVRDAAAA
+ARTWTERAGVAGIPVSALCRPDGDHLRSWLRLTFCKSEDTVAEAVARLTRHAADLRAG*
+>NZ_CP097650.1_802
+MDGTQPTPRSAPHDVDVDAPWRRTAAAAGLLGDAGPVPTVFETMTGLAVEHGAVNLGQGF
+PDADGPDALLRLAADAVLAGPNQYAPGTGDPALRRAVAEHRRRHWGVTEDPATQVMITTG
+ATEGIAATVLAFVRPGDEVVTVEPFYDSHAATIALAGGRHVSVPVEAPDFLPDPARVAAA
+MTDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLILADEVYDHLVYEGEHVGLRS
+VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY
+LPTDDAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA
+VQWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000772.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000772.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f050fd7a5ff177b5059c379e9ad07229eac939ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000772.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_850
+MPELPEAEVVRRGLARWATDAVAAELEVLDPRSLRRSPGGADALRERLRGARLAEPARRG
+KFLWLPLAEGDDAVVVHLGMSGQILVDEPGAADQRHLRLRLPVTAVDGSARELRFVDQRI
+FGGWWLDALRPDDAAGGERIPTTAAHIALDPLHPLFDPAAVHARLARRRSTLKRALLDQS
+LVSGIGNIYADEALWGARLHPERPTERMRRADTLRLLAAVQDVMRRALEVGGTSFDALYV
+NVDGRSGYFARSLAAYGRTGQPCRRCAAEGVDSRIVREPFMNRASHLCPRCQPRPRRRRA
+AAADA*
+>NZ_CP033200.1_581
+MPELPEAEVVRRGLARWATDAVAAELEVLDPRSLRRSPGGADALRERLRGAQLAEPARRG
+KFLWLPLAEGDDAVVVHLGMSGQILVDEPGAADQRHLRLRLPVTAADGSARELRFVDQRI
+FGGWWLDALRPDDAAGGERIPTTAAHIALDPLHPLFDPAAVHARLARRRSTLKRALLDQS
+LVSGIGNIYADEALWGARLHPERPTERMRRADTLRLMAAVQDVMRRALEVGGTSFDALYV
+NVDGRSGYFARSLAAYGRTGQPCRRCAAEGIDSRIVREPFMNRASHLCPRCQPRPRRRRA
+VAADA*
+>NZ_CP040019.1_2017
+MPELPEAEVVRRGLARWATDAVAGALQVHDPRSLRRSPGGAEALRARLEGARLAEPARRG
+KFLWLPLADADEAVVVHLGMSGQILVDEPGAPDQRHLRLRLPVTAADGAARELRFVDQRI
+FGGWWLDALHPDFAAGGEPIPATAAHIALDPLHPLFDADAVHARLARRRSTLKRALLDQS
+LVSGIGNIYADEALWGARLHPERPTERMRRADTRRLMAAVQDVMRRALAVGGTSFDALYV
+NVDGRSGYFARSLDAYGRTGQPCRRCAAEGVESRIVREPFMNRASHRCPRCQPTPRRRRT
+ATPADGPARP*
+>NZ_CP083691.1_1908
+MPELPEAEVVRRGMARWASGARAADLDVLDARSVRRSPGGAEALRERLSGAVLAEPARRG
+KFLWLPLEDADDAVVVHLGMSGQVRVDEPGAPDQRHLRLRLPITAADGSDRELRFVDQRL
+FGGWWLDPVVVGPETGDAVPASAAHIALDPLHPDFDPDAVHRRLVRRRSTLKRSLLDQTL
+VSGIGNIYADEALWAARLHPERPTQRMARAQTRAVLAAVQDVMRRALAVGGTSFDALYVN
+VDGRSGYFARSLEAYGRTGQPCRRCTAEGRRTLIVREPFMGRASHRCPVCQPVPRRSPSR
+*
+>NZ_CP097650.1_808
+MPELPEAEVVRRGLARWATDAVAAELEVLDPRSLRRSPGGADALRERLRGARLAEPARRG
+KFLWLPLAEGDDAVVVHLGMSGQILVDGPGAADQRHLRLRLPVTAADGSARELRFVDQRI
+FGGWWLDALRPDDAAGGERIPTTAAHIALDPLHPLFDPVAVHARLARRRSTLKRALLDQS
+LVSGIGNIYADEALWGARLHPERPTERMRRADTLRLLAAVQDVMRRALEVGGTSFDALYV
+NVDGRSGYFARSLAAYGRTGQPCRRCAAEGVDSRIVREPFMNRASHLCPRCQPRPRRRRA
+AVADA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000773.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000773.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df5f157359f2dfabb6a5503a28b954b09c9d89d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000773.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_851
+MSHPPAASWTPEPLPRPEPPRDDAPPVARRRRRWPWVVGLLAVLLAALLGLGAWYTSSLG
+RTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYTLAVDTVELLLGVSIHHVLEVDFQGFRGV
+TNALGGVEVCNPRAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVENQQR
+YLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPTKEKKAQAAGGPAP
+VLTLLTGTTPAPVLGEDPCDD*
+>NZ_CP033200.1_582
+MSHPPAASWTPEPLPRPEPPRDDAPPVARRRRRWPWVVGLLAVLLAALLGLGAWYAGSLG
+RTFDDHRQTVDVGALEQAAGDGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVDTVELLLGVPIHHVLEVDFQGFRGV
+TNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVKNQQR
+YLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPEKEKKAQAAGGPAP
+VLTLLTGTTPAPALGENPCDD*
+>NZ_CP040019.1_2016
+MSQPPAASWTPEPLPRPARSPEPPRPARRRRWPWVLGVLAAVLVVLLALGAWYAVSLART
+FDDHRQTVDAGALEQAGGGEPVNVLVLGSDSRGGEGEEDMGERSDAMMLVHLPADRSQVF
+VMSVLRDSWVEIPGHGEAKVNAAFDLGGYPLAVDTVEQLLGVPVHHVVEMDFQGFRGVTN
+ALGGVEVCNPVAFSSGQTSPSYYPRGPVLLQDTAALRYVRERHAFDDGDVSRVQNQQRYL
+AGAVERFLSPQILGNPARTTEVVATFSDHLGVDAGLTSGVVASLAWQLRGVRAGDVEMFT
+VPRAGFGYSPDGDSIVELDEAKLADLRSALKDDDVQRYVAEHESEDGQDASAAGADPAPV
+LALLAQPAPTPAVGEDPCAD*
+>NZ_CP083691.1_1907
+MTQPPQQPWIPPERPGGAADPLEGLRGPAPAAPPTSTPPATRRSGGGRARRRRPLRRFLA
+VLGVLALLLVVALGAYGLLLARTFDGHRQTVSAAAFADPGNDGPVNFLVLGSDSRAAEDS
+AETSQRSDTMMLVHVPADRRHVYVISVLRDSLVEIPGRGQRKANAAYELGGPELTAAMLD
+KLLGVPVHHLAELDFQGFRGMTTALGGVEVCNPHAFSSGQKNPSFYPRGRIELKDTAALR
+YVRERHAFPEGDVMRVQNQQRFVRGAVAAFLDPAVVLNPPRAVDVVAGLSDHLTVDEGLD
+SATLASLAWQLRGVDRSALTMFTVPRAGYGTSPDGQDVVLLDADRMAALRDALQRDDVES
+YLRAHDPEALAAGEDVQPALAAAPGATPLLTELAAAPPAGEGTLLGEDPCGG*
+>NZ_CP097650.1_809
+MSHPPAASWTPEPLPRPESPRDDASSVARRRRRWPWVVGVLAVLLAALLGLGAWYAGSLG
+RTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVDTVELLLGVPIHHVLEVDFQGFRGV
+TNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVKNQQR
+YLAGAMDRFLSPEILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPTKEKKAQAAGGPAP
+VLTLLTGTTPAPALGEDPCDD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000774.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000774.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c6187d7b69149a487b00388a41d0b5ae73d3568
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000774.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_852
+MTTESRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAVPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGAAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VRVVRTLGNGVDLARLAVAPRRERAAGELHVLYLGNMGESQGLERLIDAAATLRRTRPGV
+RVRLVGEGTRRPALEARNAELGSPAEILGPVHGAAVAEQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGLVTGEAARTLEAAGGADVIGPDVDDLVRHLTALADDPHRTDVG
+AGGRDWVRRHADLPAVARRYERVLRRVAGR*
+>NZ_CP033200.1_583
+MTTEPRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAIPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGVAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VRVVRTLGNGVDLARLAVAPRRERDAGELHVLYLGNMGESQGLERLIDAAATLRRTRPGV
+RVRLVGEGTRRPALEARNAELGSPAEILGPVHGAAVAQQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGLVTGEAARTLEAAGGAEVIGPDVDDLVRHLTALADDPHRTDVG
+AGGRDWVRRHADLPAVARRYERLLRRVAGR*
+>NZ_CP040019.1_2015
+MPTEPRRPRVLLITHSYRPERTPPARRWAAVVAALRAGGWDVDVVAPGGLRAVAGDDGER
+ILRTPRLPAGRSGRNGRFLEAAVHAVLAVPRGLAARRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGVAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VERVETLCNGVELAGLARAPARRREPGDLHVLYLGNMGESQGLERLVEAAAELRQSRPGV
+RVRLVGAGTRRGELEARNAELGSPAEILPACYGEEAAAQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGMVTGEAARTLEDAGGADVIGSRVADLVAHLTALADDPARTDVG
+EGGRPWVRLHADLPSVARRYVRLLGQLVPDYRRHA*
+>NZ_CP083691.1_1906
+MGERRTRAGGRAPRLLLVTHSYRPERTPPARRWAAVVQALRAAGWEVDVLVPGGLRTRVG
+EHGERLRPTPRLLGSGDGRNGRFAAAAVHAVLAVPRGLVLPRPDVVVATLPALPVVVAGR
+ALAVLRRRPLVVEMRDAWPDLAREAGVHPGLLGTLMERVVTGGQRAADLVVTVTEGFAAT
+LRGRGMRRVEVLANGVDLERVPVAPPRDRTAGELHVLYLGNLGESQGLERLVEAAARQRA
+THPGVHVRIVGDGTRRAALEALNAELEAGVEFVPPVSGAALTEQYAWADTLVVCLRPDWP
+SFRHTIPSKTYEALAVGRHVTGQLSGEAALMLERSGAADVVGPGVEDLVAHLDALADDPA
+RTRVGDAGRRWAAAHGDLPTTARRYEALLRRVAARPSRRTRTETTA*
+>NZ_CP097650.1_810
+MTTEPRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAIPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGAAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VERAETLCNGVELAGLAWAPARRREPGDLHVLYLGNMGESQGLERLMEAAAELRQSRPGV
+RVRLVGAGTRRGELEARNAELGSPAEILPACYGEDAAAQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGMVTGEAARTLEDAGGADVIGPRVADLVAHLTALADDPARTDVG
+EGGRPWVRRHADLPSVARRYVRLLGQLVPDYRRHA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000776.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000776.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2686ea014c36ab6ab74d84594311d159ab475acc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000776.fa
@@ -0,0 +1,29 @@
+>NZ_CP042169.1_865
+MSADPLTPSVVVDEASMTYRVLSAEAVQPRRGLRGRVRAARGVRTTEVQALQPLSFVVGR
+GESVGVIGTNGSGKSTLMKLITGQMRPTTGHIYATSTPVMLGVNAALVRQVSGEDNIRLG
+CLAMGMSRAEAEAKRDAVVALSGLDDHALQLPLKAYSSGMAARLQFAIATSVDPDILVID
+EALNTGDAQFRERTRQRLDELREQAGCVFLVSHSLSTIQEMCQRVIWIERGVLTMDGSPR
+AVTRGYNLYARAMAQGRTEEAQEILERKQSELVRERIAWSGGERPTGITAL*
+>NZ_CP033200.1_596
+MSAEPLTPSVVVDEASMTYRVLSAEAVQPRRGLRGRVRAARGVRTTEVQALQPLSFVVGR
+GESVGVIGTNGSGKSTLMKLITGQMRPTTGHIYATSTPVMLGVNAALVRQVSGEDNIRLG
+CLAMGMSRAEAEAKRDAVVALSGLDDHALQLPLKAYSSGMAARLQFAIATSVDPDILVID
+EALNTGDAQFRERTRQRLDELREQAGCVFLVSHSLSTIQEMCQRVIWIERGVLTMDGSPR
+AVTRGYNLYARAMAQGRTEEAQEMLERKRSELVRERIAWTGGERPTGITAL*
+>NZ_CP040019.1_2004
+MSGSRPLDPAVVLDEAGMTYTVRSSDTGARRAGIGGMLRGVRGVRTDQVQALAPLSLIVD
+RGESVGIIGTNGSGKSTLMKLITGEIHPTTGRVYATSTPVMLGVNAALVRQISGEDNIRL
+GCLAMGMTTAEAAEKRDDVVRLAGLDDQALQLPLKAYSSGMASRLQFAIATSVDPDILLI
+DEALNTGDAQFRARTRARIDELRARAGCVFLVSHSLTTLKQMCSRVIWIEQGILTMDGNP
+EVVTGNYARYTRHRSNGADEVAERLLAEARAGVKRVAVRWAGGQRPSGVIAD*
+>NZ_CP083691.1_1899
+MTDTTVDYALVLDRVSMTYRVPSSAADSVAALPAWRRGLARALRQPPRVPVHALHEMTLG
+LEQGRTLGLVGRNGSGKSTLSQIIAGKLAPSTGRVLATATPMMLGVNAALVPAMSGRQNI
+VLGCLALGMAKDEVMAKTPEIAASTGLGEAIDLPIETYSSGMSARLRFAIATSRDPEVLV
+IDEALNVGDSQFRARAKERMQELKRKAGAVVLVSHDNKTILDSSNKVLWLDKGRPVMEGS
+PQRVMDRYEQYNEMLAAQKVDEARAFVEDLRTTYRPRVVLPATDMHLPSVQEVEFSPRHA
+L*
+>NZ_CP097650.1_815
+MPNLTGLDNIRIGLLAMGLTPAEVHDRIPQVAELADIGKSIRMPMRTYSSGMRARLRFAI
+SVASQPDIIMIDEALATGDDAFRERSNQAMRDLIARSGTGFLVNHSAGVIREMCTRVVWM
+DEGAIIEDGDTLDVMQHYSYFMSALRKHGEEKALEARARYETTEAERIVALKGTTGH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000778.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000778.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a33a10539a1983535fc65937b8f726a5665f7e3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000778.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_867
+MPKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLN
+IIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAG
+LRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALLE
+AVGHQVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLP
+AHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPV
+LVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGDGRAAER
+TVSAIAELLGVGERLPAFDGGDPA*
+>NZ_CP033200.1_598
+MPKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLN
+IIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAG
+LRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALLE
+AVSHQVPFEDERLAGLEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLP
+AHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPV
+LVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYSAMSQAVNPYGDGRAAER
+TVSAIAELLGVGERMPEFAPDDRG*
+>NZ_CP040019.1_2006
+MKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLNI
+IQPRQTLNGVFARTLDGLDAILEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAGL
+RSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALLEA
+VGHQVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLPA
+HRNPVVREAILPEIEGRANVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPVL
+VMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGDGRAAERT
+VSAIAELLGVGERLPAFDGA*
+>NZ_CP083691.1_1901
+MPLKIMPIYGTRPEAIKMAPIVNALRADDRFECFTTVTGQHREMLDQVNAIFGITPDADL
+DIMRPNQTLNGIMSVMLEGLDELLVRERPDAVVVQGDTTTSTAGAIAAFYRGIPVVHAEA
+GLRSGDLFSPFPEEANRKITSQIASLHLAPTSVSRANLEREAIDSAAITVTGNTVIDALL
+ETVAQQLPFTDPRLAELAERRAADPQSRVLLVTTHRRENQGEAMRGVGRALARLAQSHPN
+LTIVLPAHRNPVVREAVLPTLEGIDSVIVTEPLPYGEFTRMMDLADVVLTDSGGVQEEAP
+SLGKPVLVMRDNTERPEAVHAGTVRLIGTDEERLVEETSLLLTDPDAYAAMAHAVNPYGD
+GRAGLRTVAAIAQLLGVGDRLDEFGA*
+>NZ_CP097650.1_817
+MPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLNIIQP
+RQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAGLRSF
+DILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALLEAVSH
+QVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLPAHRN
+PVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPVLVMR
+ENTERPEAVTAGTVRLIGTDEEVVVTEVTRLVTDEAAYTAMSQAVNPYGDGRAAERTVSA
+IAELLGVGERLPAFDGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000780.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000780.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d817f1bb2f1a2476aa448331b022470b727fb60e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000780.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_872
+MCETGHVEIVLIISVVLALLVGGLIVGLLDRRPAPPKGSYQGVRDADDPRPGPRHAAPGG
+STAVLERPDAEEATVDVAEPEVVEEVETAPAAPELERPEAAGSRLSRLRARLLKSNNVFG
+KGLLALLSQDRIDEDVWDEIEETLLMADLGTEPTMELVDRLKARVTVEGTRDPEQVRALL
+REELVAMVDPSMDRRLAATRRDGRPAVTLVVGVNGVGKTTTVGKLARVLVAEDRDVVLGA
+ADTFRAAAAEQLATWGARVGVPTVRSEKEGADPASVAFEAVAEGIRAEADVVLVDTAGRL
+QNKSNLMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLD
+GTAKGGIVVAIQRQLGVPVKLIGLGEGADDLAPFTAEGFVDALLAD*
+>NZ_CP033200.1_600
+MLIVSVVAALLLGGVLVGLLDRRPAPPKGSYQGVRDADDPRPSPRHAAPSGSTAVLERPE
+VDEAPAVVAEPEPAVVEEVEPAPAKPEYERPEAAGSRLARLRARLLKSNNVFGKGLLALL
+SQDRIDDDVWDEIEETLLMADLGTEPTLELVDRLKARVTVEGTRDPEQVRTLLREELVAM
+VDPSMDRRLAATRKGDRPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFRAA
+AAEQLATWGARVGVETVRSEKEGADPASVAFEAVELGIAEGVDVVLVDTAGRLQNKANLM
+DELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKGGI
+VIAIQRQLGVPVKLIGLGEGPDDLAPFTAEGFVDALLTD*
+>NZ_CP040019.1_2002
+MCQTGHVEIVLIISVVLALLVGGLIVGLLDRRPAPPKGSYQGVRDADDPRPAPRHAAPGG
+STAVLERPEAEEAPVDLVEPEVVEEVEAEPAAPELERPEAAGSRLARLRARLLKSNNVFG
+KGLLALLSRDRIDEDTWDEIEETLLMADLGTEPTMVLVDRLKSRVTVEGTREPEQVRELL
+REELVAMVDPSMDRRLAASRRDGRPAVTLVVGVNGVGKTTTVGKLARVLVAEDRDVVLGA
+ADTFRAAAAEQLATWGARVGVPTVRSEKEGADPASVAYEAVAEGIRLEADVVLVDTAGRL
+QNKSNLMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLD
+GTAKGGIVVAIQRQLGVPVKLIGLGEGADDLAPFTAEGFVDALLAD*
+>NZ_CP083691.1_1897
+MITVIVISVVLALLLGVVLVGLLDRPVAPPKGTYTELRDSDDPAPAGLVADPSSAPAPEE
+ALEETGRAGSHAAAPVAEPVEAAEAPERQLERPEAAGTRLQRLRARLLKSNNVFGKGLLA
+LLSRDHIDEDVWDEIEETLLMADLGTEPTMELVDRLKARVTVDGTRDPESVRALLREELV
+AMVDPSMDRRLAATPHDGHPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFR
+AAAAEQLATWGARVGVETVRSDVEGADPASVAFEAVKTGIEREADVVLVDTAGRLQNKAN
+LMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKG
+GIVVAIQRQLGVPVKLIGLGEGADDLAPFSAEGFVDALLAA*
+>NZ_CP097650.1_819
+MLIVSVVAALLLGGVLVGLLDRRPAPPKGSYQGVRDADDPRPSPRHAAPSGSTAVLKRPE
+VDEAPAVVAEPEPAVVEEVEPAPAKPEYERPEAAGSRLARLRARLLKSNNVFGKGLLALL
+SQDRIDDDVWDEIEETLLMADLGTEPTLELVDRLKARVTVEGTRDPEQVRTLLREELVAM
+VDPSMDRRLAATRKGDRPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFRAA
+AAEQLATWGARVGVETVRSEKEGADPASVAFEAVEHGIAEGVDVVLVDTAGRLQNKANLM
+DELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKGGI
+VIAIQRQLGVPVKLIGLGEGPDDLAPFTAEGFVDALLAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000783.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000783.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f319f463cba6a48f1ae039c0bd2cfdb3a172469
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000783.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_875
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAAEAPAEDAEKSE*
+>NZ_CP033200.1_603
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAEEAAEAPAEDAEKSE*
+>NZ_CP040019.1_1999
+MAVKIRLKRFGKIRAPYYRIVVADSRTRRDGRAIEEIGKYHPTEEPSYIEVDSERAQYWL
+SVGAQPTEQVAALLKITGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKAEE
+PKAKESAEAETPAEEAPEAPAEDAEKSE*
+>NZ_CP083691.1_1894
+MAVKIRLKRFGKIRAPYYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKITGDWQKFKGEAGAEGTLKTKGEKEAFVAPAKESVILPEEPKQEE
+APAESAEAEAPVEEAADAEAPAEDAEKAE*
+>NZ_CP097650.1_822
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAEEAAEAPAEDAEKSE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000787.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000787.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c54ffd9dd7e4c820c0bf5c314a6a3ef605e1636d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000787.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_879
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGHGVRETFRV
+RKVSFGIGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK*
+>NZ_CP033200.1_607
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGYGVRETFRV
+RKVSFGIGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRADAK*
+>NZ_CP040019.1_1995
+MHILDSLDSNSLRSDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRNGYGVRETFRV
+RKVSFGVGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK*
+>NZ_CP083691.1_1890
+MHILDSFDKASLREDIPAFGPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGHGVRETFRV
+RKVSFGVGVERVFPVHSPVIDKIEVLTKGDVRRAKLYYMRDRHGKAARIREKRADAK*
+>NZ_CP097650.1_826
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGYGVRETFRV
+RKVSFGIGVERVFPVHSPIIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000795.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000795.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30811d59274a1e5db21887fa46e7b30c75ebbda4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000795.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_887
+MAPSSSVRPAPAPRAPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLHSLIDYVAGTA
+ATAGTPPVDDDAPARHGPSAPDVLPELDIEDLRGWLAAMSGSGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQERVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WERLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA*
+>NZ_CP033200.1_615
+MAPSSSARPAPAPRAPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLRALIDHVAGTA
+GTSGSPAADDDAPARHVPSAPDVLAELDIEDLRGWLAAMSGAGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQDRVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WQRLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA*
+>NZ_CP040019.1_1986
+MASSSSSARPAAARAFAPSPRDAAWLEAFEEHLRHERNRSPQTVRAYATDLRDLVAHVAS
+GTWGGHPGTATSEAAVEADAVAPDVFAEVDVEDLRGWLAAMTDAGLARTTLARRVAAVRT
+FTGWLRREGLREDDPALRLRSPRPAATLPHVLQEQQAERLLAGAQARVAEAAVGDDPAAH
+ALALRDAALLELLYATGARVAELSALDVDDLEPGRAVARLTGKGDRQRTVPYGAPAARAL
+DAWLRLGRPRLARDGSGPAVFLGVRGGRLGVRQVRAVVDRALEGLGDTAARGPHALRHTA
+ATHLLDGGADLRSVQEVLGHSSLRTTQVYTHVSIDRLREGYRQAHPRA*
+>NZ_CP083691.1_1882
+MHPPHAHHAPGAPLPPASARDEAWLEAFAEHLLHERGRRPRTVRAYLADLRHLAAHVTDD
+GADAFAEVDLEDLRRWLARMRDQGLSRATVARRVAAARTFLGWLHRSGLRPDDPTLRLRA
+PAPDSRLPQVLQAEQAQRLLQAAEERVHEARRADDLHGAALAARDVALFELLYATGARVA
+EVAALDVDDLDLDRRTARLTGKGDRQRTVPFGAPAAAAVERWLRVARPVLATEHSGVALL
+LGARGGRADVRVLRGAVDRALERLGDTAARGPHALRHTAATHLLDGGADLRSVQELLGHS
+SLQTTQRYTHVSVDRLRDGYRRAHPRA*
+>NZ_CP097650.1_834
+MTPSSSARPAPVPRDPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLHSLIDHVAGTA
+GTSDTPAVDDDAPARHASSAPDVLAELDIEDLRGWLADMSGSGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQERVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WQRLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000801.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000801.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09fced67c75c0047806facbb7bf0ee4ecbbe0438
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000801.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_893
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALAPWFAPGPVIVGPVVDSLVSAHVSARHTLAGLSAAAAHPRASRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD*
+>NZ_CP033200.1_621
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALAPWFAPGPVIVGPVVDSLVSVHVSARHTLAGLSAAAAHPRASRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGAGSD*
+>NZ_CP040019.1_1980
+MPEPRSAASRPVSTEGRARLRSHLGALNTAVLQRLDATLPWYRGLTPDERSALGLVAQRA
+LQGFISWFDRPKTTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPIREHVLHYSREVAFALADVYARAAEMRGAMDSRLEAVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHRVMVMAGLAPGQDQPAFIPGLRRAAAKLDCDLLVGVQAERLVLVIGSVTDAQ
+VVGEALTPWFAPGPVILGPVVDSLVEAHVSARHTLAGLGAAPAHPRAIRPTPAEDLLPER
+ALLGDPTACEALVEGVYAPLADAGTALLDTVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAVTLGRLAGSRPGVAEASA*
+>NZ_CP083691.1_1876
+MPAPRPSAPRRVSADGLARLRAHLGTFNTATLRRLDETLPWYRELTPDERSALGLIAQRA
+LQGFITSFERPQTTTVDVLRDVFGQSPTELTRAISLHRALQLIRTIVDVVETGVPDAVSE
+ADQPVVAEHVLHYSREIAFAIADVYARAAELRGAMDSRLEAVLLDAVLRGQEPDEIQHRA
+TAFGWRGGDGVMVMAGSARDGATAAFLPGLRRDAARLQCELLVGVQSRRLVLVVGSVSDP
+DAVAEALLPWFADGPVIVGPVVDSLLEAHVSAHHALAGLGAAAAHPRAGRPARSDDLLPE
+RALAGDATACAALVDGVYAALADAGPSLLETVDVYTACGHSLEGTARELYVHANTVRYRL
+RRAAEVTGWDPQRPRDAYVLQTAVALGRLSEGAPRL*
+>NZ_CP097650.1_840
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLHRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALARWFAPGPVIVGPVVDSLISAHVSARHTLAGLSAAAAHPRACRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000802.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000802.fa
new file mode 100644
index 0000000000000000000000000000000000000000..927d1af5f6e69d74638792e97926f5e17b9f44e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000802.fa
@@ -0,0 +1,85 @@
+>NZ_CP042169.1_894
+MSAAEESSQIRSGLTDQLPDKDPQETSEWIESLDGLIEERGTERAQYIMRSLMQRASAQS
+VALPYVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDGVGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEEDLDGFRQE
+KSRQGHGLPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHIAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSVTKE
+MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV
+PERRSDYHAIPLPPESAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHDRGDDVRNVIYYLTVYNEPIT
+HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSATPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF
+VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGEVERGTAAKAHEKYR
+LDDVNAGTTGIAGGDA*
+>NZ_CP033200.1_622
+MSAAEESSQIRSGLTDQLPDKDPQETSEWIESLDGLIEERGTERAQYIMRSLMQRASAQS
+VALPYVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDAVGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEQDLDGFRQE
+KSRQGHALPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHVAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSVTKE
+MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV
+PERRSDYHAIPLPPESAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHDRGDDVRNVIYYLTVYNEPIT
+HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSASPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF
+VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGEVERGTAAKAHEKYR
+LDDVNAGTTGIAGGDA*
+>NZ_CP040019.1_1979
+MSAAEESSQILSGLTQQFPDKDPQETAEWIESLDGLIEERGTERAQFIMRSLLQRAGAKS
+VGVPMVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAAAIVQRAQKEGIGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEEDLDGFRQE
+KSRQGHALSSYPHPRMMPDFWQFPTVSMGLGPMNAIFQAQTNRYLHNHGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHVAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSATKE
+MVADMSDEEIWGLKRGGHDYRKVYAAYKSAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKMTVEDIKVFRDRHRIPVTDEQIERDPYDIPYYHPGKDAPEIKYLMERRKELGGFV
+PERRAKHHSIPVPPEAAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGSRIVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAVG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVIAGTNPAVKHYDPAYSYEIAHIVRQGFEDMYGEHDRGEDVRNVIYYLTVYNEPIH
+HIDEPEDLDVEGLLKGIYRLSEGQGDGPKVQLMGSGVSLPWAVEAQGILAEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSAAPRVPYVTQKLEGAEGPVVATSDFATSWTNQIRPF
+IPNRFAALGADEFGFADTRSAARRYFLIDSHSMVVRALQLLEEEGSVEKGTAAKAHEKYR
+LDDVNAGTTGNAGGDA*
+>NZ_CP083691.1_1875
+MSAAEESSQIVSGLTSQRPDKDPQETAEWIESFDGLVDERGTERAEYIMRSLMQRAGAKS
+VALPHVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDAVGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEEDLDGFRQE
+KSRQGHALPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHVAANDKLDNLTFVVNCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVREHFFGRSSVTKE
+MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV
+PERRSTYHQIPLPPESVYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHEDGDARRNVIYYLTVYNEPIT
+HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSATPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF
+VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGGVERGTAAKAHEKYR
+LDDVTAGTTGIAGGDA*
+>NZ_CP097650.1_841
+MSAAEESSQIRSGLTDQLPDKDPQETSEWIESLDGLIEERGTERAQYIMRSLMQRASAQS
+VALPYVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDAVGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEQDLDGFRQE
+KSRQGHALPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHVAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSVTKE
+MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV
+PERRSDYHAIPLPPESAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHDRGDDVRNVIYYLTVYNEPIT
+HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSATPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF
+VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGEVERGTAAKAHEKYR
+LDDVNAGTTGIAGGDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000803.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000803.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff60b17ac710ec2d55e5598e6902deaec4c99fe9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000803.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_895
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEDALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG*
+>NZ_CP033200.1_623
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEGALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG*
+>NZ_CP040019.1_1978
+MEAGSTPTSTDSALLAELALAQGDLVQEWGYDDDVDFTFRDGLEDALGEELLTEEDQEPA
+DAVLYWWRAEDGDVTDLADALVDAQRSLDSGPVWLMTPRKGRAGHVNPADVQEAAGTAGL
+HATTGAGVSEDWAAQRLVQKRGG*
+>NZ_CP083691.1_1874
+METPSDGTSTHQELLDAYGLTAGELVQEWGYDDYIDFDFRDALEDALGEELLTEEDQEPA
+DAVLFWWRTDDGDVSDLTDALVDAQRSLDAGPVWLMTPRNGRPGHVSPTDVAEAAATAGL
+HVTTGAGGSADWAAVRLEKRGG*
+>NZ_CP097650.1_842
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEDALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000812.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000812.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34ae0cbc99120fbeb1d7b6fd409f30c34bb32587
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000812.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_904
+MARILDDITQAVGGTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG
+ELSPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQEIVRSTPNSIWAQQFANQANVQAHYTGTGPEIWDASEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE
+VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG*
+>NZ_CP033200.1_632
+MARILDDITQAVGNTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG
+ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQEIVRSTPNSIWAQQFANQANIQAHYTGTGPEIWDASEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE
+VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG*
+>NZ_CP040019.1_1967
+MAHILDDITQAVGGTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEASG
+ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQQIVASTPNSIWAQQFANQANVQAHYTGTGPEIWDATEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTELYDD
+VYAASLEESIETSRTLATQEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG*
+>NZ_CP083691.1_1861
+MAKILDNITQAVGGTPLVRLNSLTEGLPGDVAVKVEFYNPANSVKDRIGVAIVDAAEKSG
+QLTPGGTIVEGTSGNTGIALAMVGAARGYKVILTMPETMSAERRVMLRAFGAEIVLTPGA
+DGMRGAVERAQQIVRDTPNSIWAQQFANEANVRAHYTTTGPEIWDATGGAVDTFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPSDSPILSGGQAGPHKIQGIGANFVPEILDTELYDE
+VYAATFEESIATSRALGAREGILGGISTGAIVSAALKEAAKPESEGKLIVAVVCDFGERY
+ISTALFEDVRG*
+>NZ_CP097650.1_852
+MARILDDITQAVGNTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG
+ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQEIVRSTPNSIWAQQFANQANIQAHYTGTGPEIWDASEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE
+VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000817.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000817.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99691b70299e47d679756c2499e7290e556820b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000817.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_909
+MLILLPPSEGKTAPRSGAPLDLDALALADDAAVTGARADLLTRLAAVSAAPDALAALGVG
+ASLTGEVEANTRLASAPAAPGHRVFTGVLFDALDHASLSAAAKRRARASVLVFSALFGAT
+ALADRIPAFRLPVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA
+PAERTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLERVADVVARAGDG
+HGWEVELARPSGAKPGALRVILPEG*
+>NZ_CP033200.1_637
+MLILLPPSEGKTAPRSGAPLDLDSLALADDAAVTGARADLLTRLAAVSAAPDALTTLGVG
+ASLAGEVEANTRLAVAPAAPGHRVFTGVLFDALDHASLSAAAKRRARLSVLVFSALFGAT
+ALADRIPAFRLPVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA
+PAEQTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLDRVADVVARAGDG
+PGWEVELARPSGGKPGALRVILPEG*
+>NZ_CP040019.1_1962
+MLILLPPSEGKTAPRSGAPLRLEDLALAEHDAVTAARRDLLARLAEASAAPDALETLGVG
+ASLAGEVAANTSLATAPAAPGHRVFTGVLFDALDHASLSPGAKRRARDAVLVFSALFGAT
+SLADRIPAHRLSVGARLPGLPGLAAHWRPVLAPALDAVAQADGGPIVDCRSGGYAAMWKA
+PAERTATVDVFQLRGGEPTVVSHFAKHTRGLVARALLEAGARATGALDRAAEVVAAAGAG
+DVEGRRWDVELVAPSGAKPGSLRVVLPEA*
+>NZ_CP083691.1_1856
+MLILLPPSEGKTGPRSGRPLDLSSLTLADDDAVTAARAELLPRLAEASARPDALDILGVG
+ASLADEVAANTRLATAPSAPARKVYTGVLFEALDLTSLSPAAKRRAASDVLVFSALFGAT
+TPGDRIPAYRLPVGARLPGMPGLAAWWRPRLAPALDGYAEARGGVVVDCRSGGYAAQWKA
+PAERSLAVDVFQLRAGRRTVVSHFAKHTRGLVARALLEAGSRAAGTPATAADVVARAGDG
+GVPGQRWEVELVPPTGRKAGSLQVILPEE*
+>NZ_CP097650.1_857
+MLILLPPSEGKTAPRSGAPLDLESLALADDAAVTGARADLLTRLAAVSAAPDALTALGVG
+ASLAGEVEANTCLASAPAAPGHRVFTGVLFDALDHVSLSSAAKRRARASVLVFSALFGAT
+ALADRIPAFRLSVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA
+PAERTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLERVADVVARAGDG
+HGWEVELARPSGAKPGALRVILPEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000819.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000819.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bce7215723ac108ced9da4a2391f08b21a34355c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000819.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_911
+MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQEAPLSVESTYPLVEAMAAMDLGAATIDLAELAAKHKASGQDVQAFLDAELAEVKGKA
+GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR
+DSIHGPFDGTIVVDEDRDVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD
+EGLSQHLQAKGAAKVLLTAPGKGEMKNIVFGVNSDDITPQDTIVSAASCTTNGITPVLKV
+IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAILNLELTTPTSVEELNARLKQESLTGPLRGQVGYVDSPEVV
+STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ
+A*
+>NZ_CP033200.1_639
+MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQQAPLSVESTYPLVEAMAAMDLGAATIDLAELAAKQKASGQDVQAFLDAELAEVKGKA
+GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR
+DSIHGPFDGTIVVDEDRDVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD
+EGLSQHLQAKGAAKVLLTAPGKGEMKNIVYGVNSDDITPQDTIISAASCTTNGITPVLKV
+IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAILNLELTKPTSVGELNARLKQESLTGPLRGQVGYVDSPEVV
+STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ
+A*
+>NZ_CP040019.1_1959
+MADTASTQTPEWNTQQELAERMVPLLGSLYRENNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQDAPLSVAATYPLVEAMAAMDLGAANVDLAELAARHKESGQEVQAFLDAELAEVKGKG
+GEGLGEPQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLVKRASLLRR
+DSIHGPFDGTIVVDEDRNVITANGTEIQVIYSNDPTTVDYTAHGIKDALVIDNTGRWRDD
+EGLSQHLQAKGVKKVLLTAPGKGEMKNIVFGVNSDDITPEDTIVSAASCTTNGITPVLKV
+IQDDYGIDHGHVETVHAYTNDQNLTDNFHKGSRRGRSAGLNMVLTETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAILNLELNKATSVEELNARLKQESLTGVLRGQVGYVDSPEVV
+STDFVGSDRAGVVDGLATLVNNEGKNAILYVWYDNEYGYSHQVVRVVSGPRPGRDQAPSA
+RPWSASGPCCSIASASSSSSCPKGSSSVPGSQVTPGTFMRSARCARFQRRCHLPSRRLT*
+>NZ_CP083691.1_1854
+MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQEAPLSVEATFPLVEAMAGMDLGAANIDLAELAAKQQASGQDVQAFLDAELADVTGKS
+GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR
+DSIHGPFDGTIVVDEDRNVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDV
+EGLSQHLQAKGATKVLLTAPGKGDMKNIVFGVNSDDILDEDTIVSAASCTTNGITPVLKV
+IQDEYGVQHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVITETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAIINIALEKPTSVEEINARLKQESLTGDLRGQIGYVDSPEVV
+STDFVGSDRAGVVDGLATIVNNEGKNAILYVWYDNEYGYSHQVVRVVEKMAGQQVPSFPK
+A*
+>NZ_CP097650.1_859
+MADTASTQTPEWNTQQNLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQEAPLSVESTYPLVEAMAAMDLGAATVDLAELAAKQKASGQDVQAFLDAELAEVKGKA
+GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR
+DSIHGPFDGTIVVDEDRDVIIANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD
+EGLSQHLQAKGAAKVLLTAPGKGEMKNIVFGVNSDDITPEDTIVSAASCTTNGITPVLKV
+IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAILNLELNTPTSVEELNARLKQESLTGPLRGQVGYVDSPEVV
+STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ
+A*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000824.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000824.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b85b4370d0f1904bc5f179ba27d6d85f9aba7a20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000824.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_927
+MTSHPRSPAPSRPSGRWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGLLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAALAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHIVALVWLMTTVVKDILDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGARDRLLLPPAGLGLQPLGESAGR*
+>NZ_CP033200.1_650
+MTSHPRSPAPSRPSGRWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGLLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAALAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHIVALVWLMTTVVKDILDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGAPDRLLLPPAGRGLQPLGGSADR*
+>NZ_CP040019.1_1893
+MRRAGLAPTPAPPGLPERETAPPEPAVAVRQGTWAAVLIMVGSWGVGWLPMTPDSVFSGS
+TLLNPLRVNLPGVLASTLLLASGSLLLVRAWLVLGRSLRGRWEGHGRLVSRAAWQWSAPL
+MLALPIFSRDVFSYLQQGRLFALGLDPYTQGVSALPGWFMQGADSIWAESPSPYGPLFLL
+CAEAIWRVTGGQIELSVTAFRLLALAGLALCLWAVPRLAEAAGRCGAWAAWVCVANPLFL
+LYMIAGVHNDALMSGLMLAGIVLMVRVPRRRLHALWGIVLIALSVAIKPLTALVLPFVGL
+LLPTGWDRFRRADPGLRRRDRLGPWITTAAIALAVLTILGAGSRLWFGWVPAMLTSGDAA
+FPYAPVGVLGLLLGAAADGLAGLPARAVAGGFYTLMTLAALGFGAWLALRRRAPEPVSAA
+AAVLFVAVVTAPIVQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTALAVLLLTGVGVV
+DQISVAQWLPVAAVRALTAVVVLAGIAWIVVRDPATAPLFPGRRRPPREVVEPREAVGPR
+EPGAPPGPPTAAPDAEFPPDALAADPDRRRRPAPDRRPARPGETVTSQPRRPADTRTGSA
+AAPPSPAALRPGPRWIGILVGLTAVAAVVGLLTKQWCRVNGWAAPGVHVHMCYSDFAQLF
+PTRGLSDGYFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPDSGDLHERTVMYFDVNALGV
+VLCWVVLVIATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAHRPT
+LAGLLIGLGTALKLYPLFFFGAILVLALRTGRWRGLITSLAAGVAAWLAVNVPFMLTAFD
+QWSRFYTFSGDRAVSFSSTWLSLAWTGWSGETFSTLQNGMFALFCAGIAWLGLSARHRPR
+MAQLCFLIVASFLLWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWMESA
+RITSGGAFADGAWWITAWYASGIVAHIVALVWLMVTVVKDILDPSRDPVRRTALAQGAPT
+IAPGVAEDPHAGVYAGAPDRLVLPPAGRGLQPAEGATSGS*
+>NZ_CP083691.1_1841
+MSSHPRAADAAPRPAAGLRPAGRPSPRWIGVLIAVTAAAAVVGLLTKQWCRLNGWATPGV
+HVHMCYSDFAQLFPTRGLSDGYFPFYTPLPEEQWMEYPALLAVVAGASSWLVPSTGTLAE
+RTVTYFDVNAAGVVLCWMAVVVATAFTARGRSKDALLVAVAPGIILTSMLNWDLWAVMLA
+ALALWAWSEDRPVLSGLLLGLGAAMKLYPLFFFGALLVLALRTGRWRGFLGALAAGAAAW
+LAVNVPFMLTAFDQWSRFYTFSGDREVSFSSMWLAFTWTGLSGSAFSVISNGLFALCCVG
+VAYLGLSSRHRPRLAQLCLLIVAAFLLLGKVYSPQFVMWLIPLVVLATPRRKQFWIWQAA
+EFFHWAGVWMESARITSGGEFGGTWVTVWYASGIVLHMATLIWICVTVIRDIRDPERDPV
+RRSALEQGVEPLAPGVAEDPNAGVFTGAADRFLLPPAGHGLQPTR*
+>NZ_CP097650.1_872
+MTSHPRSPAPTRPSARWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWFVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGMLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAAVAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHVVALVWLMTTVVKDVLDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGARDRLLLPPAGRGLQPLGESAGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000836.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000836.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab4328ad12bfa1173f00e9e59f8876679fa4cacc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000836.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_943
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLQIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA*
+>NZ_CP033200.1_667
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA*
+>NZ_CP040019.1_1879
+MTQFPAGLPTGTPSMPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGSQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIQAQEINRMRVWMEQTLASLTN
+RTPEEVSRDIDRDKFLSAEQALEYGLVDEVLASRKITRPAG*
+>NZ_CP083691.1_1823
+MTQFPAGLPVGTPSQAAPSARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGSQVDDAS
+ADDIMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHANEINRMRVWMEQTLASLSN
+RTPEDVSRDIDRDKFLSAEGAKEYGLVDEVLAPRKITRTGA*
+>NZ_CP097650.1_885
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000838.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000838.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26b068a74f954eedf182dfa09d22788193052bd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000838.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_945
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD*
+>NZ_CP033200.1_669
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD*
+>NZ_CP040019.1_1877
+MSENTQPVVDFYFDPTCPFAWITSRWILEVEKVRDIQVKFHQMSLYMLNEGRDLPEDYRR
+STDRGLIPGRGTQHVGAEHPERLAEWYTALGTRIHNEGQKDYEAALTGAAVDLGLDPAPI
+LAATETDAEDERLREKQRAAEELVGNDVGTPVVSFNGTAFFGPVLTRIPRGEEAGRIFDG
+AVALAEYPYFYEIKRARTTDPQFD*
+>NZ_CP083691.1_1821
+MSENTAPVVDFYFDPTCPFAWITSRWILEVEKVRDLSVTFHQMSLYMLNEGRELPEDYRR
+HTDRGLMPGRATLHVGEHHPELLSDWYTAVGTRIHNEGNQDYEAVVTGAAAELGLDAAPI
+LEATRTDAADDDLRAKQRAAEELVGNDVGTPVVSFDGTAFFGPVMTRIPRGEEAGEIFDA
+AVRLAQFPYFYEIKRARTTDPQFD*
+>NZ_CP097650.1_887
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000840.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000840.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b91f6dffeb193d9ff6ea9e7a0b48aa87aa8d9770
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000840.fa
@@ -0,0 +1,80 @@
+>NZ_CP042169.1_947
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLTRLAATVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVASLSFAASAGDAEVLPTVAQVLGGIRKAKSEAKVKQRTEVRSA
+VVTGPADWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPVDDD*
+>NZ_CP033200.1_671
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLTRLAATVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVAALSFAASAGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA
+VVTGPTEWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPVEDD*
+>NZ_CP040019.1_1874
+MAENTQGTDTPIDASTASTPAAGAVAVPDKPGLEGLEEKLTARWAQEGTYAFDPRTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMTGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPTKPYIEGYTPPAQPAKNQRDWDVVSRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWSMTYRTIDDVSRAVSQRAFLRNVAAGDAYLSEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYPFTAADGTQVFIETTRPELLASCSALVAHPEDERYQPLFGTMVRSPLFDVEVEV
+KAHELAKPDKGSGIAMVCTFGDLTDVTWWRELQLPTRTLIGRDGRFAAETPEWISSEAGR
+AFYAESIAGKTVFSAKEAVVTALTEAGLMDGEPKKVQHAVNFYEKGDKPLEIVTSRQWYI
+RNGGRDADRREQLIARGRELDWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYRL
+DAEGEPVYDEPIVPEDAALPVDPVAETAPGFTEDQRDQPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEEFFANVFPFDLRPQGHDIIRTWLFSTVVRADALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILEEFGSDAVRYWASSARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATRDAVVRTPDDAARVTNALDASLLARLATTVEQATAAFDAYDYARALNVTE
+SFFWQFTDDYVELIKDRAYGGHGEAEQASVVAALATTLDSLLRLLAPFQPFATEEVWSWW
+RTGSVHRAPWPGLESEAAGLRAAAEGGDPQVLAVVAQVLGRVRKAKSEAKVKQRTQVRTA
+TVRAAAAQLDALRGGLADLKGAGNVADVTLTEADGELEVTDIELAPAEEA*
+>NZ_CP083691.1_1818
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDDAFFSSVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLARLAVSVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVASLSFAASSGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA
+VVTGPAEWLEKLRGGLADLKAAGNIADLSLTQGEAGEAAPLTVSDVQLAPVEDD*
+>NZ_CP097650.1_889
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLARLAATVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVAALSFAASGGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA
+VVTGPADWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPAEDD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000845.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000845.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60e6185ba258ddb3efb88d2abd041e3522063306
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000845.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_952
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF*
+>NZ_CP033200.1_676
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIVREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAENEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF*
+>NZ_CP040019.1_1869
+MTLTHAPDPGTVSPAGPDVLDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPPIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF*
+>NZ_CP083691.1_1813
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF*
+>NZ_CP097650.1_894
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000847.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000847.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd4dad6139339d64ae3d8d110f1352647a39c088
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000847.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_954
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLVARLEAPTAGVV
+KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA
+H*
+>NZ_CP033200.1_678
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNIIARLEAPTAGVV
+KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA
+H*
+>NZ_CP040019.1_1867
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLIARLEAPTAGVV
+KAPRQGAAFMFQDAALFPWLTARGNIELALRFAGVPAAERRGRAGELLRLVHLGDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFGALDAITRDLLHVELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA
+H*
+>NZ_CP083691.1_1811
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLIARLEAPTAGVV
+KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVPAAGRRERAGELLRLVHLGDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHVELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAAHHDAPAAAALTAAITARLGQEIRRHA
+H*
+>NZ_CP097650.1_896
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLVARLEAPTAGVV
+KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA
+H*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000859.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000859.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69c8c9c47014d590c9f2d957f1e307ec73d14868
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000859.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_969
+MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAVAGRARKDAVLRHMAE
+ALRANTAAILTANREDRSRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV
+VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA
+VLIQVLREALVDQGFDANIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYVDASAPKQMAVDIALNSKTHRTSVCNAAETLLLHRDAEETGREVL
+RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLGQ
+AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQIRR*
+>NZ_CP033200.1_693
+MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAVAGRARKDAVLRHMAE
+ALRANTAAIITANREDRSRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV
+VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA
+VLIQVLREALVDQGFDANIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYVDASAPKQMAVDIALNSKTHRTSVCNAAETLLLHRDAEETGREVL
+RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLGQ
+AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQIRR*
+>NZ_CP040019.1_1853
+MENQESTAPQDQSAGQEAEAPSQEVVDAIRQRAEWARLAVPELATAGRTRKDAVLRHMAE
+SLRSNAAAIITANQEDRARGAEAGTSAALLDRLKLDEPRVEALALGLEALAALPDPVGAV
+VRGGTLPNGVRMTQTRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAQSTNA
+VLIQVLREALADQGFDPNVVQGIDDLGRPGVAALMATRGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYLDASAPKDMAVEIALNAKTHRTSVCNAAETLLIHREAEETGREVL
+RALMRGGVLLHVDEAAKAWLPGPTDRGDHARDAVDATEEDWGTEYLDMDMAVRIVDSLDQ
+AIEHIGRWSTGHTEAIVTNDLAAAEQFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQVRR*
+>NZ_CP083691.1_1778
+MTTEHTETEPAERVQQTPTPEQGASADGRPGADVVAEVRSRSARARAAAPELARAGRERK
+DALLRSMADAVRAAAASILAANAEDLARGEENGTSAAMLDRLRLDEPRLESLAVALEDLA
+SLPDPVGAVVRGGDLPNGIHMQQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNAVLLRG
+GSAAEHTNAVLIQVLREALRDQGFESDLVQGIDDLGRPGVAALMSTRGAVDVLIPRGGRE
+LIQRVVAEARVPVIETGEGNVHLFIDASAPADMAVDIALNAKTHRTSVCNAAETLLLHKD
+AERAGREVLRALTRAGVLLHVDEASRARLPSPADRGQDAREPQAASDEDWGREYLDMEMA
+VRTVDSIDEAMEHVRRWSTGHTEAIVTNDLANADRWVSEVDAAAVIVNASTRFTDGGQLG
+LGAEVGISTQRMHARGPMGLEELTTTKWVLRGAGQVRR*
+>NZ_CP097650.1_911
+MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAIAGRARKDAVLRHMAE
+ALRANTAAILTANREDRGRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV
+VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA
+VLIQVLREALVDQGFDPNIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYVDASAPKQMAVDIALNAKTHRTSVCNAAETLLLHRDAEETGREVL
+RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLDQ
+AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQIRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000860.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000860.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e396d46297394eded5fd6c15ba96b1bdf344c188
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000860.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_970
+MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ
+HHGTGRGSHTSGH*
+>NZ_CP033200.1_694
+MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ
+HHGTGRGSHTSGH*
+>NZ_CP040019.1_1852
+MLNTSLVLAAAEGPHVVNELPIPTVWYGIIVFALLMAALLATMSMRSRALRLPEPTTAVQ
+HHGTGHGSHTPGH*
+>NZ_CP083691.1_1777
+MLNSALVLAAAEEGHHVVNELPIPPVWFGIIVFLLLMAGLLAILSMRSVGLRHAEPTTAV
+QHHGTHGTGSHSAGH*
+>NZ_CP097650.1_912
+MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ
+HHGTGRSSHTSGH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000864.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000864.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4185c382f6dcaadd435b94d993ec23110dd904ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000864.fa
@@ -0,0 +1,49 @@
+>NZ_CP042169.1_977
+MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG
+ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP
+VAEKTDREMDRLIAKIDELTAEIDAAAPWEHPRAAELDKISFRHWLEQQSDDPEAIDNVS
+IYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKRVEGGMQSVSLAMAAELG
+DDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAV
+LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL
+VQEIYDNTNRGENLAGGAPGKEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL
+GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY
+QHVDGAIRMGEAAALAIAEREATDAGQPTG*
+>NZ_CP033200.1_701
+MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG
+ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP
+VAEKTDREMDRLIAKIDELTAEIDAAAPWEHPRAAELDKISFRHWLEQQSDDPEAIDNVS
+IYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKRVEGGMQSVSLAMAAELG
+DDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAV
+LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL
+VQEIYDNTNRGENPAGGAPGEEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL
+GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY
+QHVDGAIRMGEAAALAIAEREATDAGQPTG*
+>NZ_CP040019.1_1843
+MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG
+ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP
+VAEKTDREMDRLIGNIDELTAEIDAAAPWEHPRAAELDTISFRHWLEQESDDPEAIDNVS
+IYIASGMLTKPSHTFSMLQALLMAASAGSFRNLVDEDFILDQRVEGGMQSVSLAMAAELG
+DDVVLGQPVRTLRWTEPDPSTADEKNGVAADVRNGVAHDGDAGDVVALTDDYEVHARYAV
+LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL
+VQEIYDNTNRGENLAGGAPGEEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL
+GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY
+QHVDGAIRMGEAAALAIAEREATDAGQPTG*
+>NZ_CP083691.1_1207
+METPSDVIVVGAGLAGLVAARTLAEAGLSVRVLEREAEVGGRQRTRTVDGFVLDRGFQLV
+NPAYPELPRHADVDALGLRPFGAGVRVRTRRGLALLADPRREPRLAARTLRDGVRHGLLD
+ARELAALSRWAAPALAAPRVAKHRMDAPLIEAWDRAGVRGPLRDAVLEPFLRGVLADPDL
+TTSSRFTELLVRMFVLGTPGVPARGVAALPEQLAARVRAAGTRVTTGASVTAVRPAADGV
+VVDVAGGAPLHARAAVLAVGPEAFTGLLPEAATDRLPVPSRGLTTWWFRAPSAPARERFL
+AVDGTGSGPLVHTAVMTAAAPGLSPDGTPLVEATALLDPSAPAVTDAQARAHAARIWGVD
+ASDWDLLARDDVPHALPVQAAPLRLRAEARVAERVYAAGDHRDTASIQGALVSGRRVAER
+LLHELPR*
+>NZ_CP097650.1_919
+MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG
+ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP
+VAEKTDREMDRLIAKIDELTAEIDAAAPWEHPRAAELDKISFRHWLEQQSDDPEAIDNVS
+IYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKRVEGGMQSVSLAMAAELG
+DDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAV
+LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL
+VQEIYDNTNRGENLAGGAPGKEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL
+GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY
+QHVDGAIRMGEAAALAIAEREATDAGQPTG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000865.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000865.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f753b68059818cf278a7c7a5da8a71949515a79c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000865.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_980
+MYPTPMTFDVARAGRALAQVSARTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALLK
+YGVGLVPEDEFGGAGVRRIFSAEKSRRIKAMENEGGPAYEDDI*
+>NZ_CP033200.1_704
+MYPTPITFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALLK
+YGVGLVPEDEFGGTGVRRIFTAEKSRRIEAMENEGGPAYEDDI*
+>NZ_CP040019.1_1839
+MYPTPMTFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALRK
+YGVGLVPEDEFGGTGVRRIFTAEKSRRLEAMENEGGPAYEDDI*
+>NZ_CP083691.1_689
+MESQHISNGDMTRAARILVKVSAQYIAREANVTKEELRDFEKGRHDLSEKKQERVRAALE
+ELGAEFLPDGPNGGYGIRLKFGRSRIYSLERCEGEGGPRLTTESDRRTQAHVPFSEPDSN
+LPFHLEDRTTASLRILVPLRLGRLWPSHLASVPGMEARAR*
+>NZ_CP097650.1_923
+MYPTPMTFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALRK
+YGVGLVPEDEFGGAGVRRIFTAEKSRRLEVLENEGGPAYEDDI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000867.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c138b5cbf1189c43c74a213a4a669047463ed9b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000867.fa
@@ -0,0 +1,33 @@
+>NZ_CP042169.1_982
+MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRLELTTA
+GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALTEANSGRVAQALVAAGAGVAVVTEDP
+AFGLTPVRVIAQGRTLTVRLHAAWRGDHFAAETLEAIARRLQAFVRDRYAEPGDDAPGRG
+RSA*
+>NZ_CP033200.1_706
+MDEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRFELTTA
+GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP
+AFGLTPVRVIAQGRTLAVRLHAAWREDHFAAETLQALARRLQAFVRDRYAEPGDDAPR*
+>NZ_CP040019.1_1837
+MEERLLRAFVTVAEAGTVSAAAQRLDLVQSALSRQLQRLQRELRLPLFARVGSRLELTTA
+GEAFLPVARRVLAAHRQAEQAARTLASGSLAEVAIAAPGTTLIDVVLPFVATLDEDDPRP
+RVAETQLDDSLQDAVARHDLVVMPMAPGPTVQALHLIDLPVWAYVAPGHPWADRADVALE
+ELVDVRVVAPSRSFMARRVLDGAVAVAGLTAPELSEANSGRVAQALVATGAGVAVVTEDP
+AFGLVPLRVLLDGRALSVGLHAAWRADHFAAATLARIAASLQDFVRTRYPQPGPADDIPV
+TTRASPLSAAPSQ*
+>NZ_CP083691.1_1726
+MDSIAAGGRALDLDHLLDPALLRTFVAVVDEGTVTAAARELGLGQSALTRHLQRLQRDLG
+LALFAPEGARLRITPAGQAWLPVARSLLAAHAHARQAARILAAGRLTELSLGAPGTTLID
+VVIPFLTVLGEGDPAVRVTETQLDDSLQDSVARLDLVVLPSTPPDDVAALPLQSMPVWAC
+VAPGHPWADRDELDAAELAGARLVLPSRSFKARRVFDAALEVAGAAPRQVVEANSGRVAQ
+ALAANGTAVAVVTEDPAFGLRPLPIRAGGRRLEVHLHAVWRRDHFAAEEIAGVAAQLRVF
+VRRRYDVAEAQDDADGSLSRAVSVD*
+>NZ_CP097650.1_925
+MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVGGRLELTTA
+GEAFLPVAREVLVAHRRAEQAARTLASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP
+AFGLTPVRVIAQGRALAVRLHAAWREDHFATATLEKIARRLQAFVRDRYAEPGDDAPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000869.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000869.fa
new file mode 100644
index 0000000000000000000000000000000000000000..896646724249059cdcf3e433452a5f124d0304be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000869.fa
@@ -0,0 +1,33 @@
+>NZ_CP042169.1_984
+MSRADIAPARVRPRRWSVAVGGALLSITLATGGCSVAEEPGQTGGTEAGNTYLEGVLASP
+SQTSADPLAADIQFAGLLLRNHRDAIQQSDQVLGKDGVDQEIRATAERMKSEHEERAGRL
+ESMLEGWGVPSDDVRGAGAESTPSAQPESTEDAEPTQIVGDELRAGLLSDREKNVLAAAE
+PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLGEM
+GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRSFRATQKPVLPSSSS
+PSSSSASGSASASGRDAEDQRGRDAASASPSPSPADTAQATPRPSSGASPSPSASR*
+>NZ_CP033200.1_708
+MSRADIAPARVRPRRWSVAVGGALLSITLATGGCSVAEEPGQTGGTEAGNTYLEGVLASP
+SQTSADPLAADIQFAGLLLRNHRDAIQQSDEVLGKDGVDQEIRATAERMKSEHEERARRL
+ESMLEGWGVPSDDVRGAGAESTPSAQPESTEDAEPTQIVGDELRAGLLSDREKNVLAAAE
+PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLGEM
+GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRNFRATQKPVLPSSSS
+PSSSSASGPASASGRDAEDQRGRDAASASPSPSPADTAQATPRPSSGASPSSSASR*
+>NZ_CP040019.1_1835
+MPVTGDELRAGLLSEREKNVLAAADAEDAGRIYLLQMHRVYQGALTISATEAESGTDEEA
+KALAASVVADHQEDMQRMVEVLADMGAIGADASHTALPSGYTGPIKIEGTGADGGPVPSD
+FVPEPVQRVQSFRATQRPVLPTSSSPGDAEDRRGRDSATASPSPTPADTARPSPSPSSAA
+SPSPSATTGSPSGTNR*
+>NZ_CP083691.1_1728
+MNRATDATAPVCPVRWSAAAGGLLGLSLVLAGCGTSAQPVPAGSGSNTYLEGVLATPSAT
+KADPLAADQRFVASLLQNQYQVVQEADHVLSRPDMDGEVRDMAQQHKDVANQRIGDLSSR
+LQAWGLEVPAAPEPLVDDTKPSGRPTGDPSEIQASKGQQAAADIRAGLLTASDQSALVTA
+DDDAAGRIYLLQVHRLLQGGVSLAGTESDEGTDEETKKIASDLIDADRPRMQRILEKLGE
+NGVVAAVPSPTAPNSGYQGPISLPSQAGGDGANVDYTPSALYEMWSTLPPPATSSSADGS
+STGPSPSAQPTPTPADTASPRPTPGASAQPGAASSTASTTGAASTRNG*
+>NZ_CP097650.1_927
+MSRADIAPARVHPRRWSVAVGGALLSITLATGGCSVVEEPGQTGDTEAGNTYLEGVLASP
+SQTSADPLAADIQFAGLLLRNHRDAIQQSDQVLGKDGVDQEIRATAERMKSEHEERAGRL
+ESMLEGWGVPSDDVRGAGAEATPSAQPESTEDAEPAEIVGDELRAGLLSDREKNVLAAAE
+PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLAEM
+GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRNFRATQKPVLPSSSS
+PSSSSASGSASASGRDAEDQRGRDTASASPSPSPADTAQATPRPSSGASPSPSASR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000876.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000876.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a4301a1b670b3a38f22516e58656dcae6e65eb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000876.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_994
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLNGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL*
+>NZ_CP033200.1_719
+MTDITSTPATSVAGDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLDGVVLPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHAEQTLTLRSWPAEGGL*
+>NZ_CP040019.1_1820
+MTDISSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQEHNALDGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVVGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL*
+>NZ_CP083691.1_1707
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQAHNALHGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+PWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL*
+>NZ_CP097650.1_937
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000879.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000879.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8685a32a401d81bdc361c93102451f772ce4446d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000879.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_999
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPALLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLLSLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH*
+>NZ_CP033200.1_722
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLLPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH*
+>NZ_CP040019.1_1817
+MARIDHLVTSGTFSLDGETFDVDNNVWLVGGAEQCIVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGGATGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH*
+>NZ_CP083691.1_1704
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH*
+>NZ_CP097650.1_940
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDAVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000884.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59d71386a3ea98ad9d3cbaad3bab4cbce12adf20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000884.fa
@@ -0,0 +1,109 @@
+>NZ_CP042169.1_1008
+MSQAAAAGRTAAPFAHLHVASAFSAHHGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDGDAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPSTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALHRWKAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVAFAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRERTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYHAVVERFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDATLLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSLD
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEIDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQLALDLPDTELTALAPLFPDPGPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGDRAVSVQAVRAWDLHRPETLPDPDY
+LDATRQQWRDWLAADRRAAAARRSSRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR*
+>NZ_CP033200.1_731
+MSRAAAAGRTVAPFAHLHVASAFSAHYGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDEDAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPPTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALHRWKAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVASAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRARTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYHAVVERFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDAALLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDDATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSPE
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEVDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQMALDLPDTELTALAPLFPDPAPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGGRAVSVQAVRAWDLHRPQTLPDPDY
+LDATRQQWRDWLAADRRAAAARRSGRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR*
+>NZ_CP040019.1_1813
+MGLRRRARRRRGSSRVPTAANRDNPPTPELFVLVGPDADVGRHLARRRSAAGLAALRRWK
+EALPAGSLHADVVTHLSTPGRRLDAGHAVKALRTARRAGVPAVLTNAVRYAGPDGAATAD
+VLDAVRALSSLDAVHDLQPNGQGWLKPTAAMHRVAHEVASAADERAAPLLEATRRLAEAC
+VLDPEADLGWGVPRVPEAAVIGIEGPPERVLRERTYAGLAARYPRLHAGGRLTSAAEARD
+LEARAEHELGIITRLGFSSYFLTVAAVVDLIEGMGVRVAARGSGASSLVNHALRISNVDP
+VANGLIMERFLSDARSTLPDIDIDVESARRHEIYRAVFERFGAERTTLMSMQNAYRARGA
+VRDAGLALGMPEPEVDGIAKQLWRFSASSFREALERMPELGGLSRRIESGRAEGSRQLDL
+LVDLTERLDRLPRHISMHPCGVILGDAALLHRTPVQPSGMGLPMSQFDKHDMDPMGFLKL
+DILGVRMQSAIAYTLAEVERTTGERVDLEQVPLDDPATYAMIRTTHTLGCFQIESPGQRE
+LVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPARYPHPDLRPVLAETHGV
+TVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHRVEEAFRAGALARGYSLDVIDEVWA
+TLAAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPEAFMAAILEHDPGMYPARLMVAEARRM
+GIPVLPVDVNASSRHVRVEWVPWHPELDGPPAEDAGAGGGEPGDVVARPHAEGGAEADLA
+EGAGRGPGRWGIRLPLTGLSGLSEAETERLDAGRPYRSLADVRDRARPTARNLERLAQLG
+ALDCLLPAGGASRTDLVHHLELQHSATRGSGPGRAAARSRSARPRQVDGQLALDLPDTEL
+AALTPLFPDPSVAARVRTELELTALDVTAHLMDSHAPYLDALGVTRAADLLGLRTQSRVL
+VAGVRVATQTPPMRSGKRVVFLSVDDGTGCVDASFFTEAQHASGEMLFSARLLLIEGTVR
+RTGPRAVSVQAVRAWDLHRPESLPDPDYLDATRRQWREWLAADRRAAAARRRGQEDAGAP
+RLPDIPHHGTGGWPVKVALGGAGAPSPSSDARAPAGRGVSAGAGPGAAGQGAAARVGAGG
+VPADRRPIPVPHPDTWELLPTPER*
+>NZ_CP083691.1_1697
+MSAFPHLHVASAFSAHHGVSWPADLAAAAAAADMDLLACTDRDGLYGTVKHVGACLARRI
+TPIVGVDLAVRWDEDEPAGRVVVLARGGCHGTGYRALCRLVSAAHARTAGGAAGGAPWVL
+VAEVAAAAAGPIPTGANPGNPPTPELFVLVGPDSDVGRHLARRRTAAGLAALRRWRAALP
+AGATRAEVVSHLSAPGRRLDTGHAVKMLRTARTARVAPILTNAVRYAAPDGAATADVLDA
+VRALSALDAVHDLQPNGQGWLKPTAAMEALAAEIAHAADEHPAALLESTRALAEACALDP
+ETDLGWGRPRVPEASVVGTVGDPRQVLRERTRAGLAARYPHLHTGAGLPGTTQAARDLQD
+RAEQELGIIDRLGFAGYFLTVAAVVELIEGMGVRVAARGSGASSLVNHALRISHVDPMAN
+GLIMERFLSDARSTLPDIDIDVESARRHEIYRAVVDRFGAERTTLMSMQNAYRARGAVRD
+AGLVLGMEEDEVDGIAKQLWRFSASSFRDALDRMPELSSLAARIDAGRAAGRHQLDLLVD
+LTERLDRLPRHISMHPCGVILSDAALLDRTPVQPSGMGLPMSQFDKHDMDPMGFLKLDIL
+GVRMQSAIAYTLQEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQIESPGQRELIG
+KLEPREFNDLTVDISLFRPGPMQSDMVRPFLEHRHGWAPAHYPHPHLEPVLAETHGVTVF
+HEQVLRTLDVMTGCGLARADELRRLVGGPEEHRVETFFRTAALENGYSLDVVDEVWHTLH
+AFGSFGFCKAHGAAFAVPTYHSAWLKTHHPEAFMAAVLEHDPGMYPARLMVAEARRMGIP
+VLPVDVNASTRHVHVEWVPSHPEVDGADPTTDPATGAPGRWGIRLPLTSLSGLSAAEVDR
+LDAGRPYATLADVRDRARPTARSLERLAQLGALDSLLPAGGASRTDLVHHLELQHSATRS
+TDPGRTARRSRTARPRQVDGQLALDVPDTELTALTPLFPEPSRDAAVRTELDLTALDVTA
+HLMDSHAPYLDALGVTRAEDLLSLRSQSRVLVAGVRVATQTPPMRSGKRVVFVSVDDGTG
+CVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGARAVSVQGVRAWDLHRPERLPDPDYL
+DATREQWRAWLAADRRAAAARRRGETPVGAVPDIPHHSTGGWPVKVRADVAVGRERAAVE
+RPAPAPSSRPIPVPHPETWELLPTPES*
+>NZ_CP097650.1_948
+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_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000886.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000886.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8be188ac7c85b15200c8d5810e2e16a997f41ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000886.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1010
+MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT
+CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA
+ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETRQILADVWDRAAQDHAARQAANARAAGEHPRPGAGGPA*
+>NZ_CP033200.1_733
+MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT
+CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA
+ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETRQILADVWDRAARDHAARQAANARAAGEHPRPGAGGPA*
+>NZ_CP040019.1_1810
+MTRPEASDADARDLARASADASATDGFALPGAPDAFERFWNAHRMAYVTQGSDQVKDEHT
+CPFCAAPQRSDEASLIVHRGRAAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTAEEAAEMA
+ELTQTAMLALGHATRAAGYNLGMNQGSVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETREILAGVWDEAAADHARLQEANARAAAERAGRRDEDRP*
+>NZ_CP083691.1_1695
+MTTTPHDDAAEVSADGAPAGERPYGDPAADAAALDGFELPGTPDAFDRLWNPHRLAYIQK
+GPEQVKDEDTCPFCAAPGRDDASALIVHRGATCFVILNLFPYNPGHLLICPYRHIPMYTD
+ATAEETAELADLAQTAMIAFELATRPKGYNLGMNQGVAGGAGIAAHLHQHVVPRWTGDGN
+FLPIIAQTKNMSQTLGQTREILADVWPQALAEHAERRARNAAAAAQAPRADA*
+>NZ_CP097650.1_950
+MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT
+CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA
+ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETRQILAGVWDRAARDHAARRAANARAAAEHPRPGAGDPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000887.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000887.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b6134ee25f2fe738d34e2e337ad344f5712a33f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000887.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1011
+MLDRHARDLTTRLFTPVAHTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT
+AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG
+ACLALGMLVSYVRAKAEALGWSAHVGIAERAERLVAALVVAGLTGLGLPPVVLAVTLGLL
+AAASLVTVGQRMAAVRRQARDDA*
+>NZ_CP033200.1_734
+MLDRHARGVTTRLFTPVARTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT
+AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG
+ACLALGMLVSYVRAKAEALGWDAHVGIAERAERLVATLVVAGLTGLGLPPVVLAVTLGLL
+AAASLVTVGQRMVAVRRQARDDA*
+>NZ_CP040019.1_1809
+MLDRHARGATTRVFTPVARALLRAGVSPDAVTVVGTLGVSLGALVLFPLGELFWGTLFIT
+AFVFSDLVDGIMAREAGTTGRWGAFLDSTLDRVQDAAVFLGLSLWGFGVGGEPAVGTLAA
+VCLALGMLVSYVRAKAEALGLTANVGIAERAERLVAALVLAGLTGLGLPPAFLAATLGLL
+AAASLVTVGQRVAAVRSQTRRAA*
+>NZ_CP083691.1_1694
+MLDRRARGTTTALFTPLARRLLRAGVTPDAVTVAGTVGVSAAALLLYPAGHLFWGTIVIT
+LFVFSDVLDGVMAREAGTTGPWGSFLDSTLDRVQDAAIFLALSWWGFGVGAHPAVGVLAG
+VCLALGMLVSYARAKAESLGFTAAGGIAERAERLIVTLVFAGLTGLGLPSAVLTAVLGLL
+ALASLITVAQRVAGVRRQSRTA*
+>NZ_CP097650.1_951
+MLDRHARGVTTRLFTPVARTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT
+AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG
+ACLALGMLVSYVRAKAEALGWDAHVGIAERAERLVATLVVAGLTGLGLPPVVLAVTLGLL
+AAASLVTVGQRMAVVRRQARDDV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000891.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000891.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0fb82b3ef5949934fd5849f5435eef9b0355e0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000891.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1015
+MAQIVHLADRSPQVTPDQLLAGFHPSYRFGTVSFDTYIPDPAHPTQAQAVERLRRFAADL
+GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT
+NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG
+SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAAVEATAQENFPD
+AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD
+KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK*
+>NZ_CP033200.1_738
+MAQIVHLADRSPQVTPDQLLAGFHPSYRFGTVSFDTYIPDPAHPSQAQAVERLRRFAADL
+GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT
+NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG
+SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAVVEATAQENFPD
+AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD
+KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK*
+>NZ_CP040019.1_1803
+MAQIVHLADRSPQVTPDQLLAGFHPSYRFGEVSFDTYIPDPAHPSQAQAVERLRRFAAAL
+GRGSGSGGGFLSGLFGGGRKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVE
+YTNLVGALSFRKAVDVLKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVHLVATSNTL
+PGSLGEGRFAAQDFQREIQVLAEQFEVIRVDGEDYRHRGLSAAPDPLPDDQVVSTAEANF
+PDSGVLAVDDFDALTAMLSRVHPSRYRELVKDVDVIALHDVKTITEQATALRFVVFADRL
+YDKDVPVVASGVPFDDLFTQEMMHGGYMKKYFRTVSRMTALVREGQLGIAEEK*
+>NZ_CP083691.1_1690
+MPQTVHLADRSPQVSADQLLAGLHPSYRFGEVSFDSYIPDPAHPSQAQAVERLRRFAASL
+GGPRGGSGGGGFLGGLFGGGRKRGPEPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTF
+VEYTNLVGALSFRQAVDVLKGYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSN
+TLPGSLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPEPLADDAVESTAQA
+NFPHADVVSVDDFAALTAMLSRVHPSRYRELVKDVDVAAFHDVQTITEQATALRFVVFAD
+RLYDKDVPVVASGVPFDQLFTSEMMHGGYMKKYFRTVSRMTALVREGQTGETVEK*
+>NZ_CP097650.1_955
+MAQIVHLADRSPQVTPDQLLSGFHPSYRFGTVSFDTYIPDPAHPSQAQAVERLRRFAADL
+GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT
+NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG
+SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAAVEATAQENFPD
+AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD
+KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000892.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16ce85fc754c5aa242d3ccf69b46a2e7a5d2b3b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000892.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_1016
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPVSAATGLQAVRAAAFGGGSHAAPAVAPDGLS
+SRPASAEGGDRVTA*
+>NZ_CP033200.1_745
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPVSAATGLQAVRAAAFGGGSHAAPAVAPDGSS
+SRPASAEGGDRVTA*
+>NZ_CP040019.1_1802
+MTQPRLAHQTPLGRMYARSLTGLPEVPSITTVIGMERTDLDGWIGWMAAQSVTQDPRLAE
+SVGSAARLKQVARQSADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTLAETRAKLIE
+HGEGAYADRFDEWWDLYDVRPLAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTG
+RDGRVKALDPKVVMQLTAGLKAEESLVDAEAGTWEEWRHGQAEMLLGVALGETEVAVHQA
+NPGVLPRHWHKFWALRQVWKHAQAADDAGPALRVIGPPPPSVPLHRG*
+>NZ_CP083691.1_1689
+MYARSLSGLPEVPSITTVIGMERTDLDGWVGWMAANAVAQDPRLGESLGSPARLRQVAKQ
+SADAAARYRDAAAERGDRVHDYAEQVALRALGRPHTMAASREELQRHGEGAYADRFDEWW
+DLYDVQPVAAEITVWNHSVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDAEAGTWEPWAHGGAEMLLGVALGETEVAVHQANNAALPRHWHKFWA
+LRQVWKHALAVDDAGPALRVIGPPPVSVPGAAGGLSAARAAAFGAPPAVAHDPGTSAPAD
+RLQP*
+>NZ_CP097650.1_962
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPASAATGLQAVRAAAFGGGSHAAPDVAPDGSS
+SRPASAAEGGDRVTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000893.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000893.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87117676a4d64bd178a80875a186568e63d3632f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000893.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1017
+MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPGAPAAGTGAAR*
+>NZ_CP033200.1_746
+MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPAVPAAGTGAAR*
+>NZ_CP040019.1_1800
+MSVLPVRTVPDPVLRTPARPVPAGMDVRALVADMVETMHAVGGVGLAAPQVGVGLRVFVF
+DVQGVAGHVVNPVLETGEETVREPGEGCLSVPGLRYHPARAAEAVVRGVNVDGHPVEHRG
+TGLVARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRTARRVGAERAAAVGSVF
+AAPAAPPTPARAPRGGTR*
+>NZ_CP083691.1_1688
+MTVLTLRTVPDPVLRTPAAPVAAGQDVRALVEDMVETMHAVGGVGLAAPQVGVGLRVFVF
+DCAGASGHVLNPVLETFGSPVREPGEGCLSVPGLRYHPARAERAVVRGVDVDGNPVEHRG
+EGLLARCLQHETDHLDGILYVDRLDGDDRREARRRLRADAPDPEAERIRARRDALAGSVF
+GARPSVSPSAARTTPRRGAQ*
+>NZ_CP097650.1_963
+MTVLPVRTVPDPVLRTAASPVPAGADVRALVADMIATMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPTRAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPAVPAAGTGAAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000894.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000894.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8144d63e800506c015a3f17b89f9f2d63f2ca2ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000894.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1018
+MTAPTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRRVLTPSPVAVVAEE
+ARLPVLKADRLRGPEGADALQAIRALEADVAVVVAYGALVPAEALQTPRHGWLNLHFSAL
+PAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVAADETAGTVLTDLAER
+GGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPAAEVAARINGVTPEPG
+AWGWLTADDGAAPARFKLDGVAPVRAGDDGWPSVLDAAVPGQILVAAKAAWLRTAGGAVR
+LSRVQPAGRKLMPAADWARGAAAGAALLAGEALAHHEEQARRDAAARAAARQAARNATEQ
+DEEARA*
+>NZ_CP033200.1_747
+MTAPTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRRVLTPSPVAVVAEE
+ARLPVLKADRLRGPEGADALQAIRALEADVAVVVAYGALVPAEALQTPRHGWLNLHFSAL
+PAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVAADETAGAVLTDLAER
+GGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPAAEVAARINGVTPEPG
+AWGWLTADDGAAPARFKIDGVAPVRPGDDGWPTALDAAAPGQILVAAKAAWLRTTDGAVR
+LSRVQPAGRKLMPAADWARGAAPGAALLAGEALAHHEDQARQEAAARAAARQAARNATAQ
+DEEARA*
+>NZ_CP040019.1_1799
+MTATTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPIGRRRVLTPSPVAVVAEE
+AGVPVVKADRLRGPAGEPALEAVRALEPDVAVVVAYGALVPAEALALPRHGWLNLHFSAL
+PAYRGAAPVQRAVMAGEPEIAADVFQLEEGLDTGPVHARLTRAVAPDETAGQILADLAER
+GGPLVLELLGRIADGTAAPRPQEGEPSHAPKLTAADGLVDPARPAAEVAARINGVTPEPG
+AWGWLTVGEGGEPARFKLDGVAPATPADADWPADLDAAPPGALRTAGRAAWLRTADGAVR
+LGRVQPAGKKLMPAADWARGAADGAALLAGEALAAHTARLGQEAAARAARREAARETEAH
+A*
+>NZ_CP083691.1_1687
+MSIPETALSPDAGSAPARSLRVLFAGTPEAAVPVLRALVGSAHEVAGVLTRTDAPVGRKR
+VLTPSAVARAAAESAPDVPVLKADRLRGPEAAEVLEAIRALEADVAVVVAYGALVPAEAL
+TIPAHGWLNLHFSHLPAYRGAAPVQRALMDGVERTGADVFQLEEGLDTGPVFARIGRDVA
+PEDTAGDLLAALAEDGGPLVLEVLDALAAGEARSVPQTGEPTHAPKLTAADGLVDAAAGT
+REVAARINGTTPEPGAWGWLVPAGEADAAPARLKLGGVVPTHPGEDGWPEAAEAAAPGAI
+VAAGGTAWLRTAGGAVRLDQVQPAGKKPMSAADWARGLTAPVRLLAGDELAAHLAALDAE
+AARRAAQQAAARAAQAGEGA*
+>NZ_CP097650.1_964
+MTAPTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRRVLTPSPVAVVAEE
+AGLPVLKADRLRGPEGADALQAIRVLEADVAVVVAYGALVPVEALQIPRHGWLNLHFSAL
+PAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVAADETAGAVLTDLAER
+GGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPAAEVAARINGVTPEPG
+AWGWLTADDGAAPARFKLDGVAPVSAGDDGWPSALDAAAPGQILVAAKAAWLRTAGGAVR
+LSRVQPAGRKLMPAADWARGAAAGAALLAGEALAHHEEQARREAAARAAAREAARNATAQ
+DEEARA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000895.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000895.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ef7c2cbfbe87f8965b4ca0558571a221de049ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000895.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_1019
+MSREGQAGQGRGERGARGERGRAPRPDPQDRRDAQGRTRNRGRSGAGRKYSAQAPSQRSR
+TADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDA
+ILTRCVDRPLEQIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNA
+VLRRVAERPLEEWLADVAPADGGDAALAVRASHPVWIVRALRQALAAHRGTRHIADRDAE
+LAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSALHSGGDAGRLPGVR
+EGVLRVQDAGSQLTARALAQAPVPAAEGRAERWLDLCAGPGGKAALLAALAAERGATLVA
+NEVAPHRADLVRQALAAVPADAWTVRTGDGRTIADAPEAAPAFDRVLVDAPCTGLGALRR
+RPESRWRRTPADLAELTGLQAELLDAAVSVLAPGGVLAYVTCSPHVAETVVQVQDLVRRH
+PELELLDARTALDTVALDDLRLDEAEPAGAPKPGDVVARTAQLWPHRHGTDAMFLALLRA
+PGA*
+>NZ_CP033200.1_748
+MSRERQPGQGRGERGARGERGRAPRPDAQDRRDAQGRTRNRGRSGAGRKYSAQAPSQRSR
+TADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDA
+ILTRCVDRPLEKIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNA
+VLRRVAERPLEEWLADVAPADGGDAALAVRASHPVWIVRALRQALAAHRGTRHTADRDAE
+LAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSALHSGGDAGRLPGVR
+EGVLRVQDAGSQLTARALAQAPVPAAEGRAERWLDLCAGPGGKAALLAALAAERGATLVA
+NEVAPHRADLVRQALAAVPAGAWTVRTGDGRTIADAPEAAPAFDRVLVDAPCTGLGALRR
+RPESRWRRTPADLAELTGLQAELLDAAVAVLAPGGVLAYVTCSPHVAETVVQVQDLVRRH
+PELELLDARTALDAVALDDLRLDEAEPAGAPEPGDVVARTAQLWPHRHGTDAMFLALLRA
+PGA*
+>NZ_CP040019.1_1798
+MSGEGQGRQGRGRGGSGGGSRGGAGGGSRGGSRNGSGGGPRGGSHGGPRGGSGGARRESG
+GEERRDAQGRTRSRGRSGAGRRYSAQAPAQRSRTADPARRVAFEVIRAVHAEDAYANLVL
+PGRIRQARLDRRDAGFATELAYGTLRGIGLYDAVLARCVDRPLEKIDPPVLDALRLGAHQ
+LLAMRVPAHAALDATVALVRAEIGAGPSGFVNAVLRRVAERPLEDWLADVAPAEGGDAAL
+AVRASHPVWIVRALRQALAAHRGTRHVADRDAELGALLEADNASPVVNLVALPVPGGREG
+LSAALEDGAEPGPLAPDSALHAGGDAGRLTGVREGVLRVQDAGSQLTARALAAAPAAAAE
+GRPERWLDLCAGPGGKAALLAALAAERGATLVANEVAEHRAELVRQALGAVPAAAWTVRA
+GDGRAIADAPEAAGGFDRVLVDAPCTGLGALRRRPESRWRRTPADLAELTGLQSELLDAA
+AAVLAPGGVLAYVTCSPHVAETTVQVQDLLRRRPELELLDAGAVLSEVALGDLRLDEGEP
+GGDEAAGAAAPDDVAARTAQLWPHRHGTDAMFLALLRAPSDTPESPERTRG*
+>NZ_CP083691.1_1686
+MSAGQDGSTGRGAGQGGRGRGGAEGRQGPGGRQGAGGQDRRDAQGRQLNRGASGTGRHRT
+TLAPKERARRADPARRVAFEVVRAVHAEDAYANLVLPARIRQGRLDRRDAGFATELTYGT
+LREQGLYDAVLARCVDRALDALDAPVLDALRLGAHQLLGMRVPAHAALDATVALVRAEVG
+AGPAGFVNAVLRRVSERPREDWLAEVAPADGGDTARAVRHSHPAWIVRALRQALAGHPGT
+ADVEDRDAELEALLVADNAAPVVNLVGLPVPGGREALASALGDGAEPHPLTPDAALHAGG
+DAGRLPGVREGVLRVQDAGSQLTARALAAVPAASGRDAGGRKAERWLDLCAGPGGKAALL
+AALASERGATVLANEVAPHRADLVRSALAGVPASAWEVRTGDGRTIAEDAPAGGFDRILV
+DAPCTGLGALRRRPESRWRRTPADLAELTGLQAELLDAAVGVLAPGGVLAYVTCSPHVAE
+TLVQVQDLLRRHPVLEQLDAPAALQDVAVADLGLAAPEDADPVLARTAQLWPHRHGTDAM
+FLALFRAPVA*
+>NZ_CP097650.1_965
+MSRERQPGQGRGERGARGERGRAPRPDPQDRRDAQGRTRNRGRSGAGRKYSAQAPSQRSR
+TADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDA
+ILTRCVDRPLEKIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNA
+VLRRVAERPLEEWLADVAPADGGDAALAVRASHPVWIVRALRQALAAHRGTRHIADRDAE
+LAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSALHSGGDAGRLPGVR
+EGVLRVQDAGSQLTARALAQAPVPAAEGRAERWLDLCAGPGGKAALLAALAAERGATLVA
+NEVAPHRADLVRQALAAVPADAWTVRAGDGRTIADAPEAAPAFDRVLVDAPCTGLGALRR
+RPESRWRRTPADLAELTGLQAELLDAAVAVLAPGGVLAYVTCSPHVAETVVQVQDLVRRH
+PELELLDARTALDAVALDDLRLDEAEPAGAPKPGDVVARTAQLWPHRHGTDAMFLALLRA
+PGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000897.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000897.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3dc532a20a55bb8124ec453056b9d9f8328cbe0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000897.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1021
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWARWRQARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR*
+>NZ_CP033200.1_750
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWARWRRARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR*
+>NZ_CP040019.1_1796
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARKVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWVRWNEARRGRSEHATAITPEWAGLGGRAFL
+VLGMLIGTLALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLVWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLVGFFVWLRAKDRDKPAVETLLPDGPEEHAAR*
+>NZ_CP083691.1_1684
+MQWLVDVFNWTIPVAGGGLLMREVVGNVFGLASALGGMARKVWAWPVGILGNLLLLTVFL
+ASLFNDAPHATLLGQAGRQVMFIAVSVYGWKRWRDAQRGRADHAPAITPEWAGWGNRAFL
+AVALVLGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSSGYYASAVMYAFYGVFTLTGFFVWMRARDRDKPAVETLLPDGPAPEEAAR*
+>NZ_CP097650.1_967
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWVRWRQARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000899.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000899.fa
new file mode 100644
index 0000000000000000000000000000000000000000..108ea3aff13e1b5f967b5062007b55ea5eac7b77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000899.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1025
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TEQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD*
+>NZ_CP033200.1_754
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD*
+>NZ_CP040019.1_1793
+MAVVAAQWHTEIMDGLIAGARAAAADLGLEPVLVRVPGTVELSVAAARLAEDFDAVVVLG
+VVVRGDTPHFDYVCQAVTQGVTEVSVRTGTPVGFGVLTVDTEQQARDRAGLPGSREDKGR
+ESLEAAVLTELALRDVQA*
+>NZ_CP083691.1_1680
+MSGAGAPTLALTTLTDADRAAAGSLRVAVVAAQWHTEIMDGLIAGSRAAAADLGIDVDLV
+RVPGTVELSVAAARLAATHDVVVVLGVVVRGGTPHFDYVCQSVTQGVTEVSVRTGVPVGF
+GVLTVDTVEQARDRAGLPGSQEDKGREALEAAVLTELALRAALG*
+>NZ_CP097650.1_971
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000906.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000906.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6ec63cad48ce6dfba317e6113f9a5028863a90f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000906.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1043
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGVALMAVGVVVGIVAGKAGAGRGQHGH*
+>NZ_CP033200.1_772
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGLALMAVGVVVGIVAGKAGAGRGQHGH*
+>NZ_CP040019.1_1785
+MSHTANTEHTTRRAARNGAVEDVVVTEDGRVLNDPTHLELPDHGNTPGGWAMVALVLVGF
+VAGCIGLLADWMIVVWIGVALIVVGVLVGIVAGRGGSARSGHRAH*
+>NZ_CP083691.1_1671
+MSHTEATVNHTAQAGAHAAGHTTGHTASREVVVTEDGRVLNDPTHAKVPGHGNSPAAWAM
+AGLVVLGFLAGCIGLLNDALVIVWIGVAVIVVGVLVGIVGGKAAGRSDH*
+>NZ_CP097650.1_991
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGLALMAVGVVVGIVAGKAGAGRGQHGH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000908.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000908.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95d25090e87f3cf03595aac48391596601204cef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000908.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1045
+MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEEARQDPAFEA
+ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG
+ARTLKDAINEALRDWVASVDTTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR
+LPDAVAACVGGGSNAMGLFHGFLDDPGVELYGFEAGGEGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGQERIIIVNLSGRGDKDVATAAAWF
+GLGTATEEKDPLEEMTPGEEQ*
+>NZ_CP033200.1_774
+MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEQARQDPAFEA
+ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG
+ARTLKDAINEALRDWVASVDNTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR
+LPDAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGEGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGEERIIIVNLSGRGDKDVATAAAWF
+GLGTAAEEKDPLEEMTPGEEQ*
+>NZ_CP040019.1_1783
+MSADRPSTEPTVEFEGPYQGQSGPYFGDYGGQWMPESLMAALQEVQRTYEEARQDPAFEG
+ELRTLFRDYVNRPSLLSDVPRFAADSPGVRIMLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG
+ARTLKDAINEALRDWVASVDTTHYLLGTVTGPHPFPAMVRYFHSVIGEEARQQVLAQTGR
+LPHAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGDGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLNDTGRAVYEPVTDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDTPEGEERIIVVNLSGRGDKDVATAAAWF
+GLGQADAEKDPLEELTPGEEQ*
+>NZ_CP083691.1_1669
+MTSTESVDVAGPFQDQPGPYFGRYGGQWMPESLMAALKEVADTYEAARQDPEFLAELEDL
+YANYVNRPSLLTEAPRFAAEVPGVRIFLKREDLNHTGSHKINNVIGQALLARRMGKTRLI
+AETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVIPVTIGARTLK
+DAINEALRDWVASVDTTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQTGRLPDAV
+AACVGGGSNAMGLFHGFLDDPEVELYGFEAGGDGVETGRHAASITLGRTGVLHGARTYLM
+QDEDGQTIDSHSISAGLDYPAVGPEHAFLNDTGRATYEPVTDTECMDALLRLTRTEGITP
+AIESAHALAGALRLARRWRDEGLVGEGTPEGEERIIIVNLSGRGDKDVATAAAWFGLGEA
+DEQKDPLEEMTPGEEQ*
+>NZ_CP097650.1_993
+MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEQARQDPAFEA
+ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVIPVAIG
+ARTLKDAINEALRDWVASVDNTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR
+LPDAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGEGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGQERIIIVNLSGRGDKDVATAAAWF
+GLGTAAEEKDPLEEMTPGEEQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000909.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000909.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7347c95204edf2cbd929a6353cb3348495e4672
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000909.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1046
+MTVNSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAADNGADVIELGLPYTDP
+VMDGPVIQAATQAALQAGFHVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGALARELAAGAVREG*
+>NZ_CP033200.1_775
+MTVHSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQTALQAGFRVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGTLTRELAAGTVREG*
+>NZ_CP040019.1_1782
+MTVHSKTAAALDAARRAGRTGLVAYLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQASLRAGFRVADVFEIIRRVTQRVDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWLEASDRHGLDRVFLTAPSSTDERVRLAVESSRGFVYAVS
+VMGVTGARDAVSTAAETVVRRAEEAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALGEGGPQAVGALARELAAGAVREG*
+>NZ_CP083691.1_1668
+MSTPDQQHEATAEKPSTAGDAIERARAAGRTALIGYLPAGYPSIDESVEAAVQLGENGVD
+VIEIGLPYSDPVMDGPVIQAATSHALANGFHTRDVFEVVRRITERTEAAVVVMTYWNLVD
+RMGVDEFARRLAEAGGAGLVTPDLVPEEAGEWFEASEEHGLDRIFLTAPSSSDERVRLAV
+ESSRGFVYGVSVMGVTGARGKVSDAAERVVARAKAAGARNVCVGLGISSADHVREIGSYA
+DGAIVGTALVKALRDGGPEAVGALARELAAGTAKES*
+>NZ_CP097650.1_994
+MTVHSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQTALQAGFRVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGTLTRELAAGTVREG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000911.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000911.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c893ee30c7d19ca5c2d02e4c5eb5d22856699b9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000911.fa
@@ -0,0 +1,135 @@
+>NZ_CP042169.1_1048
+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*
+>NZ_CP033200.1_777
+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*
+>NZ_CP040019.1_1779
+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*
+>NZ_CP083691.1_1666
+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*
+>NZ_CP097650.1_996
+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_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000914.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000914.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f224ff55c66caeb3d9ecc2ba6cb6a0adcbe298b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000914.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1051
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG*
+>NZ_CP033200.1_780
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG*
+>NZ_CP040019.1_1776
+MPMTTPAEGTGLRAVVAEDETLIRLDLVEVLTGAGYEVVAEAGDGAAAVAAVREQRPDIV
+VMDVQMPVMDGIAAASEIAQDRLAPVVMLTAFSQRDLVERARTAGAMAYVVKPFTEHDLV
+PAVELAVARFEELRSLESEVRDLGDRLETRKLVDRAKSVLQDRLRLSEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVR*
+>NZ_CP083691.1_1663
+MTIPAESADPTAGLRVVVAEDEALIRLDVVETLTHAGHTVVAEVGDGQAAVAAVREHRPD
+IVVMDVMMPVMDGIAAAGEIAAERLAPVVMLTAFSQRDLVERASQVGAMAYVVKPFTEKD
+LLPAMELAVARFDQLRGLEEEVRGLEDRLATRKLVDRAKSLLQAHMGLSEAESFRWIQKT
+SMDRRLTMREVAQTVVDQIGA*
+>NZ_CP097650.1_999
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000916.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000916.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9410219a3486622372a573f99e1a64206059d0af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000916.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1053
+MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV
+EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR
+EERHAAAGRIAQHYAGQGPEVRR*
+>NZ_CP033200.1_782
+MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV
+EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR
+EERHAAAGRIAQHYAGQGPEVRR*
+>NZ_CP040019.1_1773
+MTIAITVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGRGDV
+ETQADALPQAFVLTAIVIAFAITVLLLTLAVTGRDDDAVADGHEAPDPLEQSAADARFPR
+EELRAAAARLGREAEARDGGRA*
+>NZ_CP083691.1_1661
+MTVALTVGLLMAGAVYLFSKRELLRVILGMVLLGHAANLAILATGGTDRRALPFVDGGPA
+PAGAADPLPQAFVLTAIVISFAVTVLLLVLAVTGRADDAVAAPGERPDVREAAAADARFP
+LAERHAAARTLTGSLPAAPEAGATPEREERA*
+>NZ_CP097650.1_1001
+MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV
+EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR
+EERHAAAGRIAQHYAGQGPEVRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000918.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000918.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6893ff2fa29bf752d9557ce71985ec2e3a67bb85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000918.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1055
+MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI
+ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA
+DALRAEIHDMEARMLHAMRKTGVA*
+>NZ_CP033200.1_784
+MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI
+ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA
+DALRAEIHDMEARMLHAMRKTGVA*
+>NZ_CP040019.1_1771
+MHADPSSDRPVPADGTVVLAPGRASALSWPWRWLVFWCWYAWALVTSSEAVLKDLVTPGD
+QARSGIARIRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGARGEEPGDPGATRLLYVHG
+LYADDADALRGEIHDMERRLLHAMRKQGVA*
+>NZ_CP083691.1_1659
+MTVHHPDGGVDLTPGTASAASWPLRWLLFWCWYAWALVTSSGAVLHDLLTPGDQARSGIA
+RVRSNCRTDAEVTLFSALITLTPGTLTLGTRREGAQGQEPGDPEARRLLYVHGLYADDAD
+ALRAEIHDMEARMLHAMRRTGVAR*
+>NZ_CP097650.1_1003
+MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI
+ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA
+DALRAEIHDMEARMLHAMRKTGVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000921.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000921.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c20b691dc3a199ae4e0786fe24b5dd45d224851c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000921.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1058
+MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAVISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP*
+>NZ_CP033200.1_787
+MSEHTATTPAASDRVYRPGVTPELSPAELAAACAEAGLTPELVAALGGAAISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP*
+>NZ_CP040019.1_1768
+MTDHAERADAAPAPTSDLVYRPGVTPELTDAQREAACAAAGLTPELVAALGGATVSPLAQ
+KMGIRFLELTPERAVATMPVAGNEQPAGLLHGGAHLVLAESLGSMAAKLHAGPERGVVGI
+EIGATHHRAARSGLVTGTATAIHLGGTLTTHEVVMTDEQGRRLSTARITNMVLRGRG*
+>NZ_CP083691.1_1656
+MTDTTTAPERAQALLAGLTFHAGIRPELTDEERAALATAAGMTPAVQEALGGPAVSHLAL
+KMGIRFLELSAERSVATMPVAGNEQPVGLLHGGAHLVLAESLGSLSAKVHAGPHRGAVGT
+EIGATHHRSVRSGLVTGTATAIHLGRTLTTHEIVMTDEEGRRLSTVRMTNMLLDPR*
+>NZ_CP097650.1_1006
+MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAAISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDHNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLDAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000922.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000922.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d2f1457128f1cbd44d2727146148a341b9e8e88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000922.fa
@@ -0,0 +1,85 @@
+>NZ_CP042169.1_1059
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVKAKYG
+VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLETMRLEMPEREPVEELFDALQFHRIRERVFEVFGE
+RVGEDAPPPEVEAAPEFTEATTAEDVRAFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGT
+FGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEGGLAKAVHDLKRTLKALAAPT
+EGDGLGPDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPRESAQQRAQGS
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM
+ELTGIAVDVDALTGLREDFTDAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLN
+MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE
+LEKATALLKERMGRAAELSVPLDVHVGQGRSWHDAAH*
+>NZ_CP033200.1_788
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVMAKYG
+VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGE
+RVGEDAPPPEAEAAPEFTEATTAEDVRSFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGT
+FGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEGGLAKAVHDLKRTLKALAAPT
+EGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM
+ELTGIAVDVDALTGLREDFTDAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLN
+MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE
+LEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH*
+>NZ_CP040019.1_1767
+MAADPTPEDPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTITLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVMAKYG
+VSPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLTQYGDLDGVLAHADEIKGKKGEALR
+AHLDDVRRNRRLNALVRDLDLPIGLEAMALEMPEREPVEELFDALQFNRIRERVFEVFSE
+RIGETAPAAQVEEAPEFTEAATAQDVADFLAAEAGNLLGVHVDVEGPALLPKRKVPVPGT
+FGTAVGVALVGEHAGLHVSLDADAPDPALLAALREALGEGGLSKAVHDLKRVLKAIAEPA
+EATALEAGTPLDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLAAPREPAEADAQGA
+FDLDGGAAAAERAARAADAVRAAWVVRRLSVLFTPQVLERGAQRLLQELEIPLARLLARI
+ELTGIAVDAQALETLRADFSEAAAAAQESAWASVAEETGGMKVNLGSPKQLQEVLFEHLD
+MPRTRKTKTGWSTDVDSLQDLLEQTRHPFLENLMRHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADRVAGEDAVLLSADYSQIEMR
+IMAHLSEDAGLIQAFREGEDLHSFVGSQVFGVAPDEVSSEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARRDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLAEHGMASRLLLQVHDELILEVPAAE
+LEQATALLQERMGRAAELAVPLDVHVGQGRSWHDAAH*
+>NZ_CP083691.1_1655
+MGENSTEARPRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTSMLLTMIRQQAP
+THVAVAFDLSGPTFRSAEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTKEDFEAD
+DIVATLSAQAEAQGWDVCVVSGDRDAFQLISERTQVLYPKKGVSDIPPMTAADVEAKYGV
+RPEQYPELAALVGESADNLPGVPGVGPGFAAKWLQKYGDLDGVLAHADEITGKKGEALRA
+HLDDVRRNRRLNALVRDLDLDVSLDAMELTMPEREVVEELFDALQFQRIRERVFEVFAER
+LGSAAPAAPVAEAPAAVLAATADDVHAFVSAHAGTLLGLHVEIDGPDLLPKRKVPVPGTF
+GTPVGLALAAEDAALYVDLTDADADPGLVAALGDLLAEDGAAKAVHDLKRTLKAIAVPTG
+PTALPADTSLHGVVDDVALSAYLIQPDRRDTDLATLSQAHLQEPLEAPESAAAGAQGAFD
+LDGAQEEAERTARAARAARSAWVVRRLSQAFTPQVLERGAQRLLQEMEIPLARLLARMEL
+AGIAVDGDALSALLADFTDRAEAAKESAWASVAEETGGMKVNLGSPKQLQEVLFEHLDMP
+KTRKTKTGWSTDVDSLQDLLEQTQHPFLENLMAHRDATKLRQTVEGLRETVAPDGRIHTT
+YSQTVAATGRLSSLHPNLQNIPVRTEAGRRIREAFVAAPVDGEPAELLSADYSQIEMRIM
+AHLSEDAGLIEAFNSGEDLHSFVGSQVFGVDPDDVTSEQRSKVKAMSYGLAYGLSSFGLS
+KQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARRDGFTSTIEGRRRYLPDLTSDNRQ
+LRDMAERAALNAPIQGSAADIIKRAMLDVQAGLVEQGLRSRLLLQVHDELILEVPASELD
+AATALLQERMGRAADLSVPLDVHVGHGGTWHAAAH*
+>NZ_CP097650.1_1007
+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_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000924.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000924.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc61c01cb25ddbd214d02c9ada5c70e7304f44b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000924.fa
@@ -0,0 +1,37 @@
+>NZ_CP042169.1_1062
+MSEPLPRGVTPDVAHGGLPDDLTAGVDFAALDRWPLPPEPDRQAHDAADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGEA
+GELERTATPEDAARGARTVLLPLPRSLDELDRLSRIVAAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTPRPPEEADRDVPGVGSLHLVAHAGAFG
+GAAADPGSRLLLASLADDPRPPGRLVDLGCGNGLLSVGAARLWPHVTVLATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGTEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRPVLEDLVGPTRQTARDRTFTVTVSERR*
+>NZ_CP033200.1_791
+MSEPLPRGVTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHDTADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGET
+GELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVPGVGRLHLVAHAGTFG
+GAAADPGSRLLLASLADDPRPPGRVVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRSVLEDLVGPTRQTARDRTFTVTVSERR*
+>NZ_CP040019.1_1763
+MDLGCGNGLLGVGAARLWPHVRVLATDQSAVAVASTLATARANGVADRLEAVRDDALAGR
+PDASEECILLNPPFHDGNAVDPAVAHRLVAEAARVLAPGGRLWCVWNSHLRHRPVLEAEV
+GPTRQVARDRTFTVTVSTRR*
+>NZ_CP083691.1_1652
+MDAIAQTPPRDPGPARLTATELVTPDAAGRGLPRDWTAEFPFERLGRWPLPESRERQAHD
+AADLLLVDTLAGWTADGRVPGPVAVLHDQHGAVSLPLLARGLNVRLGLDEASAARSVERN
+LDLFRDADGALPAGWGRLTVGGVDAATLADARTVLLLLPRALDALHLTAARIAVHAAPDV
+LVLGAGRDKHMTPSMNDVLARSFAAVVPGRGRSKSRVITAARPVDDATEPAPRRAQHRLG
+RLGAVTLVGGWATFGGAAADPGSLLLAGTLADRAPALPVPAPHRMRTDSGLGVDIPWATR
+AGAPDVVDAGSGNGMLSVVAARVWPEAAVLASDQSADAVASSAATAEANGLAERITAVQD
+DALGALPDASVRAVLLNPPFHDGTAVDPTVAHRMIEAAGRILAPGGELWCVWNSHLRHRP
+VLETAVGPTRQVARNRTFTVTVSTRR*
+>NZ_CP097650.1_1010
+MSEPLPRGVTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHDAADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGET
+GELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVPGVGRLHLVAHAGTFG
+GAAADPGSRLLLASLADDPRPPGRVVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRSVLEDLVGPTRQTARDRTFTVTVSERR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000925.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000925.fa
new file mode 100644
index 0000000000000000000000000000000000000000..403af2d5b080fc8e138432f08806b6cf31cd1313
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000925.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1063
+MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRLEDEAQAREMVAVLRRR
+HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV
+RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV
+SVLEASYGAAGVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE*
+>NZ_CP033200.1_792
+MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRVEDEAQAREMVAVLRRR
+HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV
+RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV
+SVLEASYGAAAVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE*
+>NZ_CP040019.1_1762
+MSAPPARCTVLPRLAAGEDGWIVHELEVRRSRFLTVLGRVADEAQARAMIAALRRRHHDA
+RHVCSAFVLGPERSVARSSDDGEPAGTAGTPMLEALTARETAPGRTDLTDVCAVVVRWFG
+GVKLGAGGLVRAYSESVSAALDTTPLVTRSRRAILAVDAPHAQAGRWENELRAAGVAVLD
+AGYGAAGVRLRVGVPDSDAQRADFAARLADITAGAGRAEPIGTEWIDHD*
+>NZ_CP083691.1_1651
+MDSPAPPAGGPVACTVLAAGALAEDGWVVHEEEVRRSRFLAVLARTPDEEAARAVVATLR
+RRHHDARHVCSAWILGPGRRRMRSNDDGEPAGTAGVPMLEALSLRDTGGGATDLTDVTAV
+VVRWFGGVKLGAGGLVRAYSDAVSRALDAAPLVRRTRRARYELAAPHGEAGRWAHELELT
+GASLEGVRWDGPQAVIDLAVPDVPDGHSALASAVARITSGSAVAAPAGHVWVDGALA*
+>NZ_CP097650.1_1011
+MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRVEDEAQAREMVAVLRRR
+HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV
+RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV
+SVLEASYGAAAVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000928.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000928.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38c60a2617e35e03a24dffea2b8368d9e1e3c0ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000928.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1067
+MSAAPPVAAVIADIVGSRALPDRDRAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGPAWYRAREAVERAHER
+AVGAATAFRAADPSLTAAVDGLVLLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQAVARSGIDRLLELDAELAAAATEVAP*
+>NZ_CP033200.1_796
+MSAAPPVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGTAWYRAREAVEHAHER
+AAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQTVARSGIGRLLELDAELAAAATEVAP*
+>NZ_CP040019.1_1756
+MTRAPQAAAVIADIVGSRRLPDREAAQEQILAAFAVAEKDVPPLRAAWATVGDEFQALHG
+VWPQAVRAVVRVSLALPPGLELRFGIGVGERRSLDDGAGDRIEDGTAWYRARAAVERAHA
+RADGAATAFVAADPSLTAAVDGVLLLRDHVLGRLKARERRLAAALLGGATQTQAARAERI
+TQSAVSQAVTRSGIDRLLELDAALAEAAAGRPGHAGAAGEGAGDEGDAG*
+>NZ_CP083691.1_1647
+MSLTDEGPVRGTAVIADIVGSRGLRDRAAAQEAILAAFAAAEEAVPARIPAWATVGDEFQ
+ALHADWAAAVRATLRVAVALPEGVELRFGLGDGVHREVTGAADDDGRPILDGSAWHRARE
+ALEAAEHRTRGLAGAYRGPDADLTAAVDGQLLVRDHVLRRLKARERRIAAALLAGRTQAE
+TATAERITQGAVSQAVARSGVRELLALDAALGALPGAGRGAKATAEEDRP*
+>NZ_CP097650.1_1015
+MSAAPPVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGTAWYRAREAVEHAHER
+AAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQTVARSGIGRLLELDAELAAAATEVAP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000935.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000935.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60b4b9d7ab199d59957c4d6f4425cf2d2064ebc6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000935.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1078
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE*
+>NZ_CP033200.1_807
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE*
+>NZ_CP040019.1_1746
+MSEESLRPEKPPTSEVLVITGMSGAGRTTAAHALEDHGWYVVENMPPPLFITLADLVARS
+PEAFPRLAIVVDVRSRAYFPELHAALQQLENNGVEYRMVFLEADEHVLVRRFEAGRRPHP
+LQGNASLLDGIRAERDMLAELKARADVVVDTTELNVHGLATEITELFSVSGPVTLRLTLM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAEVSDYVLTRPGVEDFLRSYTAM
+LAPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVQVQHRDMGRE*
+>NZ_CP083691.1_1637
+MSADEHLQPDKPPSSEVLVITGMSGAGRTTAAHALQDHGWYVVENMPPQLLGTLSDLVAR
+SPEAFPRLAIVVDVRSRSYFNELRTALQQLESTGVEFRTVFLEASDEVLVRRFEAGRRPH
+PLQGNARLLDGIQAEREILSELKERADIVVDTSALNVHGLATEVTQLFSEDGPVTVRLNV
+MSFGFKYGLPSDANFVADMRFVANPHWVPELRSKTGLDPEVSGFVLGQPGVQEFLSNYLA
+ALGPVVEGYRRENKHYATLAVGCTGGKHRSVAVAEELARRVAQWPRVSVHVDHRDVGRE*
+>NZ_CP097650.1_1027
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000938.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000938.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8b11312ce49d49210ba0894373b57edf956bfca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000938.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1081
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA*
+>NZ_CP033200.1_810
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA*
+>NZ_CP040019.1_1743
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAARDADDFAAVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEHFGSFDKFRAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARQGASGLILPA*
+>NZ_CP083691.1_1634
+MTEFVLPELDYDYAALEPHISAKIMELHHSKHHATYVKGANTALEKLAAAREAEDFASVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEFFGSFDKFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQQRFEAARNGASGLILPA*
+>NZ_CP097650.1_1030
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000945.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000945.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a9a90a6155b5ccc4f40bdd99f3eb690993f3c6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000945.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1088
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR*
+>NZ_CP033200.1_817
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR*
+>NZ_CP040019.1_1735
+MSTLGLSATGSALEAIDRHLPTLLEDRVASRLGAQDAGLWGEAAREESARRLGWIDLFED
+SRALVRHIDALSRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVMEAAFREAGIDPRSRLVAVTDPGSPLHAECES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLTADDADNPGLQ
+LGAALGGTAPLRDKLVFTDHGSGIDGLPAWAEQLIAESTGKDGTGLLPVVVADGDPETGW
+DAPDMLQVQLVGEDAPAAPAHGVQVSGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KTAARSLLDAPARERTADRTVDGVELSGPEAVVSAADLAGVLRATADLVPENGYLAVHAY
+LSRHDDAELEEVRADLARLAGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQVTGDADLDV
+EVPGRPFSLGRLIAAQAAGDARVLVEHGRPVVTLHLPHRAAGIDAIRTAARAR*
+>NZ_CP083691.1_1627
+MSTFGLTATGAALDAVDRHVPALVAERFASRLAAEDADLWGPDARDEAAKRLGWISLFEE
+SRTVAAEAAALAEELRGQGLTRVVLAGMGGSSLAPEVIAATAGAELEVLDSTDPQQVAAV
+LDHDLERTVLVVSSKSGSTVETDSQRRIVEAALAAEDIDPASRIVVVTDPGSPLEEASVE
+AGYRAVFTADPTVGGRYSALTAFGLVPAALAGVDVESLLDEAEDVLDLVTADDADNPALQ
+LGAAIGGTEPLRDKLVIQDLGSGIDGFGDWVEQLIAESTGKDGTGLLPVVVRPGDPETAW
+EAPDLLKVTLVSESEESPAGGDGVRLHGSLGALLLTWEAATAVAGRLLGINPFDQPDVEA
+AKAAARELLDSPAEEAEPGTVIHGVEVSGPESVTSADDLRGVLAAVRELVPEDGYLAVHA
+YLDRHADVDLAGIRADLASALGRPVTFGWGPRFLHSTGQYHKGGPRNGVYLQVTGDAALD
+VEVPGRPFTLGRLIAAQAAGDADVLRRLGRPVVTLRLRDRSAGIAALRTAAREA*
+>NZ_CP097650.1_1037
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPHIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000965.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000965.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc6aed3d61b0f8ef9a7a48b55cca19be7597db69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000965.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1111
+MKSEIHPDYRYVIFNDLASGEKILTRTTANSDKTAEWTDGNTYPVIDVEISAASHPFYTG
+KQRIMDTAGRVERFNARFKGFGGKK*
+>NZ_CP033200.1_840
+MKSEIHPDYRYVIFNDLASGEKILTRTTANSDKTAEWTDGNTYPVIDVEISAASHPFYTG
+KQRIMDTAGRVERFNARFKGFGGKK*
+>NZ_CP040019.1_1711
+MKSEIHPDYRYVIFNDLASGEKILTRTTANSEKTAEWTDGNTYPVIDVEISAASHPFYTG
+KQRIMDTAGRVERFNARFKGFGGSK*
+>NZ_CP083691.1_1604
+MKSEIHPDYRYVIFNDLASGEKILTRTTATSEKTAEWTDGNTYPVIDVEISAASHPFYTG
+KQRIMDTAGRVERFNARFKGFGGKK*
+>NZ_CP097650.1_1060
+MKSEIHPDYRYVIFNDLASGEKILTRTTANSDKTAEWTDGNTYPVIDVEISAASHPFYTG
+KQRIMDTAGRVERFNARFKGFGGKK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000969.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000969.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da8cbbfc16d03541c6c512c42ac9bc6972402c1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000969.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1116
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR*
+>NZ_CP033200.1_845
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELIAELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR*
+>NZ_CP040019.1_1704
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGEPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANMAGHLGKLMHGVPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAEKTAYLGADAVIAVSDGMRRDILACYPEVDPEKVHTVHNGID
+TEAWTPQTETDALEKYGIDPTRPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTPELAHEVNGLIAELRRTREGVVVIEGMIPRREVTQILSAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPIEQVADGTGAPADEDAFAADFAAALTRVLE
+DPERATAMGEAGRARAIEHFSWEAIAERTIEVYEAVLR*
+>NZ_CP083691.1_1600
+MRIDIVTKEFPPTIYGGAGVHVAELTRVLSSRADVHVHAFGGAREPDYHGATVTSYAQPA
+GFESANGAVQTLVTDLDIVGDLDGADVIHSHTWYANMAGHLGGLMHGVPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAESTAYHGAAAVIAVSEGMRRDILRCYPDVDPAKVHTVHNGID
+TQLWTPQTGTDALTKYGIDPDRPSVAFVGRITRQKGVPHLLRAALQLPEDVQLVLCVGAA
+DTPELAREVEGLIGRLRAEREGVVVVEGMIPRGEVTQILSAATVFACPSIYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVDDGVTGLLVPVEQADDGTGTPVDEEKFAADLAKALSTVLA
+DPERATAMGEAGRARAIEHFSWETIADRTMEVYAAVAR*
+>NZ_CP097650.1_1065
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000977.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000977.fa
new file mode 100644
index 0000000000000000000000000000000000000000..64041894ae34ffdd5d564d4641842ff1d8e44298
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000977.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1125
+MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT
+PLDLFDDEDDDD*
+>NZ_CP033200.1_854
+MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT
+PLDLFDDEDDDD*
+>NZ_CP040019.1_1695
+MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT
+PLEVFDDEEDDEA*
+>NZ_CP083691.1_1591
+MSSDARVALEALTSALNEHLVAAQNRRGEDDPAVEAAFFAVADAFDAYEEALYAETEEVT
+PLELFDDEDDLDEED*
+>NZ_CP097650.1_1074
+MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT
+PLDLFDDEDDDD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000982.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000982.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7cefea0bfe7a6deaf43420290b72f060ac1647d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000982.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1130
+MSGPASVRLGTIAGAPVRLSWSWLLIAAAITLAFGPQIQRALPSLGGGAYGVALGYAVLL
+ALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPAANLVL
+AGLAHLAARAVAGPSVPALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAATGSRA
+RGVEAAGWAGRVVAVGVLAAVLGPPILAGRAPDLFVVVLAAWVALTLWRGADDAVRHGRW
+SRRLETLRLEQVEAPAVALPEHLSVAEALAQADDGRRAVVAVDGAGRPRGVLDLAAAAGL
+TPERRTTTALAAVAVALAPGAVLVRDDVPAAGPDLAARLADPQTPVWVLTDAHGLVRSVV
+PRETILAAVDATRRP*
+>NZ_CP033200.1_859
+MSGPASVRLGTIAGAPVRLSWSWLLIAAVITLAFGPQIQRALPLIGGGAYGVALGYAVLL
+ALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPAANLVL
+AGLAHLAARAVAGPSVLALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAATGSRA
+RGVEAAGWAGRVVAVGVLAAVFGPPTLAGRAPDLFVVVLAAWVALTLWRGADDAVRHGRW
+SRRLETLRLEQVEAPAIALPEHLCVAEALAQADGGRRAVVAVDGAGRPRGVLDHTAAAGL
+TPARRTTTALAAVAVALAPEAVLVRDDVPAAGPDLASRLADPQTPVWVLTDAHGLVRSVV
+PRETILAAVDATRRP*
+>NZ_CP040019.1_1690
+MSGAAARRIGSLRLGSVAGAPVLLSWTWLLIAVAIVLALGPQIRRALPELGAGAYGVALG
+YAVLLALSVLVHEVAHALAGRAAGQRAEEIALTLWGGHTQFRGAHAGPLGTVLTAMAGPA
+ANLALAGLAHLAARAVDGPSVAALLLDVSVWANLLLAAFNALPGAPLDGGRMVESAVWAA
+TGSRDRGVEASGWAGRVIAAGIVAAALLAPLLQGRTPDVLFTALLIWAALTLWRGAGDAV
+ARGRWGRRLAGLRLADLELAAVAVPEHLSVAEALAHADGGRRAAVAVDGAGLPRGVLDRT
+AVGRLDAAARAGTPVAAAAVALAPQAVLEREALPEAGPELAAVLADPETPVWVLTDVRGL
+VRSVVTRERILAAVHATRRP*
+>NZ_CP083691.1_1586
+MSGPRALTLGRIAGAPVRLSPAWVAVAGAVVLLFGPQVARALPGLGGAAWLVALGYAALL
+ALSVLVHEAAHAVAGRAFGQRPQEIVLTLWGGHTQFAAPQATPVGTVVTALAGPAANVVL
+AGLAWALGAAADARGVPGLLVDATVWANLLLAGFNALPGAPLDGGRMVESAVWAATGSRD
+RGVAAAGWTGRLIAAALVIGWVAVPLVRGERPGLVVSLLLVWVAVTLWRGASESVERGRW
+GRRLAGVRLADLAIPALAVPVDADASAVLAGVPAGLAVVAVDEAGRPVGVLDRAALDGAA
+ASARVPVAAACRAVAPHAVLAADSLPPSGGALVASLATAAESAADPRPGVPGLDSTPVWV
+LTDGHGAVRSVLPRERILTALATASRPDPEEPRP*
+>NZ_CP097650.1_1079
+MSGPASVRLGTIAGAPVRLSWSWLLIAAVITLAFGPQIQRALPSLDGGAYGVALGYAVLL
+ALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPAANLVL
+AGLAHLAARAVPGPSVPALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAATGSRA
+RGVEAAGWAGRVVAVGVLAAVFGPPTLAGRAPDLFVVVLAAWVALTLWRGADDAVRHGRW
+SRRLETLRLEQVEAPAIALPEHLCVAEALAQADGGRRAVVAVDGAGRPRGVLDHTAAAGL
+TPARRTTTALAAVAVALAPEAVLVRDDVPAAGPDLASRLADPQTPVWVLTDAHGLVRSVV
+PRETILAAVDATRRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000993.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000993.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5c955ba64c9222d8ab3946d3d8be2a942a9efc6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000993.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1142
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSALAVAVGMVIGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRSGQREVDVEAELAEGPKPLDQI*
+>NZ_CP033200.1_871
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSGLAVAVGMVVGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRQGQREMDVEAELAAGPKPLDQI*
+>NZ_CP040019.1_1677
+MSEVEEVARRTRRRRRRDNPTGEMPLREHLTELRNRVIKAGVAVLLGMVVGFLIYQPVMA
+ELFRPVNELSRDGRISAIAYDTVASPFDLMLKVSLFIGLIVSSPVWLYQIWAFIVPGLKK
+AEKKYALGFIAAAVPLFLLGMGLGWLVMPQAVQFFVGFTPEGGATLPTASVYISFVTRLY
+LAFGVAMVLPVLLVGLNMLGVLPGRTIVKHWRITVFLIMLIAAIAAPGADAISMVYMAVP
+LVLLFGVAIALCLWGDRRRARRAVRREQDVEAELASGPKPLHEI*
+>NZ_CP083691.1_1574
+MTSVDEEAAGARGRRKGRKPKNPNGEMPLREHLKELRDRLIKSVLAVVLGAVAGFALYKP
+VMEVLTRPMVEARERGVNAALAFDTVSSPFDMMLKVALFIGIVVSSPVWLYQAWAFVVPG
+LTKSEKKYAVGFLGTAIPLFLAGLYLAWLVHPQAVQFFIGFTFDGTAALPTASNFLTFSI
+TLFLVFGVSMVLPVFLVGLNLLGVLPATTILKHWRIVVFLVALIAAMAAPGSDVISMFYL
+AGPLLLLFGISILVCWLNDRRRARRSRDTAEDLEAEIAAGPRSLDEL*
+>NZ_CP097650.1_1091
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSALAVAVGMVIGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRSGQREVDVEAELAEGPKPLDQI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001003.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001003.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e2d3da0409067422f91440540473f06d1e8f902
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001003.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1152
+MTSSPTARRAAPAEHRDPRGALPALAVDLLLTLLFVALGQGQHSTERGPLGLLVTAAPFL
+AGLLLMTGVTAGHRTWARAWPHGVIVWLGTVAVGMLLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR*
+>NZ_CP033200.1_882
+MTSSPTARRAVPAEHRDPRGAQPALAVDLLLTLLFVALGQGQHATERGPLGLLVTAAPFL
+AGLLVMTGLTAGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR*
+>NZ_CP040019.1_1666
+MADTLSENRSETMAQTGGMTDSPTRRHSPASPPSPLWAATALAVDAVLVVVFVALGQDQH
+TTDRGLGGLLATALPFLLGLVAATVLTAGHRTWHRVWPHGVAVWLGTVAVGMALRVLWDQ
+GGAPLSFVLVALGVLGVFLLGRRAVTAWVIRRRARV*
+>NZ_CP083691.1_1562
+MSTTPLPQDSSPAAHPSDRRRGSAPWVAFALDAALVVLFVALGQREHATDRGGLALVTAA
+APFLLAWVAGTALAGGPRTWARVWPQGVVVWAVTVAAGMGLRVLWGLGGAPVPFVLVASA
+VLAVFLLGRRWASTLLAHRATDRASRAS*
+>NZ_CP097650.1_1105
+MTSSPTARRVVPAEHRAPRGALPALAVDLLLTVLFVALGQGQHSTERGPVGLLVTAAPFL
+AGLLLMTGLTSGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001007.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9a8503b044ed856b046c0441488b7d3d01dfffe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001007.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1156
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF
+NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA
+QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS*
+>NZ_CP033200.1_886
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF
+NANCASCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA
+QLAAYVASLGAGPAIPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVDEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLTLGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS*
+>NZ_CP040019.1_1662
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF
+NANCATCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA
+QLAAYVASLGAGPAIPEDEYLDINNEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKFA
+PSLQGVEEKYIYEAMETGPQNMPVFSDANIKPEDKRDIIAYLKTIENQGSPGGLSLGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS*
+>NZ_CP083691.1_1557
+MKALSQNRRHPLVGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAAAADDITAGEKLF
+NANCASCHNMGATGTADGPSLVGVGAAAVDFQVGTGRMPMQMNGPQAQRKPNQFSEEQTA
+QLAAYVASLGAGPAVPADEDLDPNAEGVNIAKGGDLFRINCAMCHNAAAAGGALTRGKFA
+PSLEGVSEKHIYEAMETGPQNMPVFSDANLKPEDKRDIIAYLKTIEANGSPGGLQLGSLG
+PVAEGLFIWTAGLALIVGFMVWLTSRSS*
+>NZ_CP097650.1_1109
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF
+NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA
+QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001008.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8971ec3f0c1be60ff6ffd3a5c7e6d7e773d4914c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001008.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1157
+MGEKGLEGTERRSGSLEHAGEDAPRYAIDDPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVRITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG*
+>NZ_CP033200.1_887
+MGEKGFEGTEHRSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG*
+>NZ_CP040019.1_1661
+MGEKGFEGTEHGSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTLLFFVGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEADRVAATGMISEILDESQIKRRPLLRNTLIGAAVLAPLPFIAVFRDL
+DDSDNFSDEETHNFGPERLRHTMWSEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG*
+>NZ_CP083691.1_1556
+MGEKGYEGAERHSDALEHAGEESPRYAIDNPGLPPHRPRLADEDPRAAKRAERQVSVFFL
+ISVIGTVLFFIGYFGVGQVGNGESTSVLYLQNLLLGLGVALAMFGIGIGVVHWAKTLMPD
+HEVVEERHEIRTEADRAAAQGMIADILDESQIKRRPLLRNTLIGAAVLAPLPFIAAFRDL
+DNTDNFSDEAAKNFGPERLRHTMWHEGVRLVRDPTGSPIKASDVTLGSALHVIPDGLNDL
+EHGKLNEKAKAVVLVMRLDPSKVKISPGRENWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLAQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG*
+>NZ_CP097650.1_1110
+MGEKGFEGTEHRSDSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDEEIHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001014.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c95a7c803d1daaa158ac3c592eb1a21d1260d90f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001014.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1164
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRAQLERSAEAVA
+GLLREAGLQDVEIVSEIRDDGRPGGPAVIGEKPGTSDKPTVLFYAHHDVQPIGDEDLWDT
+PPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSMRLGPGMEPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSAPAAAAMMAALEDAWGVEPRAIGMGGSIPFTADLAE
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA*
+>NZ_CP033200.1_893
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSAEAVA
+GLLRAAGLQHVEIVTETRDDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEDLWDT
+PPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMDPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSATAAAAMMAALEDAWDVEPRAIGMGGSIPFTADLAQ
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA*
+>NZ_CP040019.1_1654
+MTETTPPVRDDAALVAAVRDAVDARFPQTLQTLTDLVAIPGIAWDSADRAQLERSSEAVA
+ALLRQAGLQGVEIVTETREDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEALWDT
+EPLVATEKGGRLYGRGAADDKAGIMVHLAALAALKDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLENHRARLEADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRRSASLDYPEDVFRADAGVLDSVTLAGRGPV
+ADRLWNAPALSVIGIDVPSVAESSNTIQPQARAKFSLRLGPGMDPAEAFEALKAHLEAQS
+AAVLGAEITVEAGEFGQPFDTDTSDPLAAAMMGALGDAWGVAPKEAGMGGSIPFTADLAE
+VFPDATILITGVEDPDSRAHSANESLHIEDFRRAVVAEALWFARLAG*
+>NZ_CP083691.1_1550
+MTQSTQNTPVGAAPDPELVSAIRAAVDRRFPETLQSLKDLVSIPGIAWDSMDREPLERSA
+AAVADLLRTAGLEGVETAVEERADGRPGGPAVIGGRPAVGDKPTVLLYAHHDVQPLGEEG
+LWDTPPLVATERDGRLYGRGAADDKAGIMVHLAALAALDEVCPDAGVGVRVFIEGEEEAG
+SPTFRPFLERHRDRLAADAIVVADSSNWAVGEPALTTSLRGVVSATVTVRALDHAVHSGM
+FGGPVLDAVVLMSRLIATLHDADGAVAVPGLEPRHHADVDYPEDAFRADSGILPGTRLAG
+RGALADRLWNGPALSVIGLDAPSVDTSSNTIQPAARAKISLRLGPGMDPAASLDALRAHL
+EAQSDAVLGAEITVEPGELGQPFSTDTSAPAAAAMMGALGAAFATPARETGLGGSIPFTA
+DLKELFPEATILITGVEDPDSRAHSANESLHLEDFRRAIVAEALWLAAMGA*
+>NZ_CP097650.1_1120
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSAEAVA
+GLLREAGLQEVEIVTETRDDDRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEDLWDT
+PPLEATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMEPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSAPAAAGMMAALEDAWGVEPRAIGMGGSIPFTADLAE
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001019.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001019.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10bc4150188bb20b2b57f45141df9311ccda01fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001019.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_1170
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLRGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLLLSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA*
+>NZ_CP033200.1_899
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVITEAPRWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLKGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA*
+>NZ_CP040019.1_1649
+MSAHLQKPSGMKFHKYVPYQDQIQVSLPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFESLEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLKGTQI
+TYEYSPESYTGTELEFARRISDEVAQVLEASTDRKMILNLPATVEMATPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+FSQGVDPMIDFSDMDHIKRTVEYCNQLPVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+ADAKAAGKTVDEIDWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQEMADAQGGEVSGADLWTAFQDEYLPAEAKDEQWGRYRLRSVTSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRMLGEDDMDVRVLDYTEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRAVRA*
+>NZ_CP083691.1_1544
+MRNLQKPSGMKHGKYVPYHEQIEVHLPDRTWPDKVITEAPRWCAVDLRDGNQALIDPMGP
+ERKLRMFQLLVQMGYKEIEVGFPSASQTDFDFVRQLIEGDHIPDDVSIQVLTQAREHLIE
+RTFESLEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLTGTEIT
+YEYSPESYTGTELEFARRISDEVATVLEASTDRQMILNLPATVEMATPNVYADSIEWMHR
+NLEHRDSIILSLHPHNDRGTGVAAAELGYLAGGDRIEGCLFGNGERTGNVDLVTLGMNLF
+SQGIDPMIDFSDMDHIRRTVEYCNQLPVPERSPWGGDLVFTAFSGSHQDAIKKGFEAMEA
+DAAAAGKHVDEIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHKLDLPRR
+AQIEFSHVIQELADAHGGEVSGADLWTAFQDEYLPAENKEEAWGRYRVRSVSSESGENGA
+FRMTAEIFVDHEPQTRTAEGNGPIDAFLKILGEDGQDVRVLDYTEHALSEGGSAMAAAYV
+EAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRSLRA*
+>NZ_CP097650.1_1126
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLRGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001025.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..731e74ec72c6ac7b5bce1a2949834c444e402a9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001025.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1176
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL*
+>NZ_CP033200.1_905
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL*
+>NZ_CP040019.1_1643
+MTDHYATLGVSRDASTEEIRRAYRKLARTHHPDVNPDPESAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQSGFPGGFGGGGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+APIDLEDAVFGGEQTITLDTAVRCKRCEGSCCEPGTEPETCQTCQGHGMIQRPMRSLLGT
+VMATEACPACQGFGTVIPDPCHECAGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPHETFRREGDHLATTVTVPMAAAALGTTVTLATLDGEQTVRLEPG
+VQSGHVETLAGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRELLERLAELRGEEVVHGT
+PPARGMFARLRENLRNL*
+>NZ_CP083691.1_1538
+MADHYATLGVSRDASAEEIKRAYRKLARQHHPDVNPSEEAAEEFKRISHAYEVLSDEDKR
+RVYDQTGNENGTAGGFGGGGFGGAGFGGFADIFETFMNAAGTPGGGRGPMPRARRGQDAL
+VTARIELRDAVFGGEATLQLDTAVTCERCSGTCCEPGTHPETCSTCQGQGMTQRPVRSML
+GTIMAAETCPVCRGFGTVIPHPCTECSGQGRVRVQQPLTIRIPAGVDDGTRIHLAGRGEA
+GPGGGPNGDLYVEVQVRPDEVFRREGDHLATTVTVPMAAAALGTSVTLETLDGPQEVDIE
+PGTQSGHVETLRGLGVGRLRGAGRGDLKVDVVVTTPTDVTDEQRALLEQLAGLRGEEVVH
+GAPPQSKGMFARLRENLKNL*
+>NZ_CP097650.1_1133
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPGPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001029.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d35c11f3c6d14782c887c701062321dc6d801d9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001029.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1180
+MPALPLGEPVPDDGRLPADVGQRVRAAAGDGAARTFSLYVHVPFCTVRCGYCDFNTYTAV
+DLGPGAGRGDYWESAVAELDFAADVLASSDVPARPLHTVFFGGGTPTLLPAADLVRILQA
+AVDRFGIAPGAEVTTEANPDTITPEYARELAAGGFTRLSLGMQSAVPHVLATLERTHRPE
+SVPAAVAAAREAGLEVSLDLIYGTAGESLADWRATLEAAVALAPDHVSAYSLIVEEGTKL
+GAQVARGEVADVDPDDQADKYLLAEELLGAAGYRWYEVSNWARDPQGSGVHRARHNVAYW
+EDQDWWGIGPGAHSHLAGVRFWNAKHPAAYAQRLATGVTPAVGRERPDADARRLERIMLA
+VRTVDGLPTAELVSETPGEAARIRGAIAELIAAGLLDGRAAVDGRIIPTLEGRLRNDAIV
+RALAGF*
+>NZ_CP033200.1_909
+MPALPLGEPVPDDGRLPADVGQRVRAAARDGAARTFSLYVHVPFCTVRCGYCDFNTYTAV
+DFGPGAGRGDYWESAVAELDFAADVLASSDVPARPLHTVFFGGGTPTLLPAADLVRILQA
+AVDRFGIAPGAEVTTEANPDTITPEYARQLAAGGFTRLSLGMQSAMPHVLATLERTHRPE
+SVPAAVAAAREAGLEVSLDLIYGTAGESLADWRATLEAAVVLAPDHVSAYSLIVEEGTKL
+GAQVARGEVADVDPDDQADKYLLAEELLSAAGYRWYEVSNWARDPRGSGVHRARHNVAYW
+EDQDWWGIGPGAHSHLAGVRFWNAKHPAAYAQRLATGVTPAVGRERPDADARRLERIMLA
+VRTVGGLPTAELVSETPGEAARIRGAIAELIAAGLLDGRAAVDGRIIPTLEGRLRNDAIV
+RALAGF*
+>NZ_CP040019.1_1639
+MPALPLGAPVPDDGRLPAAVGERVRAAEDGAARTFSLYVHVPFCTVRCGYCDFNTYTAVD
+LGPGAGRGDYWESAVAELGFAQRALEASAVPARPLHTVFFGGGTPTLLPAADLVRILREA
+VERFGIVPGAEVTTEANPDTVTPEYARELAAGGFTRLSLGMQSAAPHVLATLERTHRPES
+VPAAVAAARDAGLEVSLDLIYGTAGESLQDWRDTLHAAVELAPDHVSAYSLIVEEGTKLG
+AQVARGEVADVDPDDQADKYLLAEEVLGAAGFRWYEVSNWAHDPEGAGVHRARHNVAYWE
+DQDWWGIGPGAHSHVAGVRFWNAKHPAAYAQRLATGVTPAVGREQPDAAARRLERIMLAA
+RTSEGLPAAEAVSDEPGDGERVRRVTAELIAAGLLDGRAALAGRLVPTLQGRLRNDAIVR
+ALAGF*
+>NZ_CP083691.1_1534
+MPSVLPVGLPVPDDGALPPASVAAVRAASATGEPRTFSLYVHVPFCTVRCGYCDFNTYTA
+ESFGPGAGRGDYVDSALAELDFAAGVLERSRVPARPLHTVFVGGGTPTLLPAEHLVRILA
+HARERFGLAEGAEVTTEANPDTLTPEYVAELAAGGFTRLSVGMQSAVPHVLATLERTHAP
+ENVPAAVAAARASGMEVSLDLIYGTPGESLADWRTTLEAAIAMAPDHVSAYSLIVEEGTR
+FGAQVARGEVADVDPDDQADKYLLADELLSAAGYRWYEVSNWAHDPAGAGVHRARHNVAY
+WEDQDWWGVGPGAHSHVAGTRFWNAKHPAAYAQRLATGVTPAVGREMPDDEARRLERIML
+AARTVEGLDLSEVRGSLEPEALRRRVAALIGEGLVEGPAALRGRIVPTLEGRLRNDRIVR
+DLAGF*
+>NZ_CP097650.1_1137
+MPALPLGEPVPDDGRLPADVGQRVRAAARDGAARTFSLYVHVPFCTVRCGYCDFNTYTAV
+DLGPGAGRGDYWESAVAELDFAADVLASSDVPARPLHTVFFGGGTPTLLPAADLVRILQA
+AVDRFGIAPGAEVTTEANPDTITPEYARQLAAGGFTRLSLGMQSAMPHVLATLERTHRPE
+SVPAAVAAAREAGLEVSLDLIYGTAGESLADWRATLEAAVALAPDHVSAYSLIVEEGTKL
+GAQVARGEVADVDPDDQADKYLLAEELLGAAGYRWYEVSNWARDPQGSGVHRARHNVAYW
+EDQDWWGIGPGAHSHLAGVRFWNAKHPAAYAQRLATGVTPAVGRERPDADARRLERIMLA
+VRTVGGLPTAELVSETPGEAARIRGAIAELIAAGLLDGRAAVDGRIVPTLEGRLLNDAIV
+RALAGF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001040.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08dda5cf4e2158dd02be2edab959a7fd0d03588b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001040.fa
@@ -0,0 +1,65 @@
+>NZ_CP042169.1_1191
+MPHLDREFDYLVPVALDARAVPGSRVSVRFGGRAMTGWLVSREQEPATGAQLTELTGVLT
+VIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAEAAADHPVTLTG
+TDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAARAAAVVPSRLFEWDEAGALAA
+LARTVAASDGGVLLLVPDHRDLDRLCAALDEHVGEDAYARIGSEDGNTPRYRAHLAALRG
+TRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPYFHAREVVLERARATGAALLFA
+GPSRSVPVQRLVESGWLLHLGPSRAAQRELGPRVVSTADAWETARDPFAQRARLPQAAWA
+AARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCRVCAGPLGFRDARAARHGEVAC
+RWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFPRVPVHASSAQHMLGSVPPGPS
+LVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRVLARWLAAACLVRPASDGGVVV
+VTADASEAVNALVRRDPDGFAARQVAERRELHLPPAGRLAEVSGDAAAVAEYLELVEAAR
+RERPDEDIHEDPHSAPLDGGPARLPWIGPVPDPADETRSRALLIFPYAAAEATVGALRAA
+RSAASARRETAPVRVRLDPAGVL*
+>NZ_CP033200.1_920
+MPHLDREFDYLVPVALDDRAVPGSRVSVRFGGRAMTGWLVSREQEPATGAQLTELTGVLT
+VIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAETAADHPVTLTG
+TDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAARAAAVVPSRLFEWDEAGALAA
+LARTVAASDGGVLLLVPDHRDLDRLCAALDEHVGEDAYARIGSEDGNTPRYRAHLAALRG
+TRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPYFHAREVVLERARATGAALLFA
+GPSRSVPVQRLVESGWLLHLGPSRATQRELGPRVVSTADAWETARDPFAQRARLPQAAWA
+AARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCRVCAGPLGFRDARAARHGEVAC
+RWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFPRVPVHASSAQHMLGSVPPGPS
+LVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRVLARWLAAACLVRPASDGGVVV
+VTADAGEAVNALVRRDPDGFAARQVAERRELHLPPAGRLAEVTGEAAAVAEYLELVEAAR
+RERPDEDVHEDPHSAPLDGGPARLPWIGPVPDPADEIRSRALLIFPYAAAEATVGALRAA
+RSAASARRETAPVRVRLDPAGVL*
+>NZ_CP040019.1_1628
+MARVLLDSPVPHLDREFDYLIPVTLDERARPGSRVAVRFGGRPMTGWLVSREDEPATGAQ
+LTELTAVLTSVPPLTEEVLASARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAGAA
+ADHPVALAVEEAPEGEPVGAGDGIAPTVWESLEGGRAFVAAVLAGDGPRAAAVVPSRLLE
+WDEAAAMAHLARAVAAGGGGVLLLVPDHRDLDRLCAALDDAVGEEAYARIGSEDGNTPRY
+RAHLAALRGTRRIVAGTRAAAWAPVRDLRLTVLWDDGDDAWAEPRAPYFHAREVVLERTR
+RTGSALLFAGPSRSVPVQRLVESGWLLHLGPSRAAQREIGPRIVSTADAWETARDPFAQR
+ARLPQAAWGAARAALLGERPGPVLVQVARAGFIPALVCDRCRTPARCRRCAGPLGFRDAR
+AARLGEVACRWCGTRERGFRCTECGAGALRAGARGVDRTAEELGRAFPRIPVHSSSAQHR
+LGTIPPGPSLVVATVGAEPVAEDGYAAALLLDGDAQLQREGLDVPGRVLARWLAAACLVR
+PAADGGVVVVTADAGEAVNALVRRDPDGFAAHQVAERRELHLPPAGRLAEVTGEASAVRE
+YLDLVEAARRERPEEDVHEDPHSAPLDGGPARLPWIGPVPDAADETRSRALLLFPYAAAD
+ATVAALRAARSAASARRETSPVRVRLDPAGVL*
+>NZ_CP083691.1_1523
+MARVLLDSPVPHLDREFDYLVPPALDERAVPGSRVSVRFGGRETTGWLVERVAAPATHAR
+LTELAGVLTAVPPLTEHVLAVARAVAARQAGVVSDVLRSAVPPRVVSVEKEVLAELASGP
+EVDHPVQGVVADPHARLVWEELTGGTAFVASAVAGDPVRAAAVVPSRVGDWDESSALAAL
+ATAVSRAGGGVLLLVPDHRDLDRLSAALAREVGEDGFVRVGSEDGNTPRYRAHLRALTGL
+ARVVAGTRAAAWAPVQDLRLVVVWDDGDDAHAEPRAPYFHVREVALERARQSGSALLFAG
+PSRSVPVQRLVEHGWLLEVSADRASQRAASPRIVASADSWESARDPFARRARLPHAAWAA
+AGEALSGPTPGPVLVQVARAGFIPAVVCGRCRTPARCRVCAGPLAFRDRRSAERGELACR
+WCGTRERDFHCAECGFTGLRAGVRGVDRTAEELGRAFPQVPVHSSSADHRLGEVGEGPAL
+VVATVGAEPHARGGYAAALLLDGDAQLQREGLDVPVRVLTRWLAAASLVRPAAEGGTVVV
+TAEHDAAVGALVRRDPQGFAGHLLAERRELHLPPAGRLAEVTGEAGAVAEYLALVEAARR
+ERRRVGPDADPSLDLDVEARPGDATPLPWIGPVPDVADESRSRALLLFPWAASAATVDAL
+RVARSAASARRERSAVRVRLDPPGVL*
+>NZ_CP097650.1_1148
+MPERAEGWPERPIARVLLDSPVPHLDREFDYLVPVALDARAVPGSRVSVRFGGRAMTGWL
+VSREQEPATGAQLTELTGVLTAIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQV
+EKAALAEDAEAAADHPVTLTGTDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAA
+RAAALVPSRLFEWDEAGALAALARTVAASGGGVLLLVPDHRDLDRLCAALDEHVGEDAYA
+RIGSEDGNTPRYRVHLAALRGTRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPY
+FHAREVVLERARATGAALLFAGPSRSVPVQRLVESGWLLHLGPSRAAQRELGPRVVSTAD
+AWETARDPFARRARLPQAAWAAARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCR
+VCAGPLGFRDARAARHGEVACRWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFP
+RVPVHASSAQHMLGSVPPGPSLVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRV
+LARWLAAACLVRPASDGGVVVVTADAGEAVNALVRRDPDGFAARQVAERRELHLPPAGRL
+AEVTGEAPAVAEYLELVEAARRERPDEDVHEDPHSAPLDGGPARLPWIGPVPDPADETRS
+RALLIFPYAAAEATVGALRAARSAASARRETAPVRVRLDPAGVL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001041.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a65476c86f7d21aeb97f5aae5ffad359f7ca1169
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001041.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1192
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPKIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLETREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
+*
+>NZ_CP033200.1_921
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
+*
+>NZ_CP040019.1_1627
+MTDAAQPSPARHADPYTGVGGGELRLFTSESVTEGHPDKICDQISDAILDAILAADPAAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVTRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRQENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHDWVGQEQLRKDVEEH
+VIRPVIERSGLDTSGMRVIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTAVVPEER
+IIQAVNEVFDLRPAAIVKELNLLRPIYRKTAANGHFGRDDADFTWERTDRVERLRAAAGL
+*
+>NZ_CP083691.1_1522
+MSDTPTPTPSAAAQPYRGVGGGDLRLFTSESVTSGHPDKMCDQISDAILDAILAADPSAK
+VAVETLSTTGLVQVAGEVNTSAYVEIPHIVRETILDIGYDSSANGFDGAQCGVNVSIGQQ
+SSDIFAGVSRSLEAREQGSADEVDEQGAGDQGIMFGYATNETPSYMPTPIYLAHRLSERL
+TAVRRQENTPMPYLLPDGKTQVTVGYDADHRPRTVETVVVSTQHHDVVTQEQLRADVAEH
+VIRPVIERSGLDVSNARFIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYALRWVAKNVVAAGLAGRAEFQVAYAIGSARPVGLYVDTFGTNAVPEET
+IIAAVNEVFDLRPAAIVKSLNLLRPIYRKTAAHGHFGRDDADFTWERTDKVEELRRAAGV
+*
+>NZ_CP097650.1_1149
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEKH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001047.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2a3a09a3d497ff25645205d793f2eabb8247f30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001047.fa
@@ -0,0 +1,100 @@
+>NZ_CP042169.1_1198
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL
+AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV
+TSLQEHDARLQQAVAGPEAAA*
+>NZ_CP033200.1_927
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL
+AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVAHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV
+TSLQEHDARLQQAVAGPEAAA*
+>NZ_CP040019.1_1621
+MPKRPDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLHRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPADGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPRELL
+RRARTATTDRLAQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADQIRDAEVLDES
+LLRHAKRHGFSDAQIGSLRHMGADVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGRSVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVLGVYVQLGGQTPLKLAQQLADAGVPILGT
+SPEAIDLAEHRGEFARVLDRAGLVAPKNGTAVSFEDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGERMYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATEQIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAAMIGVGKSIADLQAEGVLPTAYDGATLPLGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHYDTAFAKSQAAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQIVSTGGTAEVLRRNGIPAETVAKIAEAGGEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRAYEWSV
+TSLQEHDARLQQAVEASA*
+>NZ_CP083691.1_1516
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVILVNSNPATIMTDPEL
+ADATYVEPITPEVVAKIIEKERPDAVLPTLGGQTALNTAIALDKDGVLEKFGVELIGANI
+AAIELGENRELFKGVVERAGGESARSHIVHTMEEAFAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLRRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPEDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADATLTTTMKSVGEAMAIGRSFSEALQKALRSLEQKGSELSFDRDADPASLL
+ASARTATTQRLAQTQRALYAGATLEEAFEATAIDPWFLDQLMLINEVADEVREAPQLDEA
+VLRRAKRHGFSDAQIGSLRHMDPAVVRGLRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLESEVDEHAAPSVVILGSGPNRIGQGIEFDYSCVHATLALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEATGGVAGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPEAIDLAEHRGEFARVLDEAGLIAPKNGTAVSFEDARRVADEIGYPVLVRPSYVLGGRG
+MEIVYTEEALAHYVTNATEITPTQPMLVDRFLEDAIEIDVDALYDGHELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVRTATEKIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAAMIGMGRTIAELRAAGTLPTAFDGASLPMGASVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHFDTAFAKSQAGAGGPLPTEGRVFVSV
+ANRDKRAVVGQAKRLVDLGFEIVSTGGTAEVLRRNGVPAEVVAKIADASDADGAGTVLEQ
+LHEGRVDLVLNTPSGGEARTDGYEIRAAATSLGVPVITTTAEFAACLQAIEAMRTYEWSV
+TSLQEHEERLAQAVAAEASA*
+>NZ_CP097650.1_1155
+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_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001048.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5141a3b554348c94e46c7f59c327eab2497ef7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001048.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1199
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA*
+>NZ_CP033200.1_928
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELETFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVDAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA*
+>NZ_CP040019.1_1620
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDTDRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVYSGEHAGRPEAELLAEVREQPSMAGARLAETVTTEQPYVIEPAA
+HGWEGEPLAEIAALDLGIKAATPRHLASRGIRVHVLPATAGLEEIRAVSPDGVFLSNGPG
+DPATADAQVALLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVMDNATG
+RVAITSQNHGFAVDAPLGEPVEAPETRYGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVRMLTEHRDAAAPAATEGA*
+>NZ_CP083691.1_1515
+MSTPTPETALLVLEDGTVHRGRAYGARGSTLGEAVFTTGMTGYQETLTDPSYARQIVVQT
+APHIGNTGVNDEDAESRAIWVAGYVVRDAARRPSNWRSQRTLDEELAAHGVVGIQDVDTR
+AITRALRTEGSMKAGIFSGEAAQRPEAELLAEVREQPSMAGARLAETVSAPSAYVVEPSD
+HGWDGEPIADVAALDLGIKAATPHHLAARGIRVHVLPADSDFAAIQAVRPDGVFMSNGPG
+DPATADAQVAVLREVLDAGLPYFGICFGNQIFGRALGFGTYKLPFGHRGPNQPVMDKATG
+RVEITSQNHGFAVDAPIGEVVEAPEARYGRVEVSHWSLNDDVVEGLRLLDRPAFSVQFHP
+EAAAGPHDSLGLFDRFAHTLTERRAAAPSATPEGA*
+>NZ_CP097650.1_1156
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001052.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db84dcc26b6847133f6b65b7f0222bc5ada3166b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001052.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1203
+MGTDPAAPRAARTVLSTSEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAL
+LARIEPAFDPTAAVGEVDVTLYRDDLRRGTARTPMPTRLPEVPLDGAVVVLVDDVLFSGR
+TVRAALDAIADLGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTAERVQVRLMEVDGP
+EGTGEVTEDAVSIVDRVATREG*
+>NZ_CP033200.1_932
+MGTDPAAPRAARTVLSTSEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAL
+LARIEPAFDPTAAVGEVDVTLYRDDLRRGTARTPMPTRLPEVPLDGAVVVLVDDVLFSGR
+TVRAALDAIADLGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTAERVQVRLMEVDGP
+EGTGEVTEDAVSIVDRVATREG*
+>NZ_CP040019.1_1616
+MGADPAAPRAARTVLSASEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAV
+LARIEPAFDPEAAVGEVDVTLYRDDLRRSAARTPMPTRLPAVPLDGAVVVLVDDVLFSGR
+TVRAALDAISELGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTSERVQVRLVEVDGP
+EGTGEVSEDAVSIADQADRPEQREA*
+>NZ_CP083691.1_1511
+MGGIPAAPRAARTVLTAPEIDRALTRIAHEILESNKGPEGLVLMGIPRRGVPLARRLAAV
+LHRIDPAFDPVSAVGEVDVTLYRDDLRRGTARTPAPTRLPDHPLDGAVVVLVDDVLFSGR
+TIRAALDALADLGRPAAVRLAVLVDRGHRELPIRADFVGKNLPTSTAERVQVRLTEVDGP
+DGSGEVPEDAVRIVDAPAETPREA*
+>NZ_CP097650.1_1160
+MGTDPAAPRAARTVLSTSEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAL
+LARIEPAFDPTAAVGEVDVTLYRDDLRRGTARTPMPTRLPEVPLDGAVVVLVDDVLFSGR
+TVRAALDAIADLGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTAERVQVRLMEVDGP
+EGTGEVTEDAVSIVDRVATREG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001058.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a574a89733b26f819174a135bf3b58841743d0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001058.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1209
+MRPVLRAAVLGRPIAHSLSPVLHAAAYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGAA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPAAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGANAVLFGVRDAARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPADAALPPLLDAAY
+DPWPSVLAAAWSREGGPVASGLSMLLHQGVEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG*
+>NZ_CP033200.1_938
+MRPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGTA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPSAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGADAVLFGVRDPARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPAGAALPPLLDAAY
+DPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG*
+>NZ_CP040019.1_1610
+MGAPSDVRAEASAGAPAAPRLRAAVLGRPIAHSLSPVLHGAAYGVLGLDVDYRRRDLGED
+EVGAFVAGRLGAPRTADGGDAAARGEDWLGCSVTMPLKRAVVGCAGRVSERVRLLGTANT
+LVRDHPEHPGLVSAENTDVDGILGALASAGLAERGSGGAVGILGNGGTATAAVLAAATLG
+ADEVVFGVRDAARAAEVTALADALGLAWRTVGQPELAAAAPGLRAVVATLPPRAADPLAA
+HVPVGAALPPLLDAAYDPWPSALASAWTEAGGAVASGLSMLLHQGVEQVRLFTARPRAAA
+GMPEPDWAAVTRAAARALGPAAG*
+>NZ_CP083691.1_1505
+MAGATFRAAVLGRPIAHSLSPVLHAAAYRALGLDVDYGRADLGEEEVGPWLAARLGAPGS
+AARPAGPSGGDWLGVSVTMPLKPAVVPLADELSARVRELGVANTLVRDHPDHPGSLLAHN
+TDVDGIVRALAERGLDAGAGGGAVGILGNGGTATAAVAAASLLRAETVVLGVRDAGRARD
+VVALADRLGLGVRVEAQDALVRQAADLRAVVATLPPRAADPLADKVPAGVLPPLLDAAYD
+PWPSAIARAWSAAGGGVASGLSMLLHQGVEQVRLFTERPRRAAGGVEPDWAEVTAAASRA
+LGLPGR*
+>NZ_CP097650.1_1166
+MRPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGTA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPSAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGADAVLFGVRDPARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPAGAALPPLLDAAY
+DPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001060.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001060.fa
new file mode 100644
index 0000000000000000000000000000000000000000..805715a5fec81c715a9303b35c8ce8379141ce2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001060.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1211
+MSAGQDGANAATDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDE
+LVAHARELDVVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALAEAGHPVPVRLVDERLS
+TVSAQAGLRAAGRSVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREPIR*
+>NZ_CP033200.1_940
+MASDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDELVAHARELD
+VVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALVEAGHPVPVRLVDERLSTVSAQAGLR
+AAGRSVKYSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREQIR*
+>NZ_CP040019.1_1608
+MSAGQDGAATATDAVRRGRTLGVDVGRARVGLATADPDGLIATPVATLARDARRGRDVGE
+LVAHALELDVVAVYVGLPVNLRGEHTPSTQDALDYARSVARAPAAAGHAVPVRLVDERLS
+TVSAQAGLRAAGRTVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDPEEIA*
+>NZ_CP083691.1_1503
+MSAQAAVRGRVLGVDVGRARVGLAASDPDGLIATPVETLRRDARQRRDHAELLDRARELD
+AVAVYVGLPRNLRGEHTPSTQDAVEYAAAIEALVAEAGTPIPVRLVDERLSTVSAQAALH
+RAGRTVKDSRGVIDQAAAVELLQDALEVQRRRGAWAGITVAEARA*
+>NZ_CP097650.1_1168
+MASDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDELVAHARELD
+VVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALVEAGHPVPVRLVDERLSTVSAQAGLR
+AAGRSVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREQIR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001061.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef1e388ded8a3c7a780f2db1b1153416ee2e60bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001061.fa
@@ -0,0 +1,85 @@
+>NZ_CP042169.1_1212
+MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD
+PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKEDNYWHTGQPGPGGPCSEIFYDRGP
+AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDVAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+ARIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFRALMAEQRDRARADAKAKKSGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVPSAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAESLSAGARSEVEDVVNIAIRDDHTVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLAAQAR
+DVTTSGGTSVRVLAHHAGDVAGDQLRSLALDLRARIESAGGNAAGTPVFVALTAEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALDAVVAAV
+RAA*
+>NZ_CP033200.1_941
+MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD
+PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP
+AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDIAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFRALMAEQRDRARADAKAKKAGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAEALSAGARSEVEDVVNIAIRDDHAVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLAGQAQ
+DVTTSAGTSVRVLAHHVGDVAGDQLRSLVLDLRARIESAGGNAAGTPVLVALTAEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALEAVVAAV
+RAA*
+>NZ_CP040019.1_1607
+MKSQEIARRWIAFFESKGHQHVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRAV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKEKAIPMAWELLTTSVEDGGYGLD
+PERLWVTVYEEDDEAARIWEESVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP
+EYGADGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDVAGELENKNIDTGLGLERLAML
+LQGVENMYETDQVRPVLDRAAELSGREYTSTEDPTDPHYEDDVRLRMVADHVRSALMLIG
+DGVRPGNEGRGYVLRRLIRRVIRALRLMGVTEPVLPELLPVSRDAMKGSYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARTAGGGIAGADAFELHDTYGFPIELTLEIAE
+ESGVAVDEAGFRALMAEQRDRARADAKAKKSGHTDTALYQRLRAEGQTHFTGYTEHTTES
+VVRGLLLDGEEVASASAGTELEVILDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+RGLSVHRVKVLDGEVPAGAEALGAIDLQRRLDGEKAHSGTHLVHAALHQVLGPEATQSGS
+FNKEGYLRFDFRWAESLSAGARSEVEDVVNIAIRDDHTVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIAASMDRLKAAEKQIAELQAKALQAQAGELAAQAQ
+DVTTASGVSVRVLARHVGEVAGDQLRGLVLDLRSRIESAGGNAAGTPVLVALTGEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALDAVVAAA
+RAA*
+>NZ_CP083691.1_1502
+MKSHEIARRWTAYFEKQGHLVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRAT
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKEKAIPMAWELLTTSVEDGGYGLD
+PERLWVTVYEEDDEAARIWREDVGVRPERIQRMGKADNYWNTGQPGPGGPCSEIFYDRGP
+EYGVEGGPEADDTRYIEIWNLVFMQYRLSQVRSKYDFDVAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAELAGKSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFHALMAEQRDRARADAKAKKSGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGVITGDGFSLEVLDVQAPV
+KGLSVHRVKVLDGEVPVGAEAVGRIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAEAVSAMARSEIEDVVNIAIRDDHQVLTQEMSLDEARAMGAMSLFGE
+KYGDRVRVVEINGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSDLSEMFKAPADQLKDRITATMDRLKAAEKQVADLQAKALQAQAGTLAAQAQ
+DVTTTSGASVKVLAHHAGEVAGDQLRSLVLGLRSRIESAGGNAAGTPVLVALTGEAKGRP
+LVVVATNEAARGAGLKAGAMVKLATAALGGGGGGKDDVAQGGGQDVTAVAAALDAVLDAV
+RDA*
+>NZ_CP097650.1_1169
+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_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001062.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f8b0f78c8e952db8ce8e2d7eff50207c6362d72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001062.fa
@@ -0,0 +1,19 @@
+>NZ_CP042169.1_1213
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA*
+>NZ_CP033200.1_942
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA*
+>NZ_CP040019.1_1606
+MLRSLLLVTAGAASGWLAHRALGDRAAADAAPGRSDAGPQARPGRARLDPEHLARQAGQA
+VGDAAAAALNEGARRLADRVRAEAPWAAQFLPHTGPIIEGETVEPPSPSGPGGPRPQTTI
+PTTTTQKDTHA*
+>NZ_CP083691.1_1501
+MSRITSLLLVGAGTAAGWIAHRAVESGRRAVDQEAGRRLQETLDPTRLGRSAGQAVGDAA
+AEALAQSAQAFTERLRADAPPWVSQLIGPPRDTIEGEALDTPDTTATPSSARKDPHA*
+>NZ_CP097650.1_1170
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001064.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001064.fa
new file mode 100644
index 0000000000000000000000000000000000000000..003e0eb9f5ad257309888602ba34de744e493f51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001064.fa
@@ -0,0 +1,23 @@
+>NZ_CP042169.1_1215
+MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG
+FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL
+LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG
+TAATPRA*
+>NZ_CP033200.1_944
+MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG
+FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL
+LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG
+TAATPRA*
+>NZ_CP040019.1_1603
+MSQHQPYAQDPRSTVPATTADAAYAGGPLGAADHRVLESVPDYARAQAIVDQLSDAGFPV
+EHVRIVGTGLRTVEQVLGRMTTGKAAGRGAVQGLWFGLLLGLLFSIFSPGFGFLWILLIS
+LGLGALWGAVFGAIGHAATRGRRDFSSLQTMDAASYEVQVEAAHLDRARQTLGAGPAAPR
+A*
+>NZ_CP083691.1_1499
+MSASAAHYAVLSTVPDYAHAQSTVDRLSDSGFPVEHVRVAGTGLRSVEQVTGRLTTGAVG
+VC*
+>NZ_CP097650.1_1172
+MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG
+FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL
+LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG
+TAATPRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001075.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001075.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0151069292dec54ffb32002397fe5d5d3cc18a73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001075.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1226
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL*
+>NZ_CP033200.1_955
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL*
+>NZ_CP040019.1_1592
+MNRFADWGNALYSGRVSYPFVQRWRLWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTAATDIAAGERAVTDVLAGGHATVTNIAPGTVRVQTEQLDDAQTRQVAANLQDAYG
+VGQDQVTSTFVGPTWGAAVSQQALLGLVIFVVLVTLFMAFYFRTWKMSLAAVIGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGQEEDPERTFEQNVNL
+AVNQTLVRSITTSIVGILPVGSILFIGAGLLGAGTLRDIALAIFVGIIVGTLSTLFIQAP
+LYALLRRGDEDVRDHDARAAARAARENRGDTVTDPDVAPWEDGARL*
+>NZ_CP083691.1_1485
+MNRFADWGNALYSGRISYPFVRKWKTWFLIAAALLAVAFGLTALRGGFNLGIDFRGGSEF
+TVSDAASSELDPGRAAVTDVVAGAEPTVTQVAPGTMRVQTEQLDDAQTRQVAQNLQQAYG
+VTGDHVTSTFVGPTWGQAVSQQAVIGLVIFVVLVTLFMALYFRTWKMSLAAVVGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTRGVEEDPDRTFDGSVNL
+AVNQTLVRSITTSIVGLLPVGSILFIGAGLLGAGTLRDISLAIFVGIIVGTLSTLFIQAP
+LYALLRRGDADVVAHDARVGADHDEREQEEDLADARGAVL*
+>NZ_CP097650.1_1183
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001077.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9ac1a897d515f2313846068b05af8a2a90b87b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001077.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1228
+MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG
+VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETTAAPTTDPSRLD
+DAPGTEYRADDADDPRPRRDDLA*
+>NZ_CP033200.1_957
+MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG
+VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETAAAPTTDPSRLD
+DAPGTEYRADDADDPRPRRDDLA*
+>NZ_CP040019.1_1590
+MPVATAATLPVIAQQAQGGGGSMLMLIAFAMLAVMLFLSFRKGKKVQQQQAEMRSTLAPG
+VEVMTGAGIFGTVVSVDAENQRVTIETAPGTRMDVHLQGVTNVVEPTAAAAATPADDEAR
+LDRAPGAEYGAQQPVVEPRADDAVDPRDRRGDLA*
+>NZ_CP083691.1_1483
+MPLTPLAPVLADDAAGGGNVLVLAMFAALAVMLFLSFRRGKKAQAEAADMRARLTPGQEV
+MTGAGIFGRVVAVDAAAQRVTLETAPGTRMDVHLQGIVKIEEPDVAPAADTAPAVGGAHA
+AETAPAADDTDRA*
+>NZ_CP097650.1_1185
+MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG
+VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETAAAPTTDPSRLD
+DAPGTEYRADDADDPRPRRDDLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001078.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5188437cfa00f9b66ba602ec8ec24c707025261
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001078.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1230
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLSTLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR*
+>NZ_CP033200.1_959
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR*
+>NZ_CP040019.1_1588
+MIASLSGTVEHVALDRAVIAVGGFGVQFSATPQTLATLHEGRTGSVQTHLVVKEDALTLF
+GFADRHEREVFEVLITANGVGPRLALAVLSVHHPEAVRRAVTEEDENALTRVPGVGPKLA
+RKIIVELSGRLTPTGEQVPAPEEPAAPETPEAAWHADVVQAMTGLGWSEKEALKAVEATV
+AARPELDEARDVAALLRATLRDVGTAGTVRGGR*
+>NZ_CP083691.1_1481
+MIASLSGTVEHVGLDHAVIAVGGVGLSFSATPQTLSHLHEGRDGAVQTHLVVKEDSLTLF
+GFADRAEREVFEVLLGANGVGPRLALAILAVHRPEAVRRAVTDEDEKALTLVPGIGPKMA
+RKIIVDLAGRLAPTGEVEPEAAVVEPEAAADAWHADVVQAMTGLGWSEKEAAKAVAATVA
+THPDVDASGDVAALLRATLRDVGAAAAVRGGRRA*
+>NZ_CP097650.1_1187
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001079.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aca37946c30bcca00f947c332d54540bae9c03ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001079.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1231
+MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEAVSAVLAAHRPDRA
+AVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAVTGHGDAGKEQVTT
+MVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTADLASRAGRSQFAAK
+APARARQRGQLTAAQRAWLDAERSAGGGRRR*
+>NZ_CP033200.1_960
+MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEAVSAVLAAHRPDRA
+AVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAVTGHGDAGKEQVTT
+MVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTADLASRAGRSQFAAK
+APARARPRGQLTAAQRAWLDAERSAGGGRRR*
+>NZ_CP040019.1_1587
+MVDVDARRRAALVHVEVAGTPPTASLDQRLLRIDEAVSAVLTAHAPDRAAVERMFANTNT
+PTVLGTAQAAGVAIAAAARAGIPVGLHTPSEVKAAVTGYGDAGKEQVTTMITRILGLDAP
+PRPADAADALALAIAHGWRGTALGAAAGQTGLDTSDLASRAGRSQFAAGTRSRGGRRGEL
+TAAQRAWLDAERSAGGGCR*
+>NZ_CP083691.1_1480
+MTDRPAGVVRVLGVDPGLTRCGIAVVDVDARRRAELVHVEVAGTAPEESLDARLLCIDRA
+VSAVLVRFRPERAAVERMFANNNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAV
+TGNGDAGKEQVTTMVTRILRLDAPPRPADAADALALAIAHAWRGTALGRAAGHTGLDTSG
+LASRTGASRGAAGARVRRAPKAALTPAQQAWLAAERSAGARPGRRSAG*
+>NZ_CP097650.1_1188
+MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEAVSAVLAAHRPDRA
+AVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAVTGHGDAGKEQVTT
+MVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTADLASRAGRSQFAAK
+APARARPRGQLTAAQRAWLDAERSAGGGRRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001081.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001081.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d286f37778fd907ec01e659f0059191f60c0435b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001081.fa
@@ -0,0 +1,65 @@
+>NZ_CP042169.1_1233
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARVASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRADAEVAPWDWPALSAGYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDRADALGERPVVFTTMNVPAPAAGRPALLTLDETTTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVETGEPLPA
+GTLERLEAADLWGEGHRTVEYLGATLVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA*
+>NZ_CP033200.1_962
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEATTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPA
+GTLERLEAADLWGEGHRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA*
+>NZ_CP040019.1_1585
+MTPTPASSVLPADHPLATPSELPYGLPDFSAVTDAQLAEAVRAGMAAQRAEVEQILGAAT
+APTFENTVRAFELSGQLLRRSAAMFFTLVSADGTDARQGLAEELSPELAAHEDALLLDPR
+LAERVAAIDGAGLTGEDARLLEVLRRRLDLAGAGLGEAERAELGRINTELAGLTAAYTRR
+LVADTAERAVLVTDRERLAGLSEDDLASAAAAAREAGHGGADGEGGDEAGPWLLTLSLFT
+SQPWLASLEDEALRREVFEASVGRGAAGDHETLSTAMEVVRLRLRKARLLGSASWAEHAL
+KDRAAPSTTAVEELLATMAPRAMANARTDAATAAAHAGRVGGAVAPWDWPALSAAYARER
+FAVDAGALRPHFELDRVLHAGVFAAATALYGITFEERPELAGRLYRPGIRVFEVRDEDGA
+GVGLFVADLFARSTKSGGAWMHTVRDAADALDERPVVFNTMNVPAPAPGRPALLTLDEAT
+TLFHEFGHALHGLLAKGEYVSLSGTHVPRDVVEFPSQVNEVWLREPALLAEYARHVETGE
+PLPAGTLERLEAADLWGEGYRTVEYLGATLVDWAWHSLTEDTVEAATADPAAFERRVLTE
+AGIDPELVPPRYGTGYFKHIFGNDYAAGYYSYIWAEVLDADAVEWFREHGGMTRENGRRF
+AEELLSRGETRDLLESYRAFRGRDAELEPLLRRRGLVDAAA*
+>NZ_CP083691.1_1478
+MTQITHRLPAGHPLLSPSPLPHGLPDFAAVSDADLATGMRQGMAEQRAEVEEILSSPEAP
+TFENTVRALELSGALLRRVAPMFSTLVGSDGTDARQALAEELSPELAAHEDAILLDPRLS
+ARVAAVDDAGLAGEDARLLERTRTRLEIAGAGLDEAGRAELARLNGELATLSAAYTRRLV
+ADTAARAVLVTDRERLAGLRADDLAAAAERAAAEAGHRRADAAEGAGPWLLTLSLFTSQP
+WLADLEDAGLRREVFEASVGRGSSGEHETLTTAMRIVRLRLEKARLLGAASWAEHALRDR
+AAPSVAAVEGLLGSLTGPAMANARRDAEAVAEGDAPVVPWDWPFLSAAHAREAFDVDAGA
+LRPWFELDRVLTRGVFAAATALYGLRFAEREDLAGHLYRPAIRVWEVTDEDGRGVGLFVG
+DFFARPTKSGGAWMHNVVDASAALGTRPVVFCTMNVPAPAEGRPALLTLDEATTLFHEFG
+HVLHGLLAEGEYPSLTGTAVPRDTVEFPSQVNEVWLREPSLLADYARHVETGAELPTGTL
+ERLEAADLWGEGYRTVEYLGATLLDWAWHTLTEDTVDAATADPAGFERRVLTEAGIDVDL
+VPPRYGTGYFKHVFGNDYAAGYYSYIWAEVLDADAVEWFREHGGLTRENGRRFAEELLSR
+GDTRDVLESYRAFRGRDAELEPLLRRRGLLPEGA*
+>NZ_CP097650.1_1190
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGAGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEATTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPA
+GTLERLEAADLWGEGHRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001083.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001083.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2dfd3fbc03bf0730c4014bda8871b115bfd6b50f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001083.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1235
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR*
+>NZ_CP033200.1_964
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR*
+>NZ_CP040019.1_1583
+MTDTPQTPQDPDRTDAAQASPVVGHGAGAPRGARLTDEEWARRLTPEEFQVLRRAGTERA
+YTGEYWDSHVQGVYACRACGAELFRSDEKFDSHCGWPSFFAPLAEDRVEYLKDTTLGVER
+VEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADASGAGSDDDAAGRA*
+>NZ_CP083691.1_1476
+MSQNHATVPSGADDAARPAALTDEEWARRLTPEEFHVLRRAGTERPYTGEYWDSRVQGVY
+ACRACGVELFRSEEKFDSHCGWPSFFAPLAEDRVVYVKDATLGMERIEVRCAACGSHMGH
+VFAGEGYDTPTDLRYCINSISLRLTPADVAAIGTEADPAGDRA*
+>NZ_CP097650.1_1192
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001084.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001084.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b1c5ade9961e12b95b5a25d7f08453cab4f1d7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001084.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1236
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERHHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP*
+>NZ_CP033200.1_965
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP*
+>NZ_CP040019.1_1581
+MTVIGPRRLAPVTGPRGAVAPAPAPLPAAFRRALADLRTARPRPEVRLREIAAPAGQAPH
+AVALAAEVCGSPGADDVLATGRFVLLHDPSPAARWPGGFRAVTWIRASLEPDVALDQLAG
+AVAWTWLVEALERRHAEHTQAGGTATRSIAEGFGTLGTAPDATDIELRASWTPAPRDLGA
+HLEAWSDMIGAFAGLPPR*
+>NZ_CP083691.1_1474
+MTESGPRAPAPAAGGASGAFADALADLRAAHPRPEVRLRPIPDPPGLAPFAVTLAADVLD
+PHGAEADPLATGRFVLLHDPAGSPVWRGDFRVVTYIRASLEPDVATDHLAGAVAWDWLAE
+ALERRHAAHTEAGGTATRQLAEHFGTLALEPGWTDIELRASWTPGPRDLGAHLEAWSDMI
+CAFAGLPPLADDDVPAAVPLRP*
+>NZ_CP097650.1_1193
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001085.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00035226ad971743f3a0c381901894129d20e66e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001085.fa
@@ -0,0 +1,42 @@
+>NZ_CP042169.1_1237
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVAGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERGDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA*
+>NZ_CP033200.1_966
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAIDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERDDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA*
+>NZ_CP040019.1_1580
+MTDVPEPAEPDATPRLIAEPADGVPRVTDTPAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLEPLQEALSGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVAGLPRVGLAAVLESMLGVTLAKEHSAADWSVRPLPEAMLAYAALDVELLV
+PLRAAMLELLEAEGKREWAEQEFEHVRTAPAPGPRADPWRRTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSLIAAAESQPRTVPALRQTSGFHGRAASREAPPLDHRD
+PRRRRGRRARRRPARPGARRGRPAPAPGVEGPRPARRPPPEDRQGARGPARRAAGPAHGE
+PAHPGHPAPALLGAAAAADARGRGRVPPRARGPALAGGPGGRGGHRGPAGPGPRRGLSRG
+GRRADAAVGRGPTHR*
+>NZ_CP083691.1_1473
+MTSPTSPAVATSPDPSDRPGGEQAAPTLVAEPAGGVPVVTDTPAGLAACAAALAAGTGPV
+AVDAERASGIRYGQRAFLVQLKRAGAGIWLVDPEAFEDLAPLDEALRGVEWVLHAASQDL
+PCLADCGMRPDLLFDTELAARLAGLPRVGLAAVLESQLGLTLAKEHSMADWSTRPLPVDW
+LNYAALDVELLVELRDALAVLLEEQGKLAWAEQEFEHVRTTPPAAPRQDPWRRTSGMAAL
+KRPVQLAVLRRLWQAREDLAQHRDLAPGRLLPDSALVAAASTLPRTVPELRATRGFHGRS
+AAREAPRWITAIRAGIEDAAAGQAPPRHGPGSDAPPPPRAWRDRDPLADRRLTTAKPRIA
+RAAEALGMPPENLLTPDTLRRVCWTPPETITPETVAAALAERGARPWQVEQTSAIITVAL
+LDPDPARDR*
+>NZ_CP097650.1_1194
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERGDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001086.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001086.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5c1f3034f7e202b7211633e68b8def2d2c2a4d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001086.fa
@@ -0,0 +1,69 @@
+>NZ_CP042169.1_1238
+MTSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATL
+LGLGRVLDEQAARAAAGEIQALAVTGVEGTFAAGADLSLIASITDDVGRDLALLGHAVYD
+RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP
+HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVTGDESV
+AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEALFTGARTRTRAESAQA
+EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA
+LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGQALAGLITADTDKA
+VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLERPERLVG
+FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG
+EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA
+NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE
+DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA
+AQA*
+>NZ_CP033200.1_967
+MTSVSLASFDHLPALAPDEVVTTVTVTDHALPDGAGTLALLTLDNGQGPRRPATLGPATL
+LGLGRVLDEQAARAAAGAIQALAVTGVEGTFAAGADLSLIAGLTDDVGRDLALLGHAVYD
+RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP
+HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAGDESV
+AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQA
+EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA
+LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGEALAGLITADTDKA
+VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPERLVG
+FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG
+EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA
+NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE
+DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA
+AQA*
+>NZ_CP040019.1_1579
+MTFTPAPLAPFESLLPLVPDEVLTHVAATDHVLPGGAGTLVLLTLDNGQGPRRPATLGPA
+SLLELGRAVDAQAERARAGEVQALALTGVEGTFAAGADLSLIAGIEDRTVGRDLARLGHA
+VHDRIDAFPAPTLALVNGTALGGGLELALAADHRVVAADARGFGLPEVRLGLIPGWSGVW
+RVPHLIGPEAAVEVVLKNPLDNNRMLDARTAHGLGLMDEVAEGDLLEAGLAFAARIVAGD
+DAALAAVRDHRDRDVSDAAWDRALEAMEALQAGRPGRDLPARRALQELFAGARTRTREES
+AEAEAEALHGLIGSDEFRRTVYAFLDLLQRRAKRPVGDPGKELAREVTKVGVVGAGLMAG
+QLALVFAQHLRVPVVMTDMDQERVDRGLAGVRGQVEKMVSRGRITAEQGEALAGLITAST
+DKSVYADADVVIEAVFEELEVKRTVFRELEPIVREDAVLMTNTSSLSVAAMAEVLEHPER
+LVGFHFFNPVAQMPLIEVVRVAETSDEAVATAFELSRRLRKTGVLVHDAAAFVVNRVLLR
+MMGEVQASFDEGTDAHTADHALDPLALPMTPFTLLAMVGIPVAQHVSESLQAAFGAERFP
+VSANLQRLIDAGKTAIWAKDVRRDKVEEEAAGATGETIPAGTAALIERGSSPQTAEELRR
+RVEDALAEEIGLLLAEGVVAAPEDVDLCMILGAGWPLHLGGITPYLDDCGAAERVNGTRF
+HG*
+>NZ_CP083691.1_1472
+MSHTPAPLDQFEHLSTIAPDEILTRATATDHALPDGAGTLALITLDNGQGPRRPATLGSA
+SLLELARAVDEQAARASAGEIQALGITGVEGVFAAGADLALVASLPADAETGRALGRLGH
+AVYDRIDAFPVPTVALVNGTALGGGLELALACDRRVIAPEVKALGLPEVRLGLIPGWSGV
+WRAPHLVGPEAAVALLLTNPLDNGRMIGAADAVRLGLMDSLAEGDLLAAGLTAAADAVAG
+RTVQRTADVSDAAWDRALQAFGAAQSARPGRDLPARRHLEELFAGARTRTRAESAEAEAD
+ALADLIGSAEFRRTVYAFLGLVQGRAKRPAGDPGVEQAHTVHRVGVVGAGLMAGQLALLF
+ATALRVPVVMTDLDQERVDRGLAYVRSQLERSVTKGRMKAEDAEAVAGLITGATDVSAHA
+EAEFVIEAVFEELEVKRTVFRQLEQVVSPTAILATNTSSLSVAGMAEVLEHPERLVGFHF
+FNPVAQMPLVEIVRVAETTDAAVATAFELARRLRKTAVLVNDAAAFVVNRVLLRMMGEIQ
+NSFDQGTDAHTADHALDPLAFPMTPFTLAAMVGLPVAQHVSESLQAAFGAERFPVSENLQ
+RLIEAKKTAIWAKDVKSPEEAGGATGETIPADTAALIEQGDTPQTADELRVRVEDALAEE
+IGLLLDEGVVAAPDDVDLCMILGAGWPLHLGGITPYLDDCGASERVRGARFHQA*
+>NZ_CP097650.1_1195
+MTSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATL
+LGLGRVLDEQAARAAAGEIQALAVTGVEGTFAAGADLSLIAGLTDDVGRDLALLGHAVYD
+RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP
+HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAGDESV
+AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQA
+EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA
+LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGEALAGLITADTDKA
+VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPERLVG
+FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG
+EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA
+NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE
+DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA
+AQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001092.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001092.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c260ac35789e11be5e07d12c98e672449ff30c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001092.fa
@@ -0,0 +1,85 @@
+>NZ_CP042169.1_1252
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMPDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+*
+>NZ_CP033200.1_985
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMPDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+*
+>NZ_CP040019.1_1571
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAEKLPYSLKVLLENLLRTEDGANVTAEQIK
+ALASWNPDAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPAGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAMFPIDEVTLDYLRLTGRTAEQVDLVEAYTKEQGMWHDPSSEVKYSEYLE
+LDLSTVVPSISGPKRPQDRIELSDSKDQFRKDLHNYATQDEAGEGRPSKLVDVSMEDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDSEGNDVFLKDIWPDPTEVQKIID
+ESIDTEMFTSQYGTIFDGDERWQSLETPSGSTFEWDEQSTYVRKPPYFEGMTMQPDAVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGKYLLENGVERKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGGDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+*
+>NZ_CP083691.1_1465
+MTTVDSFGSKGVLDVNGSEYEIFRLNAVEGAQKLPYALKVLLENLLRTEDGANVTAEQIK
+ALASWDPTAEPDTEIQFTPARVIMQDFTGVPCIVDLATMREAIADLGGDPSRVNPLSPAE
+LVIDHSVQIDSFGNDAAVERNMDIEYQRNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARAVMVRDVDGVKRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGQIPAGATATDVVLTITEQLREHGVVGKFVEFYGEGVGAVPLANRATIG
+NMSPEFGSTAAMFPIDDVTLDYLRLTGRSEEQVALVEAYTKEQGLWHDPSAEVQYSEYLE
+LDLSTVVPSISGPKRPQDRIVLSDSKDQFRKDLHNYATQDEAGEGRPSKLVDVHMEDGRE
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLTAKPWVKTSVAPGSRVVTDY
+YEKSGLNASLDALGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDCDFENEALGTDQDGNDVFLKDIWPDPAEVQRIID
+ESIDTEMFTSQYGTIFDGDERWQSLETPTGKTFEWDEASTYVRKPPYFEGMPAQPEPVQD
+IAGARVLLKLGDSVTTDHISPAGSFKSDTPAGQYLLANGVERKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGTGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPAGESADSLGLTGTETFAIS
+GIAELNEGRTPKTVKVTATAEDGKVTEFDAVVRIDTPGEADYYRNGGILQYVLRQIAAKA
+*
+>NZ_CP097650.1_1209
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMADGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001094.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001094.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36e64a5af44edae71d136021c48ffe3195a3217d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001094.fa
@@ -0,0 +1,61 @@
+>NZ_CP042169.1_1254
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS*
+>NZ_CP033200.1_987
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS*
+>NZ_CP040019.1_1569
+MATLSSLLRRGLLGRPVASHDVAEPRMSRWQALPVTSSNALSSLAYAPDEIVLTLVAAGT
+AALALGPLVGWGVVVVMLLIVASFRAAVAAVPQGGIYQMARTKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFAAALLPGLGLESRVLVACAALVGVLLTSLRSARLSRWALPVLVSAF
+VALTALLVAAGLWQEGQGLLGRAATSGWTQEGAGIGGTVGAVATALLALRAFSAGSVLLT
+GVEVPVSSSSAMARPAVATVRWVLAVMALTLGALTLGVMHLAQRTGVVVALDPARLRDAA
+GRPVAEADTPAPVIAQLADTVFGPGSVLSLATIAATALLLLFAARSAFRSFPALASRLAE
+DGYLPRQLRVRGDRLVHTWGVLALGAAALALVLLFRAQTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLAQTPGARARAAVRLRLTITAVAWVVTALAGVVVLVTRFAQGAWVALLAIVL
+GSLVMGRIRRHYEDVGRELAPDPEDDARALPSRVHVVVVVSTLNRPALRALAYARATRPS
+SLEAVVVDAERAVTEDVIDAWSRAGLPVPLTVVAAPYRDTVVPLVRHLRERRRRSPRDLT
+MVFIPEYVVRPGWRTLMHNRTATRQKRRLQREAGVMIGSVPWQIHEGQGDGQRSTTV*
+>NZ_CP083691.1_1463
+MSTPPSTLRRLLLGRPVASGARPAPRRGRWLALPATASNALSSLAYAPDEVILTLVASGT
+GALALGPLVGWAVVAVMVLIVLAFRAAVVAVPRGGIYRMARTKLGPRSGVVAAAALLLDF
+VFTAAVSVAAFAHHASALVPALRGHVGIVSAVALVLVLVSALRGERGSGALVTVLVAAFV
+GLLGTLVAVGLWQSGQGTLAAAPSAGLHVDGAGLGPVGDAATALLALRAFSAGSVLLSGV
+EVPLSATDRMARPAVRTARWVLTVLAVVVGTLTVGVMHLAQRTGVVVALHPDRLRTADGA
+PLAPDTAPAPVVAQLAETVFGAGSPGAVATVAVTSLLLLVAARGAFRSFPTLTARLAEDG
+WLPRQLRVRGDRMVHTGGTLALATATLLLLVLFRGRTALLVQLYVIGVLLAFALALVGML
+RLWRLKLAHTPGARARASVRVKLVVTAVGLGATALAGVVVLVTRFAQGAWVALLAIGVSA
+VVMGRIRRHYRAVEAELAPDPQDDARALPSRVHAVVVVSTLNRPALRALAYARATRPATL
+EAVVVDADRRQTERVVEDFARAGLPVPLTVIAAPYRDTVVPLVRHVRGRRLRSPRDLTMV
+FIPEHVVRGGWRRLLHNRTASRQKARLQREAGVMVGSVPWQIREGDPHRPVEGGIVACAA
+PGDVPEGVESS*
+>NZ_CP097650.1_1211
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001100.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001100.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4c4af95ec9aa3006ab8c1acf8aaf8213d250249
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001100.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1260
+MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG
+HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL
+QPVVRARFEPVDALPDSERGAGGFGSTGGFTADNTPGRTS*
+>NZ_CP033200.1_993
+MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG
+HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL
+QPVVRARFEPVDALPDSERGAGGFGSTGGFTADNTPGRTS*
+>NZ_CP040019.1_1563
+MTDSAELPVPLHALDPDLAPPAYAQPGDAGADLRAAVDVTLAPGERALVPTGVALAIPEG
+FAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTDAVELRRGDRIAQLVI
+QPVVRARFAPVDALPGSERGAAGFGSTGGFGTENAPGRTS*
+>NZ_CP083691.1_1457
+MNGPREIDVPLRALDPQLPPPEYARPDDAGADLRAAEDVTLAPGERALVPTGVALAIPAG
+FAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPVVLRRGDRIAQLVV
+QPVVQARFMAVDRLADSERGEAGFGSTGGFTPAAHDDAPGRTA*
+>NZ_CP097650.1_1217
+MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG
+HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL
+QPVVRARFEPVDALPDSERGAGGFGSTGGFTADNTPGRTS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001105.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001105.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d7057700890bcd8d31348c1a445bbd7fe24721c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001105.fa
@@ -0,0 +1,85 @@
+>NZ_CP042169.1_1266
+MGETEADRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS
+ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG
+SILMEHLAAAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA
+RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGTVHAVN
+RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG
+AEGLEAQRRLVSLARAHGMRVIGPASTGLVRTDPAIRLNASPSPGLAQRGPVSLFSQSGA
+VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS
+RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD
+ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPADTL
+VSAVRDAVCHEQADAVVVLARLGLHQADDEPERLAHALADATREARIPVLGCLTDVVSPR
+YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMAVLGALADYVHWRHQEVGEPLEPTG
+LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSVRFETAEEAVAAAERL
+GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG
+QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT
+GGVPPVDLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPERVTVLQAEVHVANAARRTD
+SARRALRGR*
+>NZ_CP033200.1_999
+MGETEAVRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS
+ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG
+SILMEHLAVAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA
+RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGAVHAVN
+RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG
+AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAIRLNASPSPGLAQRGPVGLFSQSGA
+VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS
+RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD
+ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPAETL
+VSAVRDAVRHEQADAVVVLARLGLHQADDEPERLAHALADATRDARIPVLGCLTDVVSPR
+YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMTVLGALADYVHWRRQEVGEPLEPTG
+LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSARFETADEAVAAAERL
+GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG
+QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT
+GGVPSVNLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPEGVTVLQAEVHVANAARRTD
+SARRALRGR*
+>NZ_CP040019.1_1557
+MGDTEPVRDYPSHWEADVVLRDGATARLRPITPEDADELQRMHAGQSENSIYLRYFTYKS
+ELSAKDLDRFTHVDHKDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG
+SILMEHLAVAAREHGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA
+RWRAVVESREHRAEARSVAELVAPESVAVVGASRDPQAVGSMVLRHILEGGFAGPVHAVN
+RAAGEVQGLTAHASLAEIGEEVELVVVAVPVDQVEALVPEAAAAGAAGLLVLTSGYADAG
+AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAVRLNASPSPGLAQRGPVGLFSQSGA
+VGAMVSAGAKRRGVGVSTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFT
+RITRRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGAVDSMLDQTGVLEVHTHEAMLD
+LLMAVASQPLPTGRRVVLVADSLAVDRLARDAAAEAGLDVVATVGLAGSEQGVAPPAETL
+VASVREAVAHEQADAVVVVGRLGLHQEDDDPETVARALAEATAGARMPVLVCLTDVVSPR
+YAGATLGASGPVADDAEPGSLQPGVPFYPSPQQAMSVLGALADYVRWRGEEAGEPLEPAD
+VRLHAAEDLVEAAAARAEGTELVRLSAAETEELLGHYGIAVLPSARFETADEAVAAAERL
+GFPVAVKAVDPHLRHRLDLGGVRLNVVDAASLRRNVEQMRRVLAPFGVTELEVQAMAPAG
+QACMVTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAAKLEGR
+GGVPAVDLAALEDLVGRVSVLKDDLPQVARLRFSPVLASPEGVTVLQAEVDVANAAGRTD
+SARRALRGS*
+>NZ_CP083691.1_1451
+MAEPDTETAYPSQWEADVVLRDGATARLRPIREDDVDGLRALHAGQSESSIYLRYFTFKS
+ELSAKELERFTHVDHRDRVALVIERGGRILGVGRYDRYGDSDAAEVAFNISDAAQGQGLG
+SILMEHLAVAAREQGIRRFTAEVLPENRKMLSVFQDSGFEVARHFEDGVVAVEFPIDPTA
+RWRAVVESREHRAEARSVAELVEPESVAVVGASRDPHAVGSIVLRHILEAGFTGRVHAVN
+RAAEDVQGLTAHASLKDIGEPVDLVVVAVPVAEVDAVVAEAAEAGAQGLLVLTSGYADAG
+EDGLRAQRRLVARARARGMRVIGPASAGLVRTAPDVRLNASPSPGLASRGPVGVFSQSGA
+VGAMITAGMKRRGVGMSTSLSAGNRADVSGNDAMQFFEDDPHTAAVGVYLESFGNPRKFS
+RIARRLSRTKPVVVVRSDVTGRALPPGHETRTTQAPEGAVDSMLEQTGVLEAATHEDMLD
+LLMAVATQPLPTGRRVTLVADSLALDRLGRDAAAVAGLEVVATHGLGGSEQGIAPTADDV
+VASVEAALAAGDTDAVVVVTRLGLHQDEDAAHEVAQALARVAEGATVPVLGCLTDVVSAR
+YGGARVGGAAAPAADAEPGALQPGLPLYPSPRKAMTVLGRLCDYVAWRREDAGEPIELTD
+VDVRAAEALVDRALERALGTELIRLTGAETEELLRIYGIGVLRSRRFTTPDEAVAAAEEL
+GFPVAVKAVDPYLRHRLDLGGVRLNLEDAESLRQNVRQMRAVLAPFGVTELEVQSMAPSG
+QPCMVTALEDPLLGPVVSFGMAGDATDLLGDWVHRVPPLTDQDVRRMVRSPRAAVKLDGV
+GGVPAVDLDALEDLLARVSCLKDDLPAVARLRFAPVLAAPTGTTVLSAEVDVANAAGRTD
+SARRALRAS*
+>NZ_CP097650.1_1223
+MGETEAVRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS
+ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG
+SILMEHLAVAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA
+RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGAVHAVN
+RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG
+AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAIRLNASPSPGLAQRGPVGLFSQSGA
+VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS
+RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD
+ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPAETL
+VSAVRDAVRHEQADAVVVLARLGLHQADDEPERLAHALADATRDARIPVLGCLTDVVSPR
+YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMTVLGALADYVHWRRQEVGEPLEPTG
+LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSARFETADEAVAAAERL
+GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG
+QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT
+GGVPSVNLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPEGVTVLQAEVHVANAARRTD
+SARRALRGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001107.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001107.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63ad979d4c1543267248feedddb7a1c2776565d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001107.fa
@@ -0,0 +1,108 @@
+>NZ_CP042169.1_1268
+MTDDGAPRGPGRGHDDGPRRRRGPDLSPAARRAVAAMLGLAALRAAGWILLAESLARLLT
+RMAGTLDPEGTAQLFEMLFLPPAPVGPVGAASSFAGALALGAAGVGLRALADAGQRVWGR
+RAALGVQVGVRRDLVAHRLASADGSRPRSGADAVLVTHGLQGLDDYYTEVLPALASAAVV
+PPVLGAWILTRDPLSALVVLLTVPLVPFFMVLIGRHTQERIDAAQDGLDRLSGHLVELAR
+GLPVLVGLRRAGVQRRALERASQRYHAATLGTLRTAFVSGMALELIASLSVAVMAVFIGL
+RLVYGQMDLGAGLVVLVLAAEVYLPLRDVGSAYHASEDGREAEGRARAAARAPVPEAARD
+ALADPTAAPARAAGPAAAPPGAVHLEDVGVAFGDRRVLQGVDLRAAPGTLTVLGSASGTG
+KSTLLHLLAGLLRTTDARVQGSVSGVDPDRTVWVGQHPRLLEPTVGEELDAAAGRALADS
+ERAAVLAAVALDGAAHRRPVELSPGELRRVALARALARLSTAGADRRPWLVLLDEPTAHL
+DDAAAAAVRAGVVALARAGVPGLALPPCIVVAASHDPALQRAADALVDAQGTPLAPGAAD
+GPADPEAAAPAGPEPASPAAVASPVEAEPVPASATSTAPSPAAARRARTRAALRILPWRS
+GRLWAGVAWATGTHLSAALLAGLSGWLIVTAAGRPPVLYLLSVIVLVRAFGLSRAVFRYL
+DRLATHDAVLGWASRLRLRLWDALGRRPALWGRLSRADGALSVLVADVDALRDAAPRVMV
+PVPAAVLAWLVSAGAVALLAPELAAAALVPGALGLVAIPVVVAALDRRQTQAAVRHRAGL
+LDRVAAVLAAAPDLHGLGRARAAADRLAEADAALQAPQRRAAWAAGAGRALAVLVSGGTA
+LAVALTATQTGTAAAVAAFAVLLVLSWAEPYGALAQSAQELGTLASQARAAADLMGEDEP
+GTAVPDAADPGRASATPDPTSAPMSADPEPAAPVRVTGLALRGAAVRFEGADAPLWSGVD
+LCVEPGQTAVVTGPSGAGKSTLLAVLLGFQPLAEGAYLLRTEADGRRVEAPADAAALARV
+AWTPQDALLFDSSLRGNLALARDPEDAPDDAELTAVLGRVGLGPWLAAAPEGLDTPVGAG
+GRVLSGGQRQRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRAALAGRIAVVVTH
+DERLAAEADVRLRLGVSPPRPSRGRPRPAAR*
+>NZ_CP033200.1_1001
+MTPAALRALPALLALAVLRALGWILLAESLARLITGLAMTLDPEDSARLLDLLFHPPAPV
+GPVPAAQTLSGPVLLGAAGVALRALAEAGQRVVGRRAALGAQQQVRAAVVAQRLAAADGG
+RPRSGADAVVVTHGLKSLDDHYTEALPALAATAVVPAALGVWILTHDLVSAVVAAITLPL
+VPLFMILVGRHTQERIDAAQDGLDRLAGHLLELARGLPVLVGLHRAGVQRRALQEVSQRH
+HAATMVTLRTAFLSGLALELIASLSVAVMAVFIGLRLVNGQMALLDGLVVLILAAELYLP
+LREVGAAFHASEDGREAESRARAAADAPVPAPVLDTLGPASGPDRDGGVLVQDLSVRMAG
+RQVLEGLDLTAPPGHLTALAGPSGTGKSTVLRLLAGLLRQDAAEATGRVAGVDTERTLWI
+GQHPVLTERTVAGELDLAAGGALPGPVRSAVLAAVALEGLQERDPADLSPGECRRVAVAR
+LLARLHAADGTGPWLVLLDEPTAHLDGAVAAVVVETLAALPSGAVPGLSTPQCTVLAASH
+DPTLLTAADAIVRLAPGAGPTAGSPATAMPVAAAQGRARPEPVTPRQVSLRAGLRLLPWR
+QPKLWAGIGWAAGTHVSAALLAALSGWLIVTASTRPPVLYLLAVIVLVRGFGLSRAVFRY
+LDRLTTHDAVFGWATELRLRLWDALGRQPRLWGRVGRTDGALSLLVSDVDAFRDAVPRVL
+VPAPAALLAWLATAALTWALAPELAVVALVPGAVALVVIPALVAVLDRRQTAAQVRGQGA
+LVDRVAAVLNAAGDLRGLGLTEPALRGLAVLDDRLQRPRRRAAWAAGGGRALAVAASGGI
+AVAAAAAAAHTGTSAPVAALVVLLALSWAEPYGALAAAAQHWGTLADRARATGELLGPEE
+GGAAAAPPEPAEAAEPEARVCRLRLVEAAFAHPGAPPLWTDLELDLAPGDVAVVTGPSGS
+GKSTLLAVLLGFLPLTAGRYTLETVPPTPQPDPVRPDATALARVAWTPQDALIFDSTARG
+NLALARGVADAPSDAELTAALELVGLGPWLAAAPQGLDTRVGPGGQRLSGGQRQRLAVAR
+ALVARADVVLLDEPTAHVDADEARALITDLRRALADRIVVIVTHDGRLLEDGDVPVRVGC
+*
+>NZ_CP040019.1_1555
+MTDDGAPRGPGREHDDGPRRRRGPDLSPAARRAVAAMLGLAALRAAGWILLAESLARLLT
+RMADTLDPEGTAQLFEMLFLPPAPVGPVGAASSFAGALALGAAGVGLRALADAGQRVWGR
+RAALGVQVGVRRDLVAHRLASADGSRPRSGADAVLVTHGLQGLDDYYTEVLPALASAAVV
+PPVLGAWILTRDPLSALVVLLTVPLVPFFMVLIGRHTQERIDAAQDGLDRLSGHLVELAR
+GLPVLVGLRRAGVQRRALERASQRYHAATLGTLRTAFVSGMALELIASLSVAVMAVFIGL
+RLVYGQMDLGAGLVVLVLAAEVYLPLRDVGSAYHASEDGREAEGRARAAARAPVPEAARD
+ALADPTAAPARAADPAAAPRRAVVLEDVGVAFGDRRVLQGVDLRAAPGTLTVLGSASGTG
+KSTLLHLLAGLLRTTDARVQGSVSGVDPERTVWVGQHPRLLEPTVGEELDAAAGRALADS
+ERAAVLAAVALDGAAHRRPVELSPGELRRVALARALARLSTAGADRRPWLVLLDEPTAHL
+DDAAAAAVRAGVVALARAGVPGLALPPCIVVAASHDPALQRAADALVDAQGTPLAPGAAD
+GAADPEAAAPAGPEPASPAAVASPVEAEPVPASATSTAPSPAAARRARTRAALRILPWRS
+GRLWAGVAWATGTHLSAALLAGLSGWLIVTAAGRPPVLYLLSVIVLVRAFGLSRAVFRYL
+DRLATHDAVLGWASRLRLRLWDALGRRPALWGRLSRADGALSVLVADVDALRDAAPRVMV
+PVPAAVLAWLVSAGAVALLAPELAAAALVPGALGLVAIPVVVAALDRRQTQAAVRHRAGL
+LDRVAAVLAAAPDLHGLGRARAAADRLAEADAALQAPQRRAAWAAGAGRALAVLVSGGTA
+LAVALTATQTGTAAAVAAFAVLLVLSWAEPYGALAQSAQELGTLASQARAAADLLGEDEP
+GTAVPDAADPGRASATPDPTSAPMSADPEPAAPVRVTGLALRGAAVRFEGADAPLWSGVD
+LRVEPGQTAVVTGPSGAGKSTLLAVLLGFQPLAEGAYLLRTEADGRRVEAPADAAALARV
+AWTPQDALLFDSSLRGNLALARDPEDAPDDAELTAVLERVGLGPWLAAAPEGLDTPVGAG
+GRVLSGGQRQRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRAALAGRIAVVVTH
+DERLAAEADVRLRLGVSPPRPSRGRPRPAAR*
+>NZ_CP083691.1_1449
+MTDRPPRRRGRVRAGRGPGPGLDRRARRAVGVMALLAGVRALGWILLAESLARLLTSLAM
+TLDPEASAQLFQLLFMPPAPVGPVGPVADVAGVVVLGAAGVVLRALADQGQHVAGRRAAL
+GAQVGIRRELVAHRLAATDGTRPRSGADAVLVTHGLAGLDDYYTEVLPALASAAVVPPML
+GVWILTRDGVSAAVVLLTVPLIPFFMVLIGRHTQERIAAAQDGLDRISGQLLELARGLPV
+LVGLRRAGVQRRALEKASERYHAATLGTLRTAFVSGLALELIASLSVAIMAVFIGVRLVY
+GQMDLYSGLVVLVLAAEVYLPLREVGSAYHSSEDGRAAAERAAAAVAEPVPTPALASLAW
+PGPETGQDHGTDGGMDDGMDDRTPAAGTVLLRDVSVSRGPRPVVRGADLTLRPGGLTVLG
+SASGAGKSTLLHLLAGVLRTPDVAVSGTVAGVDSDRTLWVGQHPRFLEATVDAELDAAAG
+GALAAPVRREVLRAAALADFGARAPHELSPGEQRRVALARAMSRLAADRTAVETRPWLVL
+LDEPTAHLDDASAAVVRATVGALARGAVPGLPTPPAAVLAASHDPVLQRAADALVDVEGR
+PLAPGADAAPYADPDAAGPPLAAGAPDDAGPGDAPDAPRGEGSEGRPSLRAVLAVLPWGA
+PRLWAGVGWATLTHLAAALLAGLSGWLIVTAAGRPPILYLLSVIVLVRGFGLFRAVFRYA
+DRLATHDAVLRWASELRLRLWDAMGRRPALWSRLSRADGALSVLLSDVDALRDAAPRVLV
+PVPAAVLAWAVTALLIGGLAPELAVTALVPGAVGLLVIPVVVAALDRRDTLLTARRRAAL
+LDRVSAVLGAAPDLHGLGRTREAAAALTAWDEDLQRPQRRAAWVAGLGRALAVLASGGAA
+LAAALTATQTGTSTPVAAFVVFLALSWAEPLGALAQAAQQTGTLVDQARQAAGLLGVEDE
+AASGATSAAPDEAAASAAGSSAPAGRITGVRLEDAAYAYPGSTRVLWSGLDVALESGQTA
+AVTGPSGAGKSTLLAVLLGFLTPTAGRHLLTVERDGVSREAPADPAALARVAWTPQDALV
+FDSTVRGNLALARDADDAPTDAELADTLRLVGLGRWLDAAPDGLDTPVGPGGDRLSGGER
+QRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRRALAGRIAVVATHDPRVAAAAD
+VRVRLGGDAAGHP*
+>NZ_CP097650.1_1225
+MSPSRPAAPAVERSASAAGPHPGRTRRARPPMTPAARRALPALLALAVLRALGWILLAES
+LARLITGLAMTLDPEDSARLLELLFHPPAPVGPVPAAQTLSGPVLLGAAGVALRALAEAG
+QRVVGRRAALGAQQQVRAAVVAQRLAAADGGRPRSGADAVLVTHGLKSLDDHYTEALPAL
+AATAVVPAALGVWILTHDLVSAVVAAITLPLVPLFMILVGRHTQERIDAAQDGLDRLAGH
+LLELARGLPVLVGLHRAGVQRRALQEVSQRHHAATMVTLRTAFLSGLALELIASLSVAVM
+AVFIGLRLVNGQMTLLDGLVVLILAAEVYLPLREVGAAYHASEDGREAESRARAAADAPV
+PAPVLETLAPASGPDRDGGVVIRDLSVRLAGRQVLGGLDLSALPGRLTALAGPSGTGKST
+VLRLLAGLLRQDAAEATGRVAGVDTERTLWIGQHPVLTERTVAGELDLAAGGALPGPVRS
+AVLAAVALEGLQERDPADLSPGECRRVAVARLLARLHAADGTGPWLVLLDEPTAHLDGAV
+AAVVVETLAALPSGAVPGLSTPQCTVLAASHDPTLLTAADAIVRLAPGAGPTAGSPATAM
+PVAAAQGRARPEPVTPRQVSLRAGLRLLPWRQPKLWAGIGWAAGTHVSAALLAALSGWLI
+VTASTRPPVLYLLAVIVLVRGFGLSRAVFRYLDRLTTHDAVFGWATELRLRLWDALGRQP
+RLWGRVGRTDGALSLLVSDVDAFRDAVPRVLVPAPAALLAWLATAALTWALAPELAVVAL
+VPGAVALVVIPALVAVLDRRQTAAQVRGQGALVDRVAAVLNAAGDLRGLGLTEPALRGLA
+VLDDRLQRPRRRAAWAAGGGRALAVAASGGIAVAAAAAAAHTGTSAPVAALVVLLALSWA
+EPYGALAAAAQHWGTLADRARATGELLGPEEGGAAAAPPEPAEAAEPEARVCRLRLVEAA
+FAHPGAPPLWTDLELDLAPGDVAVVTGPSGSGKSTLLAVLLGFLPLTAGRYTLETVPPTP
+QPDPVRPDATALARVAWTPQDALIFDSTARGNLALARGVADAPSDAELTAALELVGLGPW
+LAAAPQGLDTRVGPGGQGLSGGQRQRLAVARALVARADVVLLDEPTAHVDADEARALITD
+LRRALADRIVVIVTHDGRLLEDGDVPVRVGC*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001111.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001111.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37c0ff9a6ceb3444f9989522944b0c47f12981d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001111.fa
@@ -0,0 +1,89 @@
+>NZ_CP042169.1_1274
+MPQIPAAPAVLPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIV
+GTIVAVHGNPTWSWLWRSLLAETVRRARRGMAAWRVVAPDQLDMGFSERLAHTGSPSASS
+MGRADDTYRTLGGRIADLDALLAALGLRDLAATGHPLITLGHDWGGVVSLGWAARHPELV
+AGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA
+YHLPYDTAARRGGVGGFVADIPADPGHGSHPELQRVGEDLAALGRTDVPALILWGADDPV
+FLDRYLDDLRDRLPHARVHRYEGAGHLLVDDRDITAPLLQWAQLLRAGQLSDPASGLPGP
+VPHATADPGLEVDLGEEPGAREPGMVRLWDHLRDWGAPGSDHREYTALVDMAGAQAGRSL
+VGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLRVGAV
+AVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRRLLDV
+SDSLYAMVDRHRDPATGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHERLGR
+LVAMISRTLGIRPGGSLLAGFAPFALLGPALGAASVSPDMDVTKPATLTARSLADAAIAG
+QSTVLFASPAALANVVATADGLDAARRDALDAVRLVLSAGAPVHPQLMRQVRDLMPNAEV
+HTPWGMTEGLLLTDIDGETVQRLRGADDEGVCVGTALPTVSLAIAPLLEDGTAEDLILDP
+AQGHGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADIGHFDAEGRVW
+LEGRLQHVITTPEGPLGPGGPEKTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVPATRP
+ARRAGQHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRARVAR
+WAEGVLAGGRAGAL*
+>NZ_CP033200.1_1005
+MPQIPAAPAALPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIV
+GTIVAVHGNPTWSWLWRSLLAETVRRARRGMAAWRVVAPDQLDMGFSERLAHAGYPSAAS
+MGRAGDTYRTLGGRIADLDALLAALGLRDLAATGHPLITLGHDWGGVVSLGWAARHPELV
+AGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA
+YHLPYDAAARRGGVGGFVADIPADPGHGSHPELQRVGEDLASLGRTDVPALILWGADDPV
+FLDRYLDDLRDRLPRARVHRYEQAGHLLVDDRDITAPLLQWAQLLRGGQLSDPASGLPGP
+VPHATTDAAADPGLEVDLGEEPGARDPGVVRLWDHLRDWGAPGSDHREYTALVDMAGAQA
+GRSLVGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLR
+VGAVAVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRR
+LLDVSDSLYAMVDRHRDPAAGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHE
+RLGRLVALISRTLGIRPGGSLLAGFAPFALLGPALGAASVSPDMDVTQPATLTAQKLADA
+AIAGQSSVLFASPAALANVVATADGLDAPQREALDAVRLVLSAGAPVHPQLMRQVSDLMP
+NARVHTPWGMTEGLLLTDIDGDEVQRLRTADDAGVCVGSALPTVSLAIAPLLEDGSADDV
+ILDPARGHGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADVGHFDAE
+GRVWLEGRLQHVITTPEGPVGPGGPEKTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVP
+ATRPARRPGHHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRA
+RVADWAEAVLAGGKAGAL*
+>NZ_CP040019.1_1549
+MEIRSAADPEGTVRTLHVADTGPVLAAAGAEIVGTIVAVHGNPTWSWLWRSLLAETVRRA
+RRGMAAWRVVAPDQLDMGFSERLAHPGHPAAASMGRDGDTYRSLGARIEDLDALLETLGL
+RDLAATGHPLITLGHDWGGVVSLGWAGRNPELVDGVATLNSAVHHPEGAPIPAPLQAALA
+GPVLPASTVLTDAFVSVTTSLAKPALASDVRAAYHLPYETADRRGGVGGFVADIPAEPSH
+GSHAELRRVWEGVSALGRAGTPALILWGADDPVFLDRYLDDLRDRLPQARVHRYEEAGHL
+LVDDRDVTAPLLQWAQLLRAGQLDDPGSGLPGPVPHAPAASPADEDGLHVDLGEHAAPAG
+DDVARLWDHLRDWGAPGSEHREYTALVDMAGAQTGRSLVGGARRPVAVSWGELQETVSAI
+ATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLRVGGVAVVADQGLGIAGMTRAMKSARP
+RWIIGRTPGLTLARAQSWPGARISVTEPGAAQKRLLDVSDSIYAMIERHRDPAVGEPVDE
+HGSPLPEPALAADAAVLFTSGSTGPAKGVVYTHERLGRLVAMISRTLGIRPGGSLLAGFA
+PFALLGPALGAASVSPDMDVTKPATLTARSLADAAIAGQSTVLFASPAALANVVASADGL
+DAARRDALDAVRLVLSAGAPVHPQLMRQVRDLMPNAEVHTPWGMTEGLLLTDIDGETVQR
+LRGADDEGVCVGTALPTVSLAIAPLLEDGTAEDLILDPAQGHGVLGEIVVSAPHLKDRYD
+ALWHTDQQSKRDGLWRRDGRVWHRTADIGHFDAEGRVWLEGRLQHVITTPEGPLGPGGPE
+KTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVPATRPARRAGQHRDGRPKQGLAPTALA
+SAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRARVARWAEGVLAGGRAGAL*
+>NZ_CP083691.1_1443
+MPRIPAAPAALPPFDQLPGWDPDWSRLVTIRSAADLPGVERTLHVADNGPQLAALGAELA
+GTILAVHGNPTWSYLWRALLAETTRRARRGQQAWRVVAPDQLDMGYSERLEHPASPTPSE
+MGRARSTYRSLGDRLDDLDALTAALGLTDLAATGHPLITLGHDWGGVVSLGWAGRHRDVV
+AGVSTLNTAVHQPPQAKIPAPLQAALAGPVLPASTVSTDAFIAVTTSLAKPSLAPEVRAA
+YHLPYPSAERRGGVGGFVADIPVDASHGSHAALEEVSSGVSALGAQGTPALIQWGADDPV
+FLDRYLDDLRDRLPAARVHRYEEAGHLLIDDRDVVTPLLTWAQLLTAGLLADPASGLPGP
+RPHADDAAPRTSALPLLPEASRGVHVDIADHASEAGSPAGLPRLWDRLEDWGAPDSPMRE
+YTALVDMAGAETSRALFGGARRPVAVSWGEFQETVSAIATGLWEAGMRPGDRVSMLVPPG
+RDLSAALYAVLRVGAVAVVADQGLGVSGMTRAMKSARPRWVIGKTAGLTLARAQNWPGTR
+LSVSTLAAPQRALLDVSDSLYAMVDRHRAPELGVPRDAAGAPLPVPELGADAAVLFTSGS
+TGPAKGVVYTHERLGHLVRLIARTLDIRPGASLLAGFAPFALLGPALGAASVSPVMDVTK
+PATLTAAALADAAIAGQSSVLFASPAALANVVATAGDLSGEQRTALRQVRQVLSAGAPVH
+PALLRQVSALMPEAEVNTPYGMTEGLLLANIDGETIHALRRADDAGVCVGSPLPTVEFRI
+APLAEDGTPEEVTLDPAAGHGVLGEFVVSAPHLKDRYDALWFTDHQSKRDGLIRRDGRVW
+HRTADVGHFDAEGRVWIEGRAQHVLTTPDRPLAPGGPEGVVDALGPVARSAVVGVGPAGT
+QAVVVVVEAAVPAARPPRRAGHHRDGRPKQGLAPTALAASVRSALEPLPVAAVLVADHIP
+TDIRHNSKIDRPRVARWAEGVLAGGTVDGL*
+>NZ_CP097650.1_1229
+MPQIPAAPAALPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIV
+GTIVALHGNPTWSWLWRSLLAETVRRARRGMAAWRVVAPDQLDMGFSERLAHAGSPSAAS
+MGRAGDTYRTLGGRIADLDALLAALGLRDLAATGHPLITLGHDWGGVVSLGWAARHPELV
+AGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA
+YHLPYDTAARRGGVGGFVADIPADPGHGSHPELQRVGEDLAALGRTDVPALILWGADDPV
+FLDRYLDDLRDRLPHARVHRYEQAGHLLVDDRDITAPLLQWAQLLRGGQLSDPASGLPGP
+VPHATADAAADPGLEVDLGEEPGAREPGVVRLWDHLRDWGAPGSDHREYTALVDMAGAQA
+GRSLVGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLR
+VGAVAVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRR
+LLDVSDSLYAMVDRHRDPAAGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHE
+RLGRLVALISRTLGIRPGGSLLAGFAPFALLGPALGAASVSPDMDVTQPATLTAQKLADA
+AIAGQSSVLFASPAALANVVATADGLDAPRREALDAVRLVLSAGAPVHPQLMRQVSDLMP
+NARVHTPWGMTEGLLLTDIDGAEVQRLRAADDEGVCVGSALPTVSLAIAPLLEDGSAEDV
+ILDPARGHGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADVGHFDAE
+GRVWLEGRLQHVITTPEGPVGPGGPEKTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVP
+ATRPARRPGHHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRA
+RVADWAEAVLAGGKVGAL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001114.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001114.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68ea88478d737ce4797c56a11bfec2c8ea9439f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001114.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1277
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD
+ETDRLTAGA*
+>NZ_CP033200.1_1008
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD
+ETDRLTAGA*
+>NZ_CP040019.1_1545
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLPSGGALQFCGHHARAVEDALRPQAAHWQD
+ETDRLTAGA*
+>NZ_CP083691.1_1439
+MSITAVAEPAALTRADRCDRCGAQAYVRAVLPSGGELLFCGHHARGVEASLRPQAALWQD
+QTEELDGSTAA*
+>NZ_CP097650.1_1232
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQTALWQD
+ETDRLTAGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001115.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001115.fa
new file mode 100644
index 0000000000000000000000000000000000000000..003efb9a66641a513da70ab01b36a3603f5b405c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001115.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1278
+MDCKDPRVAADETERPRVTTSTTSGVQDGKETTASEATTTRTRSTAAKKSAATKSATTKG
+ATTKGATTRTTATKSAATKTAATPTAKKKATRKPTAAKTTATAKTTAAAKTTAAVKTTAT
+KKTATTRGKKATASAASAEQAEDDEEFVEARERTEAADAVEEDVVEDETATEDSDDEDAD
+GSDAPERPAMDAEAVTGTKAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDY
+LKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHL
+LEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAI
+TRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQK
+YGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVV
+AMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD*
+>NZ_CP033200.1_1009
+MDCKDPRVAADETERPRVTTSTTSGVQDGKETTASEATTTRTRSTAAKKSAAKKSAATKS
+ATTKGATTRTTATKSAATKTAATPTAKKKATRKPTAAKTTATAKTTAAKKTATTGGKKAT
+ASAASAEQAEDDEELVQARERTEAADAVEEDVVADETATEDSDDEDADGSDAPERPAMDA
+EAVTGTTAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNA
+EQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHLLEANLRLVVSLA
+KRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIR
+IPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPL
+GEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPK
+TLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD*
+>NZ_CP040019.1_1544
+MTTSTTNGAQDAPETTDSGAATTRSRSTAAKKTTAAKSTTAKGTAARKTASSTTAAKSTA
+KSAAAKGAATKAAAKTAAADGEAPAKTTTRRTAASKTTAAKSTPTKPAAKTTTRKKAAPA
+ATAKGKKATASAAAQAEQDEELADAVERTDAADAVDPDVADVVDGEAKAATEDSDDEDAD
+GSDAPDAPAMDQEAVTGTKAGSGQAVAQTKGAFVMDDSEDDAPVQQVVVAGATADPVKDY
+LKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQAEASDDYRERRDIQLIIADGRKAKNHL
+LEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAI
+TRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQK
+YGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADVVSFTLLQEQLHSVLDTLSEREAGVV
+AMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD*
+>NZ_CP083691.1_1438
+MTAGTPTERPRVTTSTTSGKQDGKETAASTTTAAAAKKTTTAAKKKTTAAAAKKPAAAKT
+ASGASTAAKKTTAKSTAAQATTTRGATTKKAAADAETEAAPAAAPRKRTSTATSTAKAAP
+KKTTRAPKKTASKAVAEEELVEEEDLELDADDVAEQASQDGDDADADGSDAPAAEDLVAT
+TEKPAETAAKGAFVMDNSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNAEQEVDLAM
+RIEAGLYAEHHFAENPPEDYRLRRDVELIIADGRRAKNHLLEANLRLVVSLAKRYTGRGM
+LFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEV
+INKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEF
+GDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKV
+YGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD*
+>NZ_CP097650.1_1233
+MDCKDPRVAADETERPRVTTSTTSGAQDGKETTASGATTTRTRSTAAKKSTATKSATTKG
+ATTRTTATKSAATKTAATPTAKKKAARKPAAAKTTATAKTTATKKTATTRGKKATASAGS
+AEQAEDDEEFVEARERTEAADAVEEDVVEDETATEDSDDADADGSDAPERPAMDAEAVTG
+TKAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNAEQEVD
+LAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHLLEANLRLVVSLAKRYTG
+RGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHM
+VEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGD
+SEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEI
+GKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001116.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbbb3fa191b83e1da248943526b7a38538b848df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001116.fa
@@ -0,0 +1,33 @@
+>NZ_CP042169.1_1279
+MEAPTSLDVPVLPARGPEDLLAYVGHALGRLPEGSLVLLTLRDGRLRAVVRVDLPPEEVD
+VGAWACAVAEVCRRDAAADATLCLALPDGARATLARPGWAAALDDALASAGRPLTAAWTC
+ARGRARPWWGSGVAEEGPLDPRAAPLSLHLMTRGSVWDRAAVPDPVPRRGPAAARADDAR
+WRPPEQDAPAARRAWLAQWESVLTGAARDRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG
+AATGDPGDEERILTAASGRAPAWDRLDALRAGLRALVPVATPAVAAQALALAGWVGWARG
+HGSDADAHLTAAAALSPDDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGRP*
+>NZ_CP033200.1_1010
+MEAPTSLDAPVLPARGPEDLLAYVGHALGRLPEDSLVLLTLHDGRLRAVVRVDLPPEEVD
+VDAWACAVAEVCRRDAAADATLCLALPDGARATLTRPGWAAALDDALASAGRPLAAAWTC
+AHGRARPWWGSSIAEEGTLDPRAAPLSLHLMTRGSVWDRAAVSDPVPRRGPAAARPDDAR
+WRPPEQDAPPARRAWLAQWEPVLTGTARGRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG
+AATGDPGDEERILTAASRRAPAWDRLDALRAGLRALVPVATPAVAAQALALAGWVGWARG
+HGSDADAHLTAAAALSPGDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGRP*
+>NZ_CP040019.1_1543
+MWLSQWESVLAGERGAAGPVTAEGTAPVSGTEEHPSADAAVLGAPLTLPSWRDALVLHAA
+VRPGDPPPEPAERERFLIAGSEQAPPWERLDRLRAGLRRLVPAAPPPAAAQALALAGWVG
+WARGQGSDAAAHLAAAAELAPDDPFVTLMRRVVDTGCVAGWAAHPDTAWRPGA*
+>NZ_CP083691.1_1437
+MRPRTLEGMDHPPAVPSAVPAGVTPPHLPVLRARGVDDLLGYAFHVLGTEPRESILLVTL
+ARARLRAVVRVDRPGRETPPAARHWAEAVAAVARRDAAADAVVCVSLTGRAGGLEPPGWW
+PPLVRALRDRGIPAREGWGVVAGHAARWPVEPGAGPGPLEEVDPRHSDLSLHLIGAGSVW
+GLRAGHRSVPTPAALDPAAPDRPHWTAARARPEAPGPWLAAWERVLDGGGLPERPAGRAR
+LGAGLEHPARRDALLIAAAGAAADELPAAERAALLTGTRDPGPDWRRLDRLWDALRALAA
+DAPAPCAAPALALAAWICWARGEGTAAGAHLDVARRLAPRDPLVGVLRRILDAGAVCAWA
+ADPRRAWTPWDPQDPASGMRG*
+>NZ_CP097650.1_1234
+MEAPTSLDVPVLPARGPEDLLAYVGHALGRLPEGSLVLLTLRDGRLRAVVRVDLPPEEVD
+VGAWACAVAEVCRRDAAADATLCLALPDGARATLARPGWAAALDDALASAGRPLTAAWTC
+ARGRARPWWGSGVAEEGPLDPRAAPLSLHLMTRGSVWDRAAVPDPVPRRGPAAARADDAR
+WRPPEQDAPAARRAWLAQWESVLTGAARDRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG
+AATGEPGDEERILTAATGRAPAWDRLDALRAGLCALVPAATPAVAAQALALAGWVGWARG
+HGSDADAHLTAAAALNPGDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGGP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001117.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001117.fa
new file mode 100644
index 0000000000000000000000000000000000000000..536abc4e90ab7b0cc6e96b68a3cb7dd69ee3cf12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001117.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1280
+MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM
+FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL
+AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPQADIVAGLLQMLELR
+AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE
+RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG
+SAPAQEDGPGRPSTGDGD*
+>NZ_CP033200.1_1011
+MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM
+FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL
+AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPEADIVAGLLQMLELR
+AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE
+RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG
+SAPAQEDGPGRPSTDDGD*
+>NZ_CP040019.1_1542
+MQDAAPIYTRHDAEAVPPGLALLVTLTGHMDAGRVSRQVRTALREHLEHRTVASFDVDSM
+FDYRARRPRMRFDRDRYRDLRLPTLEVQLVEDLIGHPFLLLAGPEPDFRWQAVVEAVLGL
+AEEWQVDSLTFLDAAPLPVPHTRRIGVTTHGTRAEAVEGLSTWSPEAEIVSGLLQMLELR
+ADEAGIPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASREIEAELE
+RQVSGSEEVQQMIAGLERNFDQNAEDQERSLLETEEGLPDGDELASAVEAYLAGRAGPDG
+SAPAQEDGPPRPSTDDER*
+>NZ_CP083691.1_1436
+MQDPTQLYTRHDAAPGDAVPDGLGVLVTLTGHLDAGHVGRQVGAGLRERLAHRTVARFDV
+DQLHDYRARRPRIRFDRERYTDLRMPALDVELMEDLLGHPFLLVAGPEPDMQWGRFTAAL
+LGLLQEWEASSATFLDAAPLPVPHTRRIGVTTHGSRADALEGLSTWSPEADVVAGLVQVL
+ELRAEEAGLPTAGYTVHVPHYVAEAGYPQAAVAALEYAGASLDLMLPTDELRDAAREVDA
+ELERQVAGSPEVQTMITGLEKNYDQNSEGQERSLLESHGELPDGDELASAVEAYLAERDE
+SVQPRPTTPAQDDEGPAPSPDPQV*
+>NZ_CP097650.1_1235
+MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM
+FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL
+AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPQADIVAGLLQMLELR
+AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE
+RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG
+SAPAQEDGPGRPSTGDGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001118.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001118.fa
new file mode 100644
index 0000000000000000000000000000000000000000..308c0f92b4810f296a9213426e17789e9a4766bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001118.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1281
+MITLDRPTLTARALEDLTASALVVGVGTGPDGPVLLTDALPAEAATALEASFELLGVRGA
+ADEVHRLPGLGGVPVPLLVLAGVGGLDDDGEAADESLRRAAGAAVRSLAGTDAVALALPA
+DTPARLAAVAEGAVLGAYAFTAQKSERARAETDTSRPVREVEVVTPLAAADADPVLRRAA
+VVGDAVCAVRDLVNTAPSHLYPATFADAVAEDLADSSVSVDVWDEDRLRAEGFGGILAIG
+QGSSRPPRLVRIEHAPADAAAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFA
+VVRAAAALDVPVKVTGWLALAENMPSGTAIRPSDVITMYGGKTVEVMNTDAEGRVVMADA
+LVAATDERPDAVLDVATLTGAQLVALGVRHTGVMGDDALRDEVVAAADAAGELAWGMPLP
+EQLRASLTSRVADISNMGDRFGGMMTAATFLREFVDAGRSEGDAAARTPWAHLDIAGPSF
+NESAAYGYTPQDATGVMVRTLVGLIEGRAR*
+>NZ_CP033200.1_1012
+MITLDRPTLTARALEDLTASALVVGVGTGPDGPVLLTDALPAEAATALEASFELLGVRGA
+EDEVHRLPGLGGVPVPLLVLAGVGGLDDDGEASDESLRRAAGAAVRSLAGTDAVALALPA
+DTPARLAAVAEGAVLGAYAFTAQKSERARAEADSSRPVRELEVVTPLAAADADPVLRRAA
+VVGDAVCAVRDLVNTAPSHLYPATFADAVAEDLADSSVSVDVWDEDRLRAEGFGGILAIG
+QGSSRPPRLVRIEHAPADAAAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFA
+VVRAAAALDVPVKVTGWLALAENMPSGTAIRPSDVITMYGGKTVEVMNTDAEGRVVMADA
+LVAATDERPDAVLDVATLTGAQLVALGVRHTGVMGDDALRDEVVAAADAAGELAWGMPLP
+EQLRASLNSRVADISNMGDRFGGMMTAATFLREFVDAGRPQDDDAARTPWAHLDIAGPSF
+NESAAYGYTPQDATGVMVRTLVGLIEGRAR*
+>NZ_CP040019.1_1541
+MITLDRPTLTARTLEDVSASALVVGVGTGPDGPVLLTDALDAPAASALEASFDLLGVRGA
+QDEVHRLPGLGGSPVPMLVLVGVGPLDDDGEVSDEALRRAAGAAVRSLAGTDAVALALPA
+DTAQRLSAVAEGASMGAYAFTALKSEKAREEAEKSRPVRGLEFVTALGAEEAEAALRRAA
+VLGDAVCAVRDLVNTAPSHLYPGTFADAVAQDLSGSSVSVDVWDEERLTAEGFGGILAIG
+QGSSRPPRLVRIEHAPAEAKAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFA
+VVRAAAALDVPVKVTGWLALAENMPSDTAIRPSDVVTMYGGKTVEIMNTDAEGRVVMADA
+LVAATDERPDAVLDVATLTGAQMVALGTRYTGVMGDDALRTEVVEAADRVGELAWAIPIP
+ENQRASLNSRVADISNMGDRFGGMMTAAAFLREFVDAGRTGEEDAPRTPWAHLDIAGPSF
+NESAAHGYTPQDATGVMVRTLMGLIEGRGR*
+>NZ_CP083691.1_1435
+MISQERPTLIARSLAEVTAPAVVVGVGAGPDGPLLLTDALPDEAAVALESSLELLEVKGR
+PDEVHRLPGLSGSRWPLLVLVGLGDLDQDGGADDEALRQASGAAVRSLAGTESVALALPA
+DTPSRLAAVAEGAALGAYAFTAFTSAGDTPGRAPVSTVELVTPLPASASEPVLRRAAVIG
+DAVCAVRDLVNTPPSHLYPASFADAVVGDLEGTDVDVRVWDEAQLAAEGFGGIVGIGQGS
+SRPPRLVRVEHAPAGARAHVALVGKGITFDTGGISLKPPASMMTMKSDMAGAATVFAVVR
+AAAALEIPVRVTGWLAMAENMPSDTALRPSDVLTMHGGKTVEVMNTDAEGRVVMADALVA
+ATDERPDAVLDVATLTGAQLVALGVRHTGVMGDEALRNEVVAAAGAAGELAWPMPIPEQL
+RPSLDSRVADISNMGERFGGMMTAAAFLREFVDAGRPAAERAESPTPWAHLDIAGPSFNE
+SAAYGYTPRDATGTMVRTLVGLIAGRAG*
+>NZ_CP097650.1_1236
+MITLDRPTLTARALEDLTASALVVGVGTGPDGPVLLTDALPAEAATALEASFELLGVRGA
+EDEVHRLPGLGGVPVPLLVLAGVGGLDDDGEAADESLRRAAGAAVRSLAGTDAVALALPA
+DTPARLAAVAEGAVLGAYAFTAQKSERARAEADTSRPVRELEVVTPLAAADADPVLRRAA
+VVGDAVCAVRDLVNTAPSHLYPATFADAVAEDLADSSVSVDVWDEDRLRAEGFGGILAIG
+QGSSRPPRLVRIEHAPADAAAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFA
+VVRAAAALDVPVKVTGWLALAENMPSGTAIRPSDVITMYGGKTVEVMNTDAEGRVVMADA
+LVAATDERPDAVLDVATLTGAQLVALGVRHTGVMGDDALRDEVVAAADAAGELAWGMPLP
+EQLRASLNSRVADISNMGDRFGGMMTAATFLCEFVDAGRPEGDAAARTPWAHLDIAGPSF
+NESAAYGYTPQDATGVMVRTLLGLIEGRAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001119.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001119.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4cd97328498d0c20ecf829cdf759666f401ba55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001119.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1282
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEEFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS*
+>NZ_CP033200.1_1013
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGINATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGSI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS*
+>NZ_CP040019.1_1540
+MADSATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKLGGTCLHWGCIPTKAYLH
+AAEVADETRNSAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLTGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYKAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVEVTIIEGLETLVPNEDPAIIKVLAREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGITMDRGFVITDERLHTGVGSI
+YAVGDIVPGLQLAHRGYQQGIFVAEEIAGNSPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVVEYNLAGNGKSSILGTGGIIKMVRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHG*
+>NZ_CP083691.1_1434
+MADSATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKVGVNATLESVDMAKVRDYKDGIVSGKHKGLAGLLKMRKVQVIEGAGK
+LVSKNEVEVDGTRYTAENIVLASGSVSKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKVFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMVRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS*
+>NZ_CP097650.1_1237
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001120.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7d2a0f331e3ba7719759dee1cc3af4f67974044
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001120.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1283
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDGAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGSSGQDEASAEEIEDK
+ATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSAQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLRTLRQRLEGGEFANELGL*
+>NZ_CP033200.1_1014
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDGAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGSSGQDEASAEEIEDK
+ATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSAQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLTTLRQRLEGGEFANELGL*
+>NZ_CP040019.1_1539
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLQEIL
+ADEDETVEVGAPLATIGDGDGGGSSESDDDAQAEESEEPAAEEAQEDEEQQEPEGEPAPE
+ERSSTQDSEEKSSGGASGGDASEVTLPALGESVTEGTVTRWLKAVGDEVEVDEPLLEVST
+DKVDTEIPSPVAGTLLEIRAEEDETVEVGAVLALVGSGSAGGSSDSSDDSAKDDSAPDEA
+SAEEIEDKATEAETGEETEEAAQDAGEEKEEKAPEASASENASREESAEQEKAAAADAPE
+ATSPGQGYVTPLVRRLAHQNDVDLSTVRGTGVGGRIRKQDVLAAALAQQAGSAESAPAQE
+QGSKEQAAAASSAPAVASSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDV
+TRIVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASED
+IAIAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGS
+VGALFDTPIINQPQVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGAD
+AGRFLTTLRQRLEGGEFANELGL*
+>NZ_CP083691.1_1433
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDEAPSAGGEDSEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLVEILANEDDTVEVGAVLARVGSGAAPAASQDPAPAADTASPEEIEDKAT
+EAPTGEQTEEAAEQAGDVKQEQAPAASPAETASAAPAASAPAAETSASEPGPGYVTPLVR
+RLAKQNGVDLSTVRGTGVGGRIRKQDVLAASLANQASSGSASPAAAEEQQTPAAASAPAP
+AAVRGETEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDMTRIVQLRGKAKASFQEKNGVK
+LTYLPFITQAVTEALKQHPKLNASFSEDNKEITYHASEDIAIAVDTDRGLLVPVVKDAGT
+LNLAGLAQKIADVAERTRTNKINPDELSGGTFSITNIGSVGALFDTPIINQPQVAILGTG
+AIVKRPMVVADADGNDTIAIRHMMYLSLTYDHRLVDGADAGRFLQTLKARLEGGEFAAEL
+GL*
+>NZ_CP097650.1_1238
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDEAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAILALVGSGSAGGGSAPSEGSSGQDEASADEIEDK
+ATEAEAPEETEEAAEAAGAEKSEETPEASPSEEASRRESAERDSAQGESAEAPAATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLTTLRQRLEGGQFADELGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001123.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001123.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75b1aa16ac774d96fb4ceb652ab092b25b7ac7d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001123.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1286
+MPETLLPPLRLLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA*
+>NZ_CP033200.1_1017
+MPETPLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA*
+>NZ_CP040019.1_1536
+MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA*
+>NZ_CP083691.1_1430
+MPHALLPPVRVLGLAPDLIDYEEGWALQRTLHADVVAGRSDGEILLLEHEAVYTAGRRTE
+DADRPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEEVLIRTAAEF
+GVTAVRVDGRAGIWITAREGDPRPDRKLGAIGLSIHDGVSMHGFSFNCSNSLTPYETIIA
+CGIADASTTTLSVETGREVTPVDVLPVLVRHLEDLGPEHIALTPTEGTPA*
+>NZ_CP097650.1_1241
+MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001124.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001124.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a42fb16ba602ee75ac6b1ed40a99cbfec6dff59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001124.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1287
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVQWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS*
+>NZ_CP033200.1_1018
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVHWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS*
+>NZ_CP040019.1_1535
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMDEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHAFNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLKVLSMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITVTQYVRPSKLHHPIDRWVKPQEFVEWSRRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLEHLAGEKTARQEASAVVAQMS*
+>NZ_CP083691.1_1429
+MTTAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNTVKGSGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDIASGRPLPLDMDEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHELNPSTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKEQELVTKSNLILGMGETDEEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVAWSQRAEEIGFAGVMAGPLVRSSYRAGKLYA
+QAMERLGREVPEHLAHLRGERTARQEAAAVVARMS*
+>NZ_CP097650.1_1242
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVQWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001126.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001126.fa
new file mode 100644
index 0000000000000000000000000000000000000000..324b84ba16c2f6a2fe82d3400de67846d3aab307
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001126.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_1289
+MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT
+AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR
+LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM*
+>NZ_CP033200.1_1020
+MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT
+AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR
+LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM*
+>NZ_CP040019.1_1533
+MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT
+AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR
+LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM*
+>NZ_CP083691.1_1427
+MSCVFPACNASSGPDYPGGVAHRASDPAPRDRSERDAAGRAEPLISRADLAGWIDGPGGG
+RAGGRWPGDLLGLPEHGPASMATAARRAGALMIDWALALVVSNLAFGGDAIATLLVFAAM
+HVVGLTLLATTVGKALCRIQVVREGTGGTAPVHRVLIRTALLCLVLPAVVVGPDGRGMHD
+RVAGTVELHM*
+>NZ_CP097650.1_1244
+MVAHYAGGVARRAPDPQDRTETTGRAEPLITRRDLAGWVDGPGGGRAGGRWPGDLLGLPE
+RGPASMATAARRMGALVLDWFIALGISWLAFDADAIATLLVFAAMHVIGLTLLATTVGKA
+VCRIQVVRVGGRPAGLLRILLRTALLCLVLPAVVVGPDGRGMHDKLADTVEIRM*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001128.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001128.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f771d6033909e65818c919cb6cd75b77dae11eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001128.fa
@@ -0,0 +1,95 @@
+>NZ_CP042169.1_1292
+MSSLSTTGALPAVPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRA
+LLLWVRLAEREPRVHHALRDPETTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAAT
+APALAQPDPADGEPWGDASATLRRLLLDSVGADPDTDRPVAAVTGKDAAVALRRAYRRQL
+AAIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIG
+MGKCGAGELNYVSDVDVVFAHAVREAADGADPDAEVPDGPRAAALAAELAAGIGRVIQGA
+APEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGER
+YIAEIWPRVWESSSRDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQ
+LVHGRADESLRVRGTLDAVRALHAASYITTRDARAFDEHYRWLRTLEHRIQLVHLRRTHL
+MPVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALS
+AEDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGAD
+PDGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVG
+DDRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLE
+AVTGALSDIDQVTVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVH
+RPRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLD
+SYREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTADAREIRRIKA
+RVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTLPALRAIARH
+GLLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGGELE
+ERYLRVTRLARQVFETRFYGL*
+>NZ_CP033200.1_1023
+MSALPDAATADAPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRAL
+LLWVRLAEREPRVHHALRDPGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATA
+PALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPLAAVTGKDAAVALRRAYRRQLA
+AIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIGM
+GKCGAGELNYVSDVDVVFAHAVREAADGADPDAQVPDGPRAAALAAELAAGIGRVIQGAA
+PEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERY
+IAEIWPRVWESSARDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQL
+VHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRIQLVHLRRTHLM
+PVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSA
+EDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADP
+DGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVGD
+DRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLEA
+VTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHR
+PRPGVDEGRAREQAEEVVRTLMALLQKPVAPPLPGERRLEVDADLRPEGRQGPLVRTLDS
+YREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAQDLSAADAREIRRIKAR
+VEAERLPRGADPARHVKLGRGGLSDVEWLVQSMQLKHAGQIEDLRVTGTLPALRAIARHD
+LLPESEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTTGGELEE
+RYLRVTRLARQVFETRFYGL*
+>NZ_CP040019.1_1530
+MSALPDAATADAPDRRALAQAGVADARRVQSLLASPEFEGADVAPLVKRLGHAADPDRAL
+LLWVRLAEREPRVHRALRDPETTARLLRLLGASEALGEFLIRRPEHLDLVLEPESAAATA
+PALAQPDPADGEEWADEPAALRRLLLEAVEADPDADRPRAGLTGADAAVALRRAYRRQLA
+AIALRDLDSADPAAVMPSVGRWLADLAGAAVDAALAVSRATLAEREGPAVDRVDLAVIGM
+GKCGARELNYISDVDVVFVHELLDPGPDAAGEAGADGADGEASDAVDGTRAAVLAAELAA
+GIGRVIQAAAPEPGLWEVDANLRPEGKDGALSRTLDSHAEYYRRWAHGWEFQALLKARPI
+AGSADLGARYLERIWPRVWESSAREGFVDSVRAMRSRVLETIAPAEREREIKLGSGGLRD
+VEFTAQLLQLVHGRADESIRVRGTLDAVRALHEASYISTRDAAAFDEHYRWLRTLEHRIQ
+LVHLRRTHLMPVKDEALRIVARSLRGAQETGPATGEDLQAAFTRVRRAVRGLHETVFYRP
+LLSTTAALSDDEVRLSAEAVRERLAALGYRDPKGALRHIEALTQGVSRRAAIQRQLLPAM
+LGWFAEGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLAASRFVGDLLEH
+SPEAVAWVGDDRELEPRGTVQLWRQADARLDRRIEAQETPAAVRHVRQVRRSETLRVALA
+DISGLLDLEAVTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYG
+SDLDALFVHRPRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGR
+QGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTAD
+AREIRRIKARVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTL
+PALRAIARHGLLPEAEVAVLEEAWLLASRIRAAVLLWTGKVGDVLPTNMRDLEAIARLSG
+VGTAGGELEERYLRVTRLARQVFEARFYGL*
+>NZ_CP083691.1_1424
+MAPTPDSHVPGPRRALVHAGVADLTRAERLLSSPELAEQDADAALAALAHAADPDSALLL
+YIRLAERDPQVHRVLAEADRARDLLRLLGASEALGEFLIRRPEHLDLVLDPARAAATAPA
+LAQQDPTDGGDWHDEPAALRALLLEAVGADPAADQPVAGLTGADASVALRRAYRRQLTAI
+ALADLASREPTLVMPAVGRWLADLAGAALEAALAVSRAELRAREGAAVDCVELAVIGMGK
+CGARELNYVSDVDVVFVHDVLEPGAPDAPSAQEAARLAAELAAGISRVLSGPAPEPGLWE
+VDANLRPEGRDGALSRTLDSHVEYYRRWAHGWEFQALLKARPVAGSPALGERYVAAVWPR
+VWESSAREGFVENVRAMRTRVLDTIARDERDREIKLGAGGLRDVEFTAQLVQLVHGRADE
+SVRVRGTLDALRVLHAASYISSRDMRAFDAAYRWLRLLEHRIQLVHLRRTHLMPVKEGPR
+RVVARSMRGAGDVHPVAGDDLQDRFSRVRREVRALHETVFYRPLLSTTAALSDEDVRLSA
+DAVQARLSALGYRDPRRALAHIEALTRGVSRRAAVQRQLLPAMLGWFADGADPDAGLLAF
+RRLSESLGSSPWFLRMLRDSTDAARRLCLVLAGSRRVGDLLEHAPESVAWIGETRELAPR
+GLSALTSEVTARLDRRSPEESAAQVIRHVRQIRQREILRTALADITGVVGLEEVGHALAD
+VDQAAVQGALRVAGQAVLDGADPLTEVVVVAMGRQGGREIAYGSDLDAMFVHRPLAGADE
+TAAAAQAEAVARQLMALLQQPAAPPLPSEQPLDVDADLRPEGRQGPLVRTLDSYREYYAR
+WAEVWERQALLRARVVAGPAGLAEEFTAWADGVRYGDELSAGDAREIRRIKARVEAERLP
+RGADPARHVKLGRGGLSDVEWLVQSLQLRHAHDEPELRVTGTLPALRALARLDLLPPSEA
+ALLEEAWLLATRVRSALVLWTGKGSDVLPTNARDLGALARLAGDACGGGVAFEERYLRVT
+RQARQVFEQRFYGL*
+>NZ_CP097650.1_1247
+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_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001131.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001131.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d88d1b1c731e1715773f6b0acc32e340418613c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001131.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1296
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNETADAWDERDDD
+WDSRPVDDAS*
+>NZ_CP033200.1_1026
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNEAADAEDARDDD
+WDSRPVDDAS*
+>NZ_CP040019.1_1527
+MSEKSEYWYNVRTQQVEEGAQSDWSQLLGPFGTREEAQGAMSRVQANNEAADAADERDDN
+WDNNPFNDAD*
+>NZ_CP083691.1_1421
+MTDTHEPGSGYWFNVRTHQIEEGPQSDWKELLGPYQTRQDAENALARVQARNEAADAEDA
+HDDAWDASPLNDAS*
+>NZ_CP097650.1_1250
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNEAADAEDARDDD
+WDSRPVDDAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001133.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001133.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b95bc32c2eac377746fd55b7e18c331fa88105ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001133.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1299
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR*
+>NZ_CP033200.1_1029
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR*
+>NZ_CP040019.1_1524
+MHCPFCRHEDSRVVDSRSLEDGSAIRRRRQCQSCGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRASGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFADAIAELRAGTDERGRPAVQPRLFSR*
+>NZ_CP083691.1_1418
+MHCPYCRHEDSRVVDSRSLEDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVSSDDLAVLAQEVEEAVRASGNAEVDAHEVGLAILGPLRRLDQVA
+YLRFASVYRDFESLSDFEDAIAELRAQEGEAPGRPAVQPRLFSR*
+>NZ_CP097650.1_1253
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001136.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001136.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b49ff2e9d799a4a742f57d864b5f3456901b98e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001136.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_1302
+MLTALIVAVLAYALDQLTKYAVESTMQLGDSVAVIPGVLRWHYILNPGAAFSIGEDHTWV
+FTIIQAVVAVAALVGIARVRSTPWALALGGLAGGVLGNLTDRLFRPPAFGRGHVVDMISV
+PHFAIFNVADSFIVCSVIGVALLVMTGRRLDGTREA*
+>NZ_CP033200.1_1032
+MLTALVVAVLAYALDQLTKYAVESTMQLGDSVAVIPGVLRWHYILNPGAAFSIGEDHTWV
+FTVIQAVVAVAALVGIARVRSTPWALALGGLAGGVLGNLTDRLFRPPAFGRGHVVDMISV
+PHFAIFNVADSFIVCSVIGVALLVMTGRRLDGTREA*
+>NZ_CP040019.1_1521
+MSAAVEAPAPAAGPGARRRAVLAALLVAVLAYALDQLTKLWVETTMELGDSVTVVPGLLR
+WHYILNPGAAFSIGEDHTWVFTVIQAVVAVAAVVGIVRARSLPWALALGGLAGGVLGNLT
+DRLFRPPSFGQGHVVDMISVPRFAVFNVADSFIVCSILAIAFLVMTGRRLDGTREA*
+>NZ_CP083691.1_1415
+MSPAAPQDALTDHRDAPARPGRGVVGAALGVATLAYALDQGTKLLVERTMELGESIVVIP
+GLLRWHYILNPGAAFSIGTDVTWLFTLIQAVVAVVALVALLRSRSRAWSVALGGLLGGVM
+GNLTDRLFRPPSFGQGHVVDMVSVPNFAIFNVADSFIVCSILTLCLLLMSGRRLDGTRES
+DAAAEA*
+>NZ_CP097650.1_1256
+MLTALIVAVLAYALDQLTKYAVESTMQLGDSVAVIPGVLRWHYILNPGAAFSIGEDHTWV
+FTVIQAAVAVAALVGIARVRSMPWALALGGLAGGVLGNLTDRLFRPPAFGRGHVVDMISV
+PHFAIFNVADSFIVCSVIGVALLVMTGRRLDGTREA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001137.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001137.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af980588769be551d6d2fba61f5917ec1ccdb678
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001137.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1303
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APAAGPAADTPEAAATPASAEESAPAAAPESADAAATSAAGVLAMAQRLHDEHVAAGEQR
+STELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQLRSFETDYRSRLTSYIE
+GQLREIRAQKRVEPPTPTA*
+>NZ_CP033200.1_1033
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APVADTPEAAETPSPVEEPAPAAAPEAADAAATSAAGVLAMAQRLHDEHVAAGEQRSTEL
+VAEAEATAARLVSDAEEQKARTLEALAEERAGLEGEVEQLRSFETDYRSRLTSYIEGQLR
+EIRAQKRVEPPTPTA*
+>NZ_CP040019.1_1520
+MALSWEDVVNKQFQPTKFREGYDQGEVDDFLDEIVGELKRLQGLNEQLTAENEALRAGGA
+VPDADAAVDAPVADADAAAVVDAGQSPAPAALADAEPGLEVEPTPSSADPASASAAGVLA
+MAQRVHDEHVAAGEQRRDELISEAEARAEALVAEAEETRTRTLEELAADKAGLEAEVEQL
+RGFETDYRSRLTAYIEGQLREIRSQERVEPAQRPA*
+>NZ_CP083691.1_1414
+MVLSWEDVVNKEFQLTKFREGYDREEVEDFLDEVVEELKRLTEENDRLRSDLDACREGAP
+AQAEASAPAAGEAAPALQAPAPVAPVEPSAPGEPVAPTDSATSAAGVLAMAQRLHDEYVA
+EGEQRRDRIIADAEAEATTVVRQAEETRTRTLSDLESRRKGLEADVERLRAFETDYRSRL
+TAYIEGQLREITAQERLEPAKGTV*
+>NZ_CP097650.1_1257
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APAAAPAADTPEAAATPASVEEAAPAAAPESADAAATSAAGVLAMAQRLHDEHVAAGEQR
+STELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQLRSFETDYRSRLTSYIE
+GQLREIRAQKRVEPPTPTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001142.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001142.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94f76bd31e20b1c49c93669f06db464cf5c3f4f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001142.fa
@@ -0,0 +1,41 @@
+>NZ_CP042169.1_1308
+MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR
+ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS
+LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF
+RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL
+AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG
+DEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPAQPQPAAQPQPAAPAQPQQAE
+RPAVRGTVPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK*
+>NZ_CP033200.1_1038
+MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR
+ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS
+LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF
+RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL
+AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG
+DEVRVTVIAAGFDKVDVTSAPAAPQAAQQQAAPQRAAAPAQPQPVPAQPQQAERPAVRGT
+VPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK*
+>NZ_CP040019.1_1515
+MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDATSAPASPQAGQFQQAPQRPAQQAQPQQQAPAPQQHQAQPA
+QQEQPQQVQPQSVRGTVPLAPQQPQQTEQRRQQDLPTVVEPDLGAGSSDLDVPDFLK*
+>NZ_CP083691.1_1409
+MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAENGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDATSAPAAPFQQQAAPQRAAAPQQPAQQAQQAPVSQQAAPQR
+PSVPGTMPLNSSSAFGGAPAQPAATQQPAAPQQPAAPQRAQQDLPTVVEPEFGSSDLDVP
+DFLK*
+>NZ_CP097650.1_1262
+MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR
+ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS
+LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF
+RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL
+AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG
+DEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPTQPHPVPAQPQPAPAQPQPAP
+AQPQQAERPAVRGTVPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001146.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001146.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8c7b3043553c8afddbb27e03ec777d53b2089e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001146.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1312
+MSPIELRPVRPRAADDAPEHRERILRRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVLKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLVLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR*
+>NZ_CP033200.1_1042
+MSPIELRPVRPRADDDAPEHRERLLHRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLGLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQASVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR*
+>NZ_CP040019.1_1511
+MSPTELHPVRTPADEEETEARSRPLQRLWRLVEGRRALDLSVLLIGGSTFLLTALGLVMV
+LSSSSVEAIGTGGGSYGLFLRQTMWAVAGLAALLLFSRLPIGWIKALAWPAFGLAVVLLS
+LVAFTPLGVTVGGNTNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALVPV
+LPGGLLLIGLVMAGSDLGTAIILALVLAAVLFVAGTHHGVFIAFSAVTVVGAIALTLLAP
+HRMVRVQAWLGDCSDASDPCFQPDHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLGVLLAYLALAVGMYRVAAGTTSPFIRLATWGIMAWLVGQAFVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLTAVGIVLAFARHERRRAEEPDARPDADDPDTDPLPV
+IPAPASQES*
+>NZ_CP083691.1_1405
+MPSTATRPEASSRASARTAVRPRLAGFWGALEGRRALDWAALLIGLCTAVLTVLGLVMVL
+SASSVEAISSSGGSYGLFLRQGGWALGGAVLLAVLRRLPVDLYRRLAWAAYLFAFLLLAL
+VAFTPLGKEVNGNTNWLQLGPVTFQPSEAAKLAMALWAAAVLQRKERLVHLVSHALVPVL
+PFGVALILLVLKGRDLGTALILAFILAVILFVAGTPGRVFAVLAGIGVVAALGMTVFAAN
+RMERVQAWLFGCEGLQGDPCMQPDHGIYALASGGWWGVGLGQSRQKWNYIPEAENDFIFT
+ILGEELGLVGTLLVLACFVGLAVGMYRVAAGASSTFVRLATWGILAWIVGQAAMNIAMVT
+GLLPVVGVPLPFISYGGSALTLSLAAVGVVLSFARHERDLLPAAEASAADPASSASPQES
+R*
+>NZ_CP097650.1_1266
+MSPIELRPVRPRADDDAPEHRERLLPRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLILVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSMLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001152.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001152.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cdc77054e585cfa23ed1a097c179a8cf8734527d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001152.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1319
+MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH
+LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR
+AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE
+KPTEEEISENRRASSARVRAVEKIRTSRTTA*
+>NZ_CP033200.1_1049
+MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH
+LRVIGIDRDVHAQAMAAERLGPLADRLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR
+AIVRARAEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE
+KPTEEEISENRRASSAKVRAVEKIRTSRTTA*
+>NZ_CP040019.1_1505
+MDADQLRPEDRHVPVMRDRVVDLLAPAVQAALDAGRAPVAVDGTLGMGGHTEAMLTRFPE
+LTVIGIDRDAHAQALAAERLGPLAERLVPFHGTYDLVPEAMAAAGVEKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEHELRRIIRRDGEERFAGPIAR
+AIVRARAEAPIETTGRLVEVIRTAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRIAKRHLSAWAASTAPPGFPVVLEEHEPVVRTLTRGTE
+KPTEEEILENRRASSAKVRAVEKIRTSRTPA*
+>NZ_CP083691.1_1398
+MDPTQPLPRDRHVPVMRDRVVDLLAPAVEAAAAAGRTPVAVDGTLGMGGHTEVLLRRFPT
+LRVVGIDRDPNALAMAQERLGPLAERLVPFHGTYDQVPEALAAAGAERMDAALYDLGVSS
+YQLDARERGFAYSYDAPLDMRMDTTAPVTAADLVAELDEQSLRRIIRRDGEDRFAGPIAR
+AIVRAREEEPILTTGRLVDVIRAVVPVSAGNKGGHPAKRTFQALRIAVNEELDILDAAVP
+AVLDALEVGGRLVVMSYHSLEDRIAKRHLQEWAASTAPPGFPVELPEHRPLVKVLTRGTE
+KPTEEEIEENRRASSAKVRAVEKIRTSRTTA*
+>NZ_CP097650.1_1273
+MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH
+LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR
+AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE
+KPTEEEISENRRASSARVRAVEKIRTSRTTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001159.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001159.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ecb94c506c4cc7213e2675888c4fe766fbfd286
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001159.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1327
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTTVADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA*
+>NZ_CP033200.1_1057
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTTTADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA*
+>NZ_CP040019.1_1496
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPVAQAPSWADEAEHRAAVAELSQVPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEEARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTSAADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRALGTRPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERVAPRR*
+>NZ_CP083691.1_1390
+MHEDPRDQIMAFGTAISEGAAPDPALDAWRELPIKQAPTWADEDDFRAAVAELSQVPPLV
+FAGEVDVLRTRLADVARGQAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQYAKPRSSDTETRDGVTLPSFRGEIVNGFEFTEEARRHDARRMVTAYHTA
+SSTLNLVRAFTQGGFADLRSVHQWNRGFMENPAYAQYEQIAAEIDRAVRFMDAAGADFEA
+MRRTEFYAAHEALLLDYERALTRLDSRTGLPYATSAHFLWIGERTRDVDGAHVDFLSRVR
+NPIGVKLGPTTTVDDVRALADRLDPEREPGRLTFITRMGADKVRDVLPGIVAGVRDEGLQ
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDELTGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPVDEADFDEHYETLCDPRLNHQQSLELAFKVTDALAHPHQD*
+>NZ_CP097650.1_1281
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTTVADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001160.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001160.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3471fb90c9058b66a9ab9c5d90269ec7325e7388
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001160.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1328
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKHEYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDRVQPIGHVLPRIRRLGMIFGEPL
+DFSDRAEAVGDPRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRTAAPPRARD*
+>NZ_CP033200.1_1058
+MSTFYWSAKTFAVAPATRLLFRPWVKGLANVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKHEYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLAALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGVPVVPIAMIGTDRVQPIGHVLPRIRRLGMIFGEPL
+DFSGRAAAADDRRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRVAAPPRAGD*
+>NZ_CP040019.1_1495
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGAAILASNHLSVSDSVFMPAMLERQV
+HFLAKKDYFTGAGPKGWITRKFFEATNQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDQAQPIGRTLPRIRRIGMIFGEPL
+DFSDRAEGVTDARVLRAVTDEIMEAIRRLSGQEYVDAYAADVKSGRVPAPPRARD*
+>NZ_CP083691.1_1389
+MSAFYWSAKTFVVAPATRLLFRPWVKGLSHVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKQEYFTGRGAKGWATKKFFEATNQLPMDRSGGAASLRSLEAGLECLREGKLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDRVQPIGRILPTLRRLGMIFGEPL
+DFSHLQGREGDHRALRQVTDEIVEAIRRLSGQDYVDVYAADVKSGRVAVPPRAGRD*
+>NZ_CP097650.1_1282
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKREYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDQVQPIGHVLPRIRRLGMIFGEPL
+DFSDRAEAVGDPRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRTAAPPRARD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001164.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..203f5c6a8e3b6965830b4eee3da3ecdc2823aa00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001164.fa
@@ -0,0 +1,105 @@
+>NZ_CP042169.1_1332
+MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN
+SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE
+NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK
+AVAGGGGRGMRRVERREDLRGSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE
+GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV
+DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVSAQLRIAAGATLPELGITQDALQVR
+GFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT
+CRGRDYATAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFLSGDVATDFIDKHPELATV
+NRSQDRGSKALQYLVDVTVNQPHGPRVEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED
+AVPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV
+AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY
+PTEVTDAFVAEAAASGVDVFRIFDALNDVEQITPAIEAVRATGTAVAEAALCYTGNMTDP
+KETLYTLDYYLGLARRMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFDLPVHLHTHD
+TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM
+EPYWESVRSAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA
+ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKEFAERPQEFDIPDSVIGFLRGELGDPP
+GGWPEPFRTKALQGRREGAGMVEISAEDSSALGEAGQTRRGVLNRLLFPGPTKEFEAHRE
+EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR
+QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQAVATIEAMKME
+AAITAQVAGTVRRVVTEGITPVNGGDLLLVIE*
+>NZ_CP033200.1_1062
+MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN
+SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE
+NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK
+AVAGGGGRGMRRVERREDLRGSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE
+GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV
+DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVGAQLRIAAGATLPELGITQDALQVR
+GFAIQCRITTEDPANGFRPDIGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT
+CRGRDYATAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFVSGDVATDFIDKHPELATV
+NRSQDRGSKALQYLVDVTVNQPHGPRIEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED
+AAPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV
+AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY
+PTEVTDAFVAEAAASGVDVFRIFDALNDVEQITPAIEAVRATGTAVAEAALCYTGNMTDP
+KETLYTLDYYLGLARRMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFDLPVHLHTHD
+TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM
+EPYWESVRSAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA
+ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKEFAERPQEFDIPDSVIGFLRGELGDPP
+GGWPEPFRTKALQGRREGAGMVEISAEDSTALAEAGQTRRAVLNRLLFPGPTKEFEAHRE
+EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR
+QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQAVATIEAMKME
+ATITAQAAGTVRRVVTEGVTPVNGGDLLLVIE*
+>NZ_CP040019.1_1491
+MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN
+SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE
+NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK
+AVAGGGGRGMRRVERREDLRGSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE
+GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV
+DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVGAQLRIAAGATLPELGITQDALQVR
+GFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT
+CRGRDYATAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFVSGDVATDFIDKHPELATV
+NRSQDRGSKALQYLVDVTVNQPHGPRVEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED
+AVPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV
+AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY
+PTEVTDAFVAEAAASGVDVFRIFDALNDVSQITPAIEAVRATGTAVAEAALCYTGNMTDP
+AEKLYTLDYYLGLARQMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFELPVHLHTHD
+TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM
+EPYWESVRAAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA
+ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKQFAERPQEFDIPDSVIGFLRGELGDPP
+GGWPEPFRTKALQGRREGAGMVEISAEDSTALGEAGQTRRAVLNRLLFPGPTKEFEAHRE
+EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR
+QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQPVATIEAMKME
+AAITAQVAGTVRRVVTEGVTPVNGGDLLLVIE*
+>NZ_CP083691.1_1384
+MSLPLDPDTTRNGAGRPAHAAAPAFSKVLVANRGEIAVRAFRACHELGARTVAVFPHEDR
+NSIHRQKADEAYRIGQEGHPVRAYLDVDEILRVAKDVGADAIYPGYGFLSENAGLARAAA
+EAGITFVGPPADVLELTGNKVEALRAAKRAGIPTLKSSDPSSDVEWLLGQAEEIGFPIFV
+KAVAGGGGRGMRRVERPEDLKDSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQVLADA
+EGNVVHLFERDCSLQRRHQKVIEMAPAPHLDEEIRQALHRDAVAFAKEMGYVNAGTVEFL
+VDTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVAAQLRIAAGATLEELGIRQEDLHV
+RGFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKL
+TCRGRDYETAVRRVRRALAEFRVRGVTTNIPFLMNVMDDPQFVAGDVATDFIDKHPELAM
+VNRSQDRGSKALQYLADVTVNKPHGERVDGIDPRDRLPGHPSDKRHEPDRSPFDGPSRNP
+GAVPPAGWRQVLAEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPA
+VAHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTP
+YPTEVTDAFVQEAAATGVDVFRIFDALNDVEQIIPAIAAVRATGTAVAEAALCYTGNMTD
+PAEELYTLEYYLGLARRMVDAGAHVLAIKDMAGLLRPAAAKELVGALRAEFDLPVHLHTH
+DTAGGQLATLLAASEAGVDAVDVAVASMAGTTSQAPMSALVAALEHTERDTGLTLEAAAA
+MEPYWESVRAIYAPFEAGLKAPTGRVYQHEIPGGQLSNLRTQAIALGLGERFEQVEAMYA
+AADDILGHLVKVTPSSKVVGDLALQLVGGGVDPDQFRERPEDFDIPDSVVGFLRGELGDP
+PGGWPEPFRTRALKGRREGSGMVQVSEEDAAALAEAGQGRRDVLNRLLFPGPTKEYEAHR
+EEFGDISTLHTRDFLYGLVPGREHVVSLGRGVRLIATLQSVSEPDEKGMRTAMLTLNGQL
+RQIQVRDRSVESSVRQAEKADAAVPGQVPAPFAGSVTVQAAVGDVVEQGAPVATIEAMKM
+EAAITAPVSGTVTRVVTQGVTPVQGGDLLLVIE*
+>NZ_CP097650.1_1286
+MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN
+SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE
+NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK
+AVAGGGGRGMRRVERREDLRGSLQAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE
+GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV
+DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVGAQLRIAAGATLPELGITQDALQVR
+GFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT
+CRGRDYAMAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFVSGDAATDFIDKHPELATV
+NRSQDRGSKALQYLVDVTVNQPHGPRIEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED
+AAPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV
+AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY
+PTEVTDAFVAEAAASGVDVFRIFDALNDVEQITPAIEAVRATGTAVAEAALCYTGSMTDP
+KETLYTLDYYLGLARRMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFDLPVHLHTHD
+TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM
+EPYWESVRSAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA
+ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKEFAERPQEFDIPDSVIGFLRGELGDPP
+GGWPEPFRTKALQGRREGAGMVEISAEDSSALAEAGQTRRAVLNRLLFPGPTKEFEAHRE
+EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR
+QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQAVATIEAMKME
+ATITAQAAGTVRRVVTEGVTPVNGGDLLLVIE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001170.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001170.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1ff46fa13b5e6668ffc201f200affcf4d3151ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001170.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1338
+MENPQNPLAGRVPDVEPSARVAASTATRPDDATPDWRGRPFLGQPGPLANLFSVELWERF
+SFYGMQAMLVYYMSWTAAEGGLGIDPAVATGIVGAYGGMVYVFCILGGWVADRLLGSERT
+MFVSAVGIMLGHIALALVPGVPGLTLGLVLVAVGSGGLKANATNLVGSLYSREDPKRDAG
+FSIFYMGVNIGALFGPLLTGLARDTMGFHVGFGLAAAGMAIGLTQYALTRKNLPTDVHRV
+PDPLPRSQYGRWGLIGLGMVAVVVALFLTDVITLDNLSDAVVVLAAVAAIAIFAVLLTST
+KVSEEERSRVKAFIPLFIGTSVFFALFQQQFTVIALYSEHRLDRNLFGWLMPMEWVNSIN
+PIFIIVFAPVFAALWTKLGTRQPATPVKFGIGIVLIGIAFLLFIPVADVAAVPLLWLTLI
+LFVCTMGELLVSPVGLSLATKVAPRSFPVMMVSLYNLSVALGTALAGSLAGSYSEQNEVG
+YFGTIGAVTLGVGLIVLAIAKPVRRGMRGVL*
+>NZ_CP033200.1_1068
+MENPQNPLAGRVPDVEPSARVAASTATRPDDATPDWRGRPFLGQPGPLANLFSVELWERF
+SFYGMQAMLVYYMSWTAAEGGLGIDPAVATGIVGAYGGMVYVFCILGGWVADRLLGSERT
+MFVSAVGIMLGHIALALVPGVPGLTLGLVLVAVGSGGLKANATNLVGSLYSREDPKRDAG
+FSIFYMGVNIGALFGPLLTGLARDTMGFHVGFGLAAAGMAIGLAQYALTRKNLPTDVHRV
+PDPLPRSQYGRWGLIGLGMVAVVVALFLTGVVTLGNLSDAVVVLAAVAAIAIFAVLLTST
+KVTEEERSRVKAFIPLFIGTSVFFALFQQQFTVIALYSENRLDRNLFGWLMPMEWVNSIN
+PIFIIVFAPVFAALWTKLGTRQPATPVKFGIGIVLIGIAFLLFIPVADVVAVPLLWLTLI
+LFVCTMGELLVSPVGLSLATKVAPRSYPVMMVSLYNLSVALGTALAGSLAGSYSEENEVG
+YFGVIGAVTLGVGLLVLAIAKPVRRGMRGVL*
+>NZ_CP040019.1_1485
+MHTPQNPPTGHEPAVEPSARVAAPTAAAPDPAAAPDWHGRPFLGQPGPLANLFSVEMWER
+FSFYGMQAMLVYYMSWTLAEGGLGIDVAVATGIVGAYGGMVYVFCILGGWIADRLLGSER
+TMFYSAVTIMLGHIALALVPGIPGLALGLILVAVGSGGLKANAANLVGALYSQQDPKRDA
+GFSIFYMGVNIGALFGPLLTGLARDSWGFHFGFGLAAVGMAIGLVQYALTRKNLPSDVHR
+IPNPLPRSQYGRWVLIALAAVAVGVVLFLTGIVTVANLADAVVVLAAVAAIGIFAVLLTS
+KKVTEEERSRVKAFIPLFIGTAVFFALFQQQFTVIALYSENRLDRNLFGWEMPMEWVNSI
+NPIFIIAFAPVFAALWTKLGPRQPGTPVKFGIGIVLIGLAFLLFIPVADVLAVPLLWLAL
+ILFVCTMGELLVSPVGLSLSTKVAPRSFPVMMVSLYNLSVALGTALAGSLAGSYSEENEV
+GYFGVIGAVTVGVGLLMLAIAKPVRRGMRGVL*
+>NZ_CP083691.1_1378
+MTHSPDSGASVAPDADLGAAQAPAPDWHGRRFFGQPGPLANLFSVEMWERFSYYGMQAML
+VYYMSWTAERGGLGIDEATATGIVGAYGGMVYVFCILGGWIADRLLGSERTMFFSAVGIM
+LGHIALALVPGVPGLILGLVLVAVGSGGLKANAANLVGSLYAKGDQARDAGFSIFYMGVN
+LGGLVGPLLTGWARQTWGFHVGFGLAAVGMAIGLTQYALTRKNLPSTVHGVPDPLPRSQY
+GRWALIGLAGLAVVAVLLLTGVVNVGNLADAVVVLAALAAIAIFAVLLTSSKVSAEERSR
+VKAFIPLFIGTAVFFALFQQQFTVVALYSENRLDRTLFGTEIPMEWVSSINPIFIIAFAP
+VFAALWTRLGDRQPSTPVKFALGILLIGAAFLLFIPASGFLAVPLLWLTLILFVMTMGEL
+MISPVGLSLSTKVAPAAFPVLMVALYNLSVALGTALAGSLAGSYTAENEAGYFGVIGGVT
+IAVGVVMLLLAPAVRRGMRGVR*
+>NZ_CP097650.1_1292
+MENPQNPLAGRVPDVEPSARVAASTATRPDDATPDWRGRPFLGQPGPLANLFSVELWERF
+SFYGMQAMLVYYMSWTAAEGGLGIDPAVATGIVGAYGGMVYVFCILGGWVADRLLGSERT
+MFVSAVGIMLGHIALALVPGVPGLTLGLVLVAVGSGGLKANATNLVGSLYSREDPKRDAG
+FSIFYMGVNIGALFGPLLTGLARDTMGFHVGFGLAAAGMAIGLTQYALTRKNLPTDVHRV
+PDPLPRSQYGRWGLIGLGMVAVVVALFLTDVITLDNLSDAVVVLAAVAAIAIFAVLLTST
+KVSEEERSRVKAFIPLFIGTSVFFALFQQQFTVIALYSEHRLDRNLFGWLMPMEWVNSIN
+PIFIIVFAPVFAALWTKLGTRQPATPVKFGIGIVLIGIAFLLFIPVADVAAVPLLWLTLI
+LFVCTMGELLVSPVGLSLATKVAPRSFPVMMVSLYNLSVALGTALAGSLAGSYSEQNEVG
+YFGTIGAVTLGVGLIVLAIAKPVRRGMRGVL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001171.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18302ffcc4ceca8b7699cee45e3152ad5317d443
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001171.fa
@@ -0,0 +1,22 @@
+>NZ_CP042169.1_1359
+MSLIRRRPAALSLATLAALALAASGCAVDDGETRAALQSAEDRLAQAEDRISELEADASD
+RVDLGQLRQEAEDALEEADQRAAEVVEDLTRSLPSGSDIVDVEALREDGKVVIEYGQSLL
+EADPQVLEDTMREAADRARDAIPDLEDVEFRVGDRTFTY*
+>NZ_CP033200.1_1099
+MSLIRRRPAALSLATLAALALAASGCAVDDGATRAALQSAEDRLAQAEDRISELEADASD
+RVDLGQLRQEAEGALEEADQRAAEVVEDLTRSLPSGSDIVDVEALREDGKVVIEYGQSLL
+EADPQVLEDTMREAADRARDAIPDLEDVEFRVGDRTFTF*
+>NZ_CP040019.1_1466
+MTTLRPRRPAVLSLAALAALSLALSGCGVDEGDAQAALESAEDRLAQAEDRISELEADAS
+NRVDLGELQRQAEGALDGADQRVGELLEDLRGRAEPLREITEQDLRDLELPRIEGLDLEA
+EAAVEDLMKSLPSGPDMADVEALREDGRVIVEYAESALEADPQVLEDTMREVAEQARNAI
+PDLKDVEFRVGDQSFRF*
+>NZ_CP083691.1_1377
+MVVPGWPASLALMTTTPRASRASRPAAALLTLAGAALALTGCAAGPDQETADALASADER
+IASAEAEIADLKDRMDRVPDTAAMQSQASEAVSSAVAQATGAAGSLGADAARRAQEAVDG
+VSGLPDAEAVQQVEDGGRVIVEYAQDALPKDPAELQARLDEAADAVRRQVPDSAGVEFKV
+GDQTFTF*
+>NZ_CP097650.1_1308
+MSLIRRRPAALSLATLAALALAASGCAVDDGATRAALQSAEDRLAQAEDRISELEADASD
+RVDLGQLRQEAEGALEEADQRAAEVVEDLTRSLPSGSDIVDVEALREDGKVVIEYGQSLL
+EADPQVLEDTMREAADRARDAIPDLEDVEFRVGDRTFTF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001173.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3cb3813a5c98cdbdd99f4331706ec5f4fc6bb444
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001173.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1362
+MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD
+IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA
+GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA
+AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD
+TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG
+NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG
+MVEISVLPGRRDELVAALTAAGWKVV*
+>NZ_CP033200.1_1102
+MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD
+IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA
+GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA
+AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD
+TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG
+NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG
+MVEISVPPGRRDELVAALTAAGWKVV*
+>NZ_CP040019.1_1464
+MSAAAETAAAVPGALPAGIPQPVLVRGTGLLGASIGIGLSAAGADVLLHDLSPAALAVAA
+DIGAGRPMRIDDDGADAGPAPALVVVAAPPDVTADVVVDSLRRWPEALVLDIASVKEAIA
+AGVRAAVDDGRLGPSDPDRHLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTLPAAV
+QAGRALALALRATPYRMDARAHDESVAMISHLPQIAASLVAARLQDTPDQALALAGNGLR
+DTTRIAASDPQLWVQILSGNAERIVPALHGLRDDLDRLIRTLEAPGAPGSRLDMARLIAE
+GNAGRARVPGKHGAPPQAFAVVTVIVDDTPGQIAAVLDEVGRTDVNVEDLRLEHASGHRA
+GMVDISVLPGRRDELVAALSAAGWKVV*
+>NZ_CP083691.1_1374
+MIPAEGGAGPAGLSGPVLVRGTGLLGASIGLGLRAAGADVLLDDPSPTALAVARDIGAGA
+VVDLDDPALAPGLVVVGAPPDVTPAVVVDSLRRWPHAVVTDIASIKGAILAEVREAATRG
+DIAPGDVARYLPGHPMAGSERSGPVAARGTLFTASPWVLCPAAETDPAALAAGEALARTL
+QATVHRMSAADHDASVALISHLPQIAASLVASRLQDAPDPSLALAGNGLRDTTRIAASDP
+HLWVQILAGNAPQIVPTLHGLREDLDRLIGTLEAPSAPGARLDVARLIAEGNAGRARIPG
+KHGAPPQAFALVTVIVDDTPGQLAALFEEIGRAGVNVEDIRLDHASGYRVGMVDVSVLPG
+RKDELVSALTDAGWKVV*
+>NZ_CP097650.1_1311
+MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD
+IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA
+GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA
+AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD
+TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG
+NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG
+MVEISVLPGRRDELVAALTAAGWKVV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001175.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001175.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d8abcde9900637e5dcafe449741020640cdd99b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001175.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1368
+MATHDAPAEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFP
+DGELNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVG
+KGDRVLVYLPMIPQAPIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGI
+EPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE
+PADCVPVRATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASD
+VGWVVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIR
+RADPEGELLKAHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANP
+VGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGSLPTLWRDDQR
+YIDSYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALGSHPAVA
+ECAVIGVADPLKGQRPSGYVVLKSGVETPEPGSEAEAALLDELRQAVRREVGPVADFRDV
+VVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVLEALAGVLRPAR*
+>NZ_CP033200.1_1109
+MATHDAPAEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFP
+DGELNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVG
+KGDRVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGI
+EPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE
+PADCVPVQATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASD
+VGWVVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIR
+RADPEGELLKDHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANP
+VGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWGDDQR
+YIDSYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALAAHPAVA
+ECAVIGIADPLKGQRPSGYVVLKSGVETPEAGSEAEAALLDELRQAVRREVGPVADFRDV
+VVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVLEALAGVLRPAR*
+>NZ_CP040019.1_1461
+MMPPPNPAPPAPTPPPTPAPLHDPEGFWLEAAEAIDWTVPPTRALDDSAAPLYRWFPDGE
+LNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRFTYAELTDAVARLAGALAARGVGKGD
+RVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGIEPK
+RRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADVDGRGGASWEDWGEAVAAAEPAE
+CVPVQATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASDVGW
+VVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIRRAD
+PEGELLQDHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANPVGL
+EQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWRDDQRYID
+SYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALASHPAVAECA
+VIGVADPLKGQRPSGYVVLKSGVPVPEPGSEAEAALLDELRQAVRREVGPVADFRDVVVV
+DALPKTRSGKILRKTMRQMADGEEYAVPSTIEDASVLDALAPVLRPGA*
+>NZ_CP083691.1_1367
+MATDTTAAPRSYADVHRRSLEDRESFWLAAAEAIDWTVPPTRALDDSAAPLYRWFPDGVL
+NTAHNCLDRHVAAGRGEELALVHDSAMTGEVTRFTYAELTAEVARLAGALAERGVGKGDR
+VLVYLPMIPQAPIAMLACARLGAVHSVVFGGFAPRELAARIDDATPDVVLTCTGGIEPKR
+RVEYLPAVAEALEIAEHPVRTVLVHHREGFATAREDVADRGGAEWEDWAEAVADAAPAGC
+VDVAATDPLYILYTSGTTGRPKGVVRDHGGHAVALRWTMENIYDVGPGQVMCTASDVGWV
+VGHSYIVYGPLLAGATTVLYEGKPVGTPDAGAFWRLIQDHGVRSFFTAPTALRAVRKADP
+EAALLAEYDVSSLRHFFAAGERLDPETQKWIEGVLGMPVIDHWWQTETGWAIAANPVGLE
+ELPVKTGSSSVPSPGFDVVVVDGLGTPVAPGEEGNIAIRLPLPPGTLPTLWKADQRYVDS
+YLTAFPGHYATGDSGIVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALASHPAVAECAV
+IGVADTLKGQRPSGYVVLRAGVERPEPGGEAEEALLAELVQTVRREVGPVADFRDVAVVE
+ALPKTRSGKILRKTMRQLADGEQVAVPSTIEDASVLEDLAAVLRPAG*
+>NZ_CP097650.1_1317
+MATHDAPTEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFP
+DGELNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVG
+KGDRVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGI
+EPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE
+PADCVPVRATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASD
+VGWVVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIR
+RADPEGELLQAHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANP
+VGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWRDDQR
+YIDSYLSAFPGHYATGDSGLVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALAAHPAVA
+ECAVIGVADQLKGQRPSGYVVLKSGVETPEAGSEAEAALMDELRQAVRREVGPVADFRDV
+VVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVLEALAGVLRPAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001176.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001176.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ef36158730ee44df203ace857320e04095aea8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001176.fa
@@ -0,0 +1,26 @@
+>NZ_CP042169.1_1369
+MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG
+RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEAALRGG
+TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD
+IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP*
+>NZ_CP033200.1_1110
+MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG
+RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEAALRGG
+TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD
+IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP*
+>NZ_CP040019.1_1460
+MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPVREALSRLVADGLAEQAPG
+RGTVVADLSLEQADQLFDLRIALESLLARRAAQRATPETAARFTALAARFQEAGEALRAG
+TDPADYYAMTAELDASLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLATSAAEHAD
+IADAVGSGAADLAEATTRVHLHHAFHHLTRRTRADETPTLLSPTEGDRP*
+>NZ_CP083691.1_1366
+MPPFTPAGVSVYSGAMRVSDRAYAALRGEILDWTLPPGTVLGEVELADRLGISRTPVREA
+LARLVADGLAAQAPGRGVVVADVSLEEAEQLFELRIALESLLARRAAERADADQAAAMGA
+LADRFLAAVPRLEAGDEPAGYYTLTDELDAGLDAAAGNPYLVSTLRTLRLHLARLRRLAA
+HDPARLASSAAEHADIAAAVAAGAADLAEATTRVHLHHAATHLTRRARAAESTTLLTPTP
+FEGAHQ*
+>NZ_CP097650.1_1318
+MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG
+RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEVALRGG
+TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD
+IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001177.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..434b9a1ab75cc5e8d431534ee46a5743057c39e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001177.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1370
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLRR
+GPIVAARAQALSHPVSTGGEGASVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHAGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG
+IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ
+TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGSWHHVDSYAPERAQREDTVALWHKVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL
+KDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP
+GELDQLNILADPAFLSEADLAAAPKGLF*
+>NZ_CP033200.1_1111
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLKR
+GPIVAARAQALSHPVSTGGAGASVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHTGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG
+IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ
+TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGSWHHVDSYAPERAQREDTVALWHRVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL
+KDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP
+GELDQLNILADPAFLSEADLAAAPKGLF*
+>NZ_CP040019.1_1459
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIVNRIIDNASVAVASLQR
+GPIVAARAQALSHPVSTGGAGATVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHAGRSGKDLIRGIATGYEVQVDLVKSICLHKHKIDHVAHIGPSASAG
+IGTLLGLDTETVFQAVGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAADRAMRGQ
+TSPVPIYEGEDGVIAWMLDGPDASYEVPLPEAGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLNKEHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGAWHHVDSYAPERAAREDTVALWHKVTTVEDPEWTRRYHSNDLTEKAFGGAVEITL
+TDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVTQEEQDRFLDAVQRVSELGP
+GELDQLNVTADPAFLSQADLDNAPKGLF*
+>NZ_CP083691.1_1365
+MKKHDVRVHPSADNLAREDQLAHKLAEVAVDPVEVLPEVEEMIINRIIDNASVAVASLKR
+GPIVAARAQALSHPVSTGGAGATVFGVDQKVSPEWAAWANGVAVRELDYHDTFLAEEYSH
+PGDNIPPILAVAQHAGRSGADLIRGIATGYEVQVDLVKSICLHKHKIDHVAHIGPSASAG
+IGTLLGLDAETVFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAADRAMRGQ
+TSPVPIYEGEDGVIAWMLDGKDAHYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHSEHPEAMDPENVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSVPYIFTV
+ALQDGAWHHVDSYAPERAARPDTVALWHKVTTVEDPEWTRRYHSNDLSEKAFGGAVEITL
+TDGTVITDQIAVADAHPLGARPFAREQYIQKFRTLAEGVVTPEEQDRFLDAVQRLSELQA
+GELDQLNVLANPAFLSEADLAAAPKGLF*
+>NZ_CP097650.1_1319
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLKR
+GPIVAARAQALSHPVSTGGEGASVFGVAQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHAGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG
+IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ
+TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGSWHHVDSYAPERAQREDTVALWHKVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL
+KDGAVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP
+GELDQLNILADPAFLSEADLAAAPKGLF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001178.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001178.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7a6b93382978de7b87c1d1c595b1bb5bf9de5bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001178.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1371
+MLYSTKTAEQKRIDLRETLKQGGAQQFPGAFTPLSAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVELDTAVKRIAAAVHARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRRQLADAGVAMVI
+YPVTLLRSAMGAAERVLNAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL*
+>NZ_CP033200.1_1112
+MLYSTKTAEQKRIDLRQTLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVELDTAVKRIAAAVHARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRRQLADAGVAMVI
+YPVTLLRSAMGAAERVLHAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL*
+>NZ_CP040019.1_1458
+MLYSTKTAEQKRVDLRAALAEGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVALRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELAPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIKDEGTQASQVDQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIDENNANL*
+>NZ_CP083691.1_1364
+MLYSKKTAAQKRIDLRETLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFEDAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELAPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIREEGTQQSQVDQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIDSNNANL*
+>NZ_CP097650.1_1320
+MLYSTKTAEQKRIDLRQTLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001179.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001179.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83c49d7081556e1981fd29b84b616dda340cf9c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001179.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1372
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT
+DEELAAFEHFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESRQDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG*
+>NZ_CP033200.1_1113
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWTGELPT
+DEELTAFERFERTHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQEVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG*
+>NZ_CP040019.1_1457
+MTETEIKKGLAGVVVDTTAISKVNPDTNSLLYRGYPVQDLAAKLPFESVALLLWNGELPT
+DEELAEFQRFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAKALFAAFPAAVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA
+NALIRPLSSYDGPEQRELPAG*
+>NZ_CP083691.1_1363
+MTETEIKKGLAGVVVDTTAVSKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWNGELPT
+DAELEEFQRFERAHRALDPEVKAAVDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAKALFAAFPAVVAYDQRRRRGQEVVEPRADLDYAQNFLWMSFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPIFIAARITGWTAHIMEQRAA
+NALIRPLSAYNGPEQRELPGK*
+>NZ_CP097650.1_1321
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT
+DEELAAFERFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001180.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001180.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9a006fe42a229efed8f7fc1cfa861cac5c5d9ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001180.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1374
+MSADPAPRGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERYRRWLEAQG
+VRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEGLTPADPAL
+DVHPPKPGARLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVVGLDVD
+DVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMAGAARSTPA
+LFVNACGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVVQELLG
+HASVTTTQVYTLVTVDSLREVYSAAHPRAR*
+>NZ_CP033200.1_1115
+MSTDPAARGSGEAEARGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERYRRW
+LEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEGLTP
+ADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVV
+GLDVDDVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMTGVT
+RSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVV
+QELLGHASVTTTQVYTLVTVDSLREVYSAAHPRAR*
+>NZ_CP040019.1_1455
+MSTDPAARGSGEAEARGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERY
+RRWLEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPFAVRSAARVLAAVRGLHRFWALEG
+LTPADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARIS
+EVVGLDVDDVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMT
+GAARSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADV
+RVVQELLGHASVTTTQVYTLVTVDSLREVYAAAHPRAR*
+>NZ_CP083691.1_1362
+MSASPELHRALDRHLDHLAVERGLASATLAAYRRDLGRYLAWLEASRVDRPADVDPGHVA
+GFLSALGTGDDGGRPLGARSAARVLSAVRGMHRFWALEGLTPTDPAADVAPPRPPERLPK
+ALPVETVTRILEAVPTAEPADLRDRALLEFLYGTGARVSEAVGLDVDDVVGVAGDRGAGR
+GDDDRLPVVRLFGKGSKERLVPVGSHAADALAAWLVRGRPALAAAATRPVPALFLNLRGG
+RLSRQSAWSILKAAAERAGVAQDVSPHTLRHSFATHLMQGGADVRVVQELLGHASVTTTQ
+VYTRVTAEALREVYASAHPRARWTT*
+>NZ_CP097650.1_1323
+MSPHAPQTSALAAPFRRHLDHLAVERGLAENTLAAYRCDLARYRRWLEAAGVRAPGDVDP
+GHVAGFLQALATGDDGGRPLAVRSAARVLAAVRGLHRFWALEGLTPADPARDVHPPKPGD
+RLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVVGLDVDDVVGLAQTG
+DDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMTGVTRSTPALFVNARGGR
+LSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVVQELLGHASVTTTQV
+YTLVTVDSLREVYSAAHPRAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001182.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001182.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df11b2374bc49af0308e4e737e46a1a2a2c18bdc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001182.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_1376
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRVTADHAALRLAQEAGAVVDEGDNGTHDLVLSRSVTASGDGTRSRATAGGRS
+VPVGLLSEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPREGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPDLAAAAARLAEAAVVLTDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG*
+>NZ_CP033200.1_1117
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDTMDETPGAVSLVEAAQQAVLAAPGDDPELAAAAARLAEAAVVLTDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG*
+>NZ_CP040019.1_1453
+MIEHLRISGLGVIGEATVDLDPGLTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGAA
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADDGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGAEAQRRALDAFGGAELAASLRAYRADHAAVSAA
+RRERDELTAHRQERAREAEALQRSLEEIDLAEPLAGEDAELRELIRRLEDVEELRAASGE
+AHARLAGAEMDALEETPGAVSLVEGARQAVLAAPGDDPALAAAAERLAEAAVVLTDIAAD
+LARYTADLDTDAASDLDAAQSRLAELTRLQRLYGPELEDVIGWAETQRPRLDELQGDSGR
+LEELEGELERLESALRERAAALTALRTAAAGRLEEAVTQELHALFMPDASFHVDLAPVGG
+DGLGPHGAEDVALALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLSAEERVEELARMLAGHGDSAAAREHARELLEASARERG*
+>NZ_CP083691.1_1360
+MIDWMQITGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGRRADAGAVRRGSR
+RAAVDAGVRLPADHPALSLAVEAGAVLDDAGDGSADLVLSRSVTASGDGTRSRAGLGGRA
+VPVGVLAEVGSALVAVHGQNDQVRLQSAAAQRHALDAFGGPQLVAAAAAYRADHTAYVAA
+RRERDLLVERQQERAREAEALQRGLEEIDRAEPEAGEDETLRALIRRLEDVEELRAAADG
+GHAHLAGPDIESGDDLPGAITLVESARAAVQAAPGDDPELAAAAGRLAEASVILGDIAAD
+LARFSADLDGDAVSDLDAAQTRLAELSRLQRLYGPELTDVLAWAEAQRPRLEELQGDSGR
+IDELEADLARLDASRRERAAELTTLRTAAAGRLEQAVTAELHALFMPDASFHVSLVPLDD
+GDPGPHGAEDVALALRPHAGAEPRPLGRGASGGELSRVMLALEVVLAETDPVPTFVFDEV
+DAGVGGEAAVSIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPEAGVTTSDVV
+TLGQQERVDELARMLAGHGDSAAARAHARELLEASAAERA*
+>NZ_CP097650.1_1325
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPELAAAAARLAEAAVVLSDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTEAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001184.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a757b4dc0fc04fadf2e22db0ef446abcb758f1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001184.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1378
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPADRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVGVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHNQLAP
+PVRADPRVLVREGLNIRDLTAEDIDGPVDLVVSDLSFISLRLVLAPLASVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRHAVVGVTAAALGAGLAPRGLARSGLAGQDGNAEFF
+LRLRRPDATAADNPAGGTSPAPPAGERAAGWVRGAHIDWS*
+>NZ_CP033200.1_1119
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVAVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP
+PVQADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSGLAGQDGNAEFF
+LRLHRPDATAADDPAGRTSPATPADERAAGWVRGAHIDWS*
+>NZ_CP040019.1_1451
+MAEAVRADVALAARGLARSRTEASALIRAGQVLVDGRPVRRASERVAPTASLTLADDGPR
+WVSRAAHKLVSALEAFPDVAVRGRRALDAGASTGGFTQVLLEGGAARVAAVDVGHGQLVD
+LVRTDPRVLVREGLNVRDLTVQDVEGEVDLVVSDLSFISLRLVMDALAGVCRPGADLLLM
+VKPQFEVGRAALPRTGVVTDPAARRDVVAAVAAAALDSGLELRGLARSGLPGQDGNVEFF
+LRLRRPAADAAGAPGTGLDDDAPAAEAVAAAWTAAAEVDWA*
+>NZ_CP083691.1_1358
+MGEARRADVALAADGLARSRTEAAALVKEGVVLVDGTPVRRPSQPVASGAVLSLLDQGPR
+WVSRAAHKLVSALEAFPVPVAGRRALDAGASTGGFTQVLLERGAARVAAVDVGHGQLVQE
+LRADPRVLVREGLNVRDLTATDVEGSVDLVVSDLSFISLRLVLDALAGVCRPDADLLLMV
+KPQFEVGRAALPRTGVVTDPRARRSAVEGVVAAALGTGLAARGVARSGLPGQDGNVEFFL
+HLRAPAAPRDGGAVAGDADEDERRRRAAALVAAADVDWS*
+>NZ_CP097650.1_1327
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVAVAGRQALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP
+PVRADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSDLAGQDGNAEFF
+LRLHRPDATAADDPAGRTSPATPADERAAGWVRGAHIDWS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001189.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001189.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ccb227df35e132613d330eaf67273f164673ce2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001189.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1383
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPHAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALEPLRRWADTPG
+SVVDAR*
+>NZ_CP033200.1_1125
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVAAELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVRLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVMAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG
+SVVDAR*
+>NZ_CP040019.1_1446
+MTENPEARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHAA
+GLLGAEDLEGMIAALDRLETDVRSGAYAPADSDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGLVATVDALLSQVQAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARTAVSPYGSGALAGSSLGLDPEAVAAELGFDSAVWNSID
+GTASRDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVKLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLAGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFETERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+EEYAAISPALTPQVREVLSTEGSLNSRDAQGGTAPAAVAAQVEALERTLEPLRRWAQTPG
+SVVDAR*
+>NZ_CP083691.1_1352
+MSENSTPRHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLTADELAGMIDALDRLEADVRSGAYAPAESDEDVHGSLERGLIERAGAELGGKLRAGR
+SRNDQVATLGRMFLRDHARVVARGVLATVDALVEQAEAHPFAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFTRDLQRLVDWDARAAVSPYGSGALAGSTLGLDPNAVAAELGFDSAVWNSID
+GTAARDVYAEFAWVAGMIGVDLSRISEEVIFWATKEAGFVRLHDSYSTGSSIMPQKKNPD
+VAELARGKAGRLIGDLAGLMATLKGLPLAYNRDLQEDKEPVFDAVDTLELLLPAVSGMIA
+TLSFNTERMAALAPQGFALATDIAEWLVRQGVPFRVAHELSGEAVQVAESRGVELWDLTD
+EEYAGISAHLTPAVREVLSTEGSLNARRGQGGTAPEAVAEQLAALKAALEPLRAFAASAG
+SVVDAR*
+>NZ_CP097650.1_1332
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG
+SVVDAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001190.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c5380996a3c27bcd8c91e8f57110909ed5ddccc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001190.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1384
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAQRNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+HVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGSDDLQDVARLSND*
+>NZ_CP033200.1_1126
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADAREEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+QVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGGDDLQDVARLSND*
+>NZ_CP040019.1_1445
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTRDKAIDYAERNELPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFSPAPDVVTIAFERGVPTALDGRALSSLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+TVDQRWTELVYDGQWFSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASERDQRLRGGDDLKDVARLANS*
+>NZ_CP083691.1_1351
+MKDRIVLAYSGGLDTSVAIGWIGEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNELPIATTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFEQGVPTALDGRALSALEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+QVDQRWTELVYDGQWFSPLKKSLDTFIDDTQKHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIYGLSAKTASEREQRLGGAADLADVARLSND*
+>NZ_CP097650.1_1333
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+HVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGGDDLQDVARLSND*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001203.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001203.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a445812e342ec9328effc84348101de91638427a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001203.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1399
+MTAAPSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEAHGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSMWRTGDPA
+SRNVFERRASLALGGYIERPVVRGLRRRR*
+>NZ_CP033200.1_1141
+MTAAPSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEARGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSTWRTGDPA
+SRNVFERRAGLALGGYVERPVVRGLRPRR*
+>NZ_CP040019.1_1430
+MTTPDSPAGVGAGPPPLRWRTRARGLWNLVNLSTPLGLVGAVVSGCALRPGPHGLIEARG
+WRHSFPGGAAFTVGDVVFTRPGLRMTEDLWRHEAGHAAQYAGMLGLPFLPAYAAAAAWST
+WRTGDPASRNPFERGAGLALGGYVERPVRRGPRRRR*
+>NZ_CP083691.1_1333
+MSAAPARPTRPRGAARLRGLWNLLNLSTPLGVVGAVLAGCPLRPGPDGLLHAEGWRHRFP
+GGAAFTVGDVVFTRPGLEMTERLWRHEGAHAAQYAACLGLPFLPLYGMSAAWSSWRTGDP
+ASRNPFERGAGLERGGYVQAAVRRGPGRGALKPAGGDLRDARRA*
+>NZ_CP097650.1_1348
+MTAARSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEARGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSMWRTGDPA
+SRNVFERRAGLALGGYVERPVVRGLRPRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001205.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001205.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60189ad848a9733a550d6bbf6834b9c333a8fa2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001205.fa
@@ -0,0 +1,37 @@
+>NZ_CP042169.1_1401
+MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV
+PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ
+AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA
+YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF*
+>NZ_CP033200.1_1143
+MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV
+PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ
+AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA
+YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF*
+>NZ_CP040019.1_1428
+MRWEAQTLRSESGAQRAAAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNAV
+PAASAMPFRWTVNPYRGCTHACRYCYARSTHAFLDLDAGEDFDRQIVVKVNVAQVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYSLMPGIIEALADSGTPFSVLTKGTLLARDVPLLQ
+AASRSVPVQVSLSLAMLDPAVAAAVEPGTPSPAARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDRDLDALMRALAAAGAARVMPGALHLRPGAKEWYLRWIRQEHPDLLAGYEQMYARSA
+YAPESYRRTLARAAGEAAARHGLTRGGAHGIRREDGPVARPVPRSTPVAVPAPAAPAQPA
+LF*
+>NZ_CP083691.1_1331
+MRWEAQTLRTGGGAQRPGAGTPAGSPATLPLPGLQRIVSPPEFAGVTFHEVLARSALNKV
+PASSAMPFRWTVNPYRGCTHACVYCYARGTHRYLDLGPGEDFDRQIVVKTNAPEVLRAEL
+SRPGWTREPVALGTNTDPYQRAEGRYRLMPGIITALADTGTPFSILTKGTLLGRDAPALQ
+AAAAQTSVQVGLSLALLDPSLAAAVEPGTPSPAARLRLISRLAEAGVEVSVMAMPLLPWL
+TDSDRQLDRLMAALADAGAHSVLAGTLHLRPGAREWFLGWIDREHPHLAADYRRMYARSA
+YAPQAYRRVVSQAAREAAARHGLRHGGAHTITREDGPGPRGGASAPLSAPAGTTGAEQAD
+TAADAVRPVIAQPTLF*
+>NZ_CP097650.1_1350
+MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV
+PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ
+AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA
+YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001210.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001210.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08b10eafb2ccc31fea946d94cba7992222950354
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001210.fa
@@ -0,0 +1,39 @@
+>NZ_CP042169.1_1408
+MHGPGAAKWRPLSHPRQQDVRFAPGRVAGSPVGTAASWRAARTEGPVRRDRVEASVCVRA
+GEAFLVSEGPSGGRGVTRRLTQRSTTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDAL
+RLAAEADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKID
+KHDYETKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPR
+QDGRNMVMVVGPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDS
+APVRNSVGDAFPEQLKAMAARTQENASAAPAETTQAPKTPAPAAPRPAAAAPAAKPASSA
+TPASAPKPAATPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAP
+KPGPRA*
+>NZ_CP033200.1_1150
+MEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKIDKHDYETKTGH
+AKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPRQDGRNMVMVV
+GPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDSAPVRNSVGDA
+FPEQLKAMAARTQENASAAPAETTQAPKTPAPAAPRPAAAAPAAKPASSATPASAPKPAA
+TPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAPKSGPRA*
+>NZ_CP040019.1_1422
+MNPSSQHRSSTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDALRLAAEADLDLVEVAP
+TAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKIDKHDYETKTGHAKKFL
+SQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPRQDGRNMVMVIGPLRT
+KADARADQRKNSEDSHRERQGGGSRRDQAAREAKARAAEKAAANAAPVKNSVGDAFPEQL
+KAMAARTQESAPAAPAASAEPKQAPKAPAKPAAQAAPKQAPKAPAKPAAAAKPAAKPAAA
+PKPAAASKPASSGKPAAPASAPKPAAKPMPAPPKPAAPRGGAAKPGPRA*
+>NZ_CP083691.1_1324
+MESSSHPRQQDVRHGRAELPGHRVSAAVAPGSDDPWRPGGTAKGPIRGRFEASRLHPQGR
+PSAWRAPGVRSHQRPANRSGTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDALRLAAE
+ADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKKQVNTVLKEVRFRLKIDQHDYE
+TKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIRLLQKFAEDVAELGTVESQPRQDGRN
+MVMVIGPLKAKAEAREEQRKSTEGTQRERKGGGSRRDQAAREAKAAAAEKAAANSAPVRN
+SIGDAFPEQLRSFAAQQTEAPAEQAPVPAPKAAPAKATPAKAPAPKPAATPAPKPPASAP
+KPPAAPKPAAAPKPAAKPMPAPPKPAAPKGAPKPGPRG*
+>NZ_CP097650.1_1357
+MHGPGAAKWRPLSHPRQQDVRFAPGRVAGSPVGTAASWRAARTEGPVRRDRVEASVCVRA
+GEAFLVSEGPSGGRGVTRRLTQRSTTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDAL
+RLAAEADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKID
+KHDYETKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPR
+QDGRNMVMVVGPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDS
+APVRNSVGDAFPEQLKAMAARTQENASAAPAETKQAPKTPAPAAPRPATKPASSATPASS
+PKPAATPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAPKPGPR
+A*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001212.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001212.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7418cbb1d5575b9595b52a58feeffee19c4e4bef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001212.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1410
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAAVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA*
+>NZ_CP033200.1_1152
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA*
+>NZ_CP040019.1_1420
+MAQSRRPDPVDPREAPAAPAPEGPRTGGRAPVAALVVAAALALQAAALLWLAGDAIAHLG
+DGVLPAGARVMLIVIYVLLGLWILVTSVALLRGRAWSRGAATAVQLFGVLLSSRLLSVGE
+PVVGGVLLAVSGIALVTLFSRPVTAHLSQAAREPSAE*
+>NZ_CP083691.1_1322
+MSSSIPASPSGRRRMPAQAVVVAGVLGLEALTLVWLAVDGVAHLGAGALPTAAGVFLVVV
+YVLLAAWVGAVCGGMVRGRRFSRGAAVAIQLFAVILSTWLMSIGAPIAGGLLLVGSGAAL
+LCLFSGAVQAHLAGPDAGRPDAGRPDVG*
+>NZ_CP097650.1_1359
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001215.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001215.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e0aaa7aa5b9cf7370db72c529648ce7582fa259f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001215.fa
@@ -0,0 +1,51 @@
+>NZ_CP042169.1_1413
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDLAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRTERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRGADEPDDAGPGAAPAA
+ATPDGGPATADEGADPAPSPEEGEPAGPARESLVTVVWGPTGAPGRTTVAVNLAAEHAVA
+GRNTLLIDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAARERWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEVAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDTGRPARRRTLIPWSVRSRRTP*
+>NZ_CP033200.1_1155
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRDADEPDDAGPGAAPAA
+ATPDDGPATAGEGADPAPSPEEGEPTAPARESLVTVVWGPTGAPGRTTVAVNLAAEHAMA
+GRNTLLVDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAAREHWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP*
+>NZ_CP040019.1_1417
+MTVRIALATTVLPGLDHIGPLERHQTRITVVRRAEDLAELLAIARSGLVDAVLVAGATEA
+VTGAFLEELARLPRPVGAAAISEVRAERRRLRALGVPCVRADAGPEPLAAAVVEAALAAA
+DGRRARADAVAEDEGGEDPVDGLDGIELTYGVLDDDPRLGPPLLGGDPERSAVSAARPEA
+GAGDEAVDDGRRGGRAGDDLVPADAAQGGVTRDGVAQDRAQDGFARDDAQDFAAWDADAA
+GRSVPDVDRPDPRDPDGDAAEHAEDRPDVEASGTPGDARVIVVWGPTGAPGRTTVAVNLA
+AEHAVAGRSTLLVDLDTYGPSVGAHLGLTEESAGVARAVRRADHGPLGPADLEAAGVRVR
+VAGAELTVLTGLTRVDRWPELRPSALTSLLAAARGRWERVVVDVGFGLEQDEELSFDVPA
+PQRNGATLAALAAADEVLAVGGPDAVSLPRLVRGTEELVEAAPEARLRVVVNRLRPAAAG
+VSPRSQVEAVWSRYASAGIPLAAFLPWDPAAADRALLGGQVLAEAAPNSALRRALAELAD
+VDPRGARRTGRRRRPTGQGPAGAARRHPQDEGAARPSRRRTLMPWSARSRRTP*
+>NZ_CP083691.1_1319
+MRVALATTLMPGRDHVGPLEQAQAEVTVVRRAEDLAELLAAARSGLVDAVLVAGDLSALA
+RGFVDEVREAPRPVAVVAMGEVRAERERVRTLGVPCLSADADPLALAAAVQSAVRARLTG
+ARPELGSETPPADPPAPAPGTPDGGDPEAVRVAAVRDREGTPRLPEPNPVRVDALAASEV
+DALFTEETSPVAAADEAGPASPDAAGPDAVTASPADTAPEDGPEGGPERGRTGRTVAVWG
+PTGAPGRTTVAVNLAAESAVAGLRTLLVDLDTYGPSVGVHLGLTEETAGLARAVHRAERG
+SVTREDLVDAAVRVRVAGGDLDVLTGLTRPDRWPEVRPGALREVLQAARDGWDRVVLDLG
+FCVEEDEELSFDVPAPQRNGATLAGLAAADRVLVVGGADAVAMPRLLRAVEALPAGVEQD
+RVRVVVNRVRPQASGVAPQAQVAGVWERYGPPIPLVAQLPWDPGAADRALLGGQVLAEAA
+PGSALRAAVLELARLDPAVAARTQSAGRGRRPAVRGLRRRLAPWSAPSPRTP*
+>NZ_CP097650.1_1362
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRDADEPDDAGPGAAPAA
+ATPDDGPATAGEGADPAPSPEEGEPTAPARESLVTVVWGPTGAPGRTTVAVNLAAEHAMA
+GRNTLLVDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAAREHWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001217.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001217.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b50474bdab8f98e3151c145f3568888fb32ed8b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001217.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1415
+MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR
+ARVREWTEADAKAR*
+>NZ_CP033200.1_1157
+MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR
+ARVREWTETDAQAR*
+>NZ_CP040019.1_1415
+MQRFLTLTDVAETLNISGQAARALIRSGELQAIQVGGRGQWRIEESWLQEYVDRQREATR
+ARVQEWAEADAKSR*
+>NZ_CP083691.1_1317
+MPQFLTLTDVAEVLNVSVGQARTLVRTGQLQAIQVGGRGQWRIEAGWLDEYVERQRELTR
+SRVAERTREDAGHGA*
+>NZ_CP097650.1_1364
+MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR
+ARVREWTETDAKAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001220.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001220.fa
new file mode 100644
index 0000000000000000000000000000000000000000..276b00e31802d97fdfc03fbfdddd9c53f711e3de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001220.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1418
+MTTLATRPRAASDRRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPKSA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG*
+>NZ_CP033200.1_1160
+MTALATRPRTASARRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPASA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG*
+>NZ_CP040019.1_1412
+MIAVACVEVETGRRALRDLSAWLSPEVLDKMTRRMDLLGLAEQDRPRARSAAAGVSRAPA
+AAPRPVGARVCEVAPGRVEASATVLCDGRARAFALRLERRISRWKVTSVEIG*
+>NZ_CP083691.1_1314
+MTHSVRADRTMIRTSADRPAHRPAQEDPMTTLAPALAHGPTRPRPVSRTAPSRRDTESAL
+LRGPARRMSAVPTGEDLVRRAEQEDDREELRRLRSLAAVVAVACVETEAGRRPVRDLAGW
+LAPETYEKMCRRVDLLERTGTRPPSGSAPRPVGARVCAVRPGAVEASATVLVAGRARAVA
+LRIERRLSRWKVTHLEIG*
+>NZ_CP097650.1_1367
+MTTLATRPRAASDRRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPASA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001221.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eab21a4a1f399a63605a71f3835ccfd199592823
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001221.fa
@@ -0,0 +1,85 @@
+>NZ_CP042169.1_1419
+MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV
+VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAQAEAAVED
+AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVMNRQREAIYTDR
+RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL
+DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPASTSLP
+GVQDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS
+RRQAERRGRRG*
+>NZ_CP033200.1_1161
+MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEANTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNREPQRVDRNDVVYKNEKVKFDAV
+VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVED
+AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVLNRQREAIYTDR
+RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGQATDWDLDQLWRDLAEIYPVGVSQEDVL
+DEVGGRGRLTAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRHWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLP
+GVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS
+RRQAERRGRRG*
+>NZ_CP040019.1_1411
+MPSIIDRVLKISDNRVLRRMQGTVDAVNLLEEDFRALSDAELRAETDTLKARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+TGRGVHVITVNDFLASYQAELMGRVFRFLGMETGVVVAGQLPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEEGSDYEVDHKKRTVGVLGPGIEKVEDHLGIANLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYDKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV
+VEDIAERHERRQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPQVLAEAEAAVED
+ANREVLEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVMNRQREAIYADR
+RSILEGEDLKDRVRRFVEDAVGNIVDATTEEGHAADWDLDQLWRDLSELYPVGITQEDVL
+EEVGGRGRLKAEDLRRELVSDALLAYEDREAQVGSEALREAERRVVLSAIGRRWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAGIREDSVSTLFKAQITAAPAPTSLP
+GIKDARGLTMTPQISVEGVEAPQRPSQLRFTGPSEDGQGAVTRAGTETGATVEAGTNRRS
+RREAERRERRS*
+>NZ_CP083691.1_1313
+MPSIIDRVLKISDNRVLKRMRGTVDAVNLLEDDFRALSDAELRAETDSFKKRLADGETLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGLALHQGNIAEMKTGEGKTLVATAPAYLNAL
+TGKGVHVVTVNDFLASYQADLMGRVYRFLGMETGVIVSGQDPATRRAQYAADITYGTNNE
+FGFDFLRDNMAWSKEELVQRGHHFAIVDEVDSILIDEARTPLIISGPAQGDISRWYGEFA
+RLVRSLERGTDYEVDEKKRTVGVLEPGIEKVEDHLGIANLYESQNTTLVQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLAGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLSGMTGTAETEAAEFTSTYGLGVVVIPPNREKQRVDRNDLVYKNEKVKFDAV
+VKDIAERHATGQPVLVGTTSVEKSEYLSTLLTKAGVRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLEQAEAAVQD
+AREKVREAGGLYVLGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDDLMRNFNPGAA
+QRIMNSASIPDDMALEFKMVSSAIQNAQSQVEGRNAEQRKNVLKYDDVMNRQREAIYADR
+RAILEGDSLGERVRGFVEDAVGAVVDAATEEGAPVDWDLEKLWETLREVYPVGISPEDVL
+EQVGGRGRLKAADLKRELVSDALLAYDDREAQVGSEALREAERRVVLAMIGRHWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGFTMFQAMLAAIKEDSARTLFHAQIAAAPAPTQLP
+GVKDARAMTMVPQISVEGVETPRQPARLHLSGPSEDGEGVEEKDLAADGAQTPAGANRAS
+RRAEARRRRRGED*
+>NZ_CP097650.1_1368
+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_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001222.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001222.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fcbb826700e382615799e702eae812cf202880dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001222.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1420
+MTMDVSYIARNLRLPESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRLRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED*
+>NZ_CP033200.1_1162
+MTMDVSYIARNLRLPESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED*
+>NZ_CP040019.1_1410
+MTMDVSYIARNLSLPESFRDHVAERTERLHTLAEGAETLEVRVTKSSHHKHSDETVRVEL
+TARGPREVVRAEADADDKQVAFDMAVTRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPNGAQMAAEDAAREQDIPEEGTPVRIREKAFPATPMTVDEAVDAMELVGHDFFLFQ
+NSETGVPSVVYRRRGWSYGVIRLDESLPADHVSATEGERAYQAREA*
+>NZ_CP083691.1_1311
+MTLDVSYIARGITLSDRFREHVEERLEKIEPLAEGAETLEVKVSRSSHHRHSDEGMRVEL
+TLRGAREVVRAEGDADDKAAAFDAALSRIAERLRRMRDRRKDRRHGKGSAASRGAGEIPF
+VPPLPAVGQADAPADEAPESGTPVSIRAKRFPATPMSVDRAVDAMELVGHDFYLFQDETT
+GVPSVVYRRRGWSYGVISLDESLPAHHVAPVEGERVYQASREADAE*
+>NZ_CP097650.1_1369
+MTMDVSYIARNISLSESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001225.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001225.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6271206db896f3f33777e28c060ca905bb4e8c10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001225.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1424
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG*
+>NZ_CP033200.1_1166
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPTFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCKLIRAESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHQVTRAGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG*
+>NZ_CP040019.1_1406
+MSRAKILVVDDDEALAEMIGIVLRNDGFEAAFAADGTAALPAFHRERPDLVLLDLMLPGM
+DGIEVCKLLRSESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLQIGDLEIDVAGHQVTRDGAAISLTPLEFDLLVALARRPRQVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG*
+>NZ_CP083691.1_1307
+MSKARILVVDDDEALAEMIGIVLRNDDFEPSFAVDGTSALPAFRSARPDLVLLDLMLPGI
+DGIEVCKQIRAESDVPIIMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEQRPAEALAIGDVRIDVAGHQVSRGGAPISLTPLEFDLLVALARKPRQVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRAKVEPDPENPTVVLTVRGVGYKAGQV*
+>NZ_CP097650.1_1373
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001230.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001230.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0553cf8d533e79d8264a011beb621d954526518b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001230.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1431
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA*
+>NZ_CP033200.1_1173
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA*
+>NZ_CP040019.1_1401
+MRQNVAMALTELALRHPVRRFARREVDFRRRILTMAVVNRTPDSFYDDGAAFALEAAVDQ
+ARAAAEAGAEWVDVGGVPFAPGPALDPGEEARRVVPLIAALRGEAAEHSEAVAGLILSAD
+TFEPAVAEAAIAAGADVVNDTSGLVHADLGRVVAASQAHLVLTHSLAHVHGPRAVVPRPR
+YGDVVAEVREHLLRTVERAVALGVPEERIIVDPGHDLNKNTLHTLEITRRLDEIAGLGLP
+VLAAVSNKDFIGESLDQHRHERLAGSLAAAVACVHGGARILRMHDAAASVSAARLLECVF
+GWREPARLVHNMGEANPAPDRTSLAEHRAGRVRAGGTR*
+>NZ_CP083691.1_1300
+MPTPSVPLAHPVHRFAHHEIDFRRRIVTMAVVNRTPDSFFDDGAGFAFDAALAQVHTAAD
+AGAEWVDVGGVPFAPGRELDPAEEAARVAPFVAAVRAGRGEGASEAARRLILSADTFQPA
+VAEAAIDAGADVVNDTTGLYYPDLGRVVAASNAHLVVTHSLAHVSGPRTVVPRPRYDDVV
+AEVREHLLRTVDRAVALGVPEERIIVDPGHDLNKTTVHTLEVTRRLDEIADLGFPVLAAV
+SNKDFIGESLDRHRHDRLAGTLASAAFCALAGARILRMHDADASVSTAHMLECILGWREP
+LLAVHNTGDVNPAADRTTPADRVPADRPPAAVPAPTHDPEEARP*
+>NZ_CP097650.1_1380
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001240.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001240.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36d8db6597fb869e7cbe1399e435a791bb057a68
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001240.fa
@@ -0,0 +1,94 @@
+>NZ_CP042169.1_1463
+MSFGQGGGGPFGGPPRDGGGTAGGQSGPFGAFGPFGGAPRGPGDDGDRGPGGPFGGGGSS
+AARGRGRPGRPSALVLTIIAVAVLVGLFVVFTNVYTDVLWFSQLGFTEVFWTEVLAKAAL
+FLIAGLGMALAVWLAIRTAWRHRPADASAAARDSLSQAQRQLEPIRRLVFLGVPLVLGVF
+AGSTAMNGWNTVLLFLNQVPYGQADPEFGLDLMFFMATLPFLTLMVGYLISVVLVSGITG
+LLVHYLYGAVRVEEGGSVRITPAARAHIGITLAVFLLLQGVNFWLNRYRTTQSQTGNWAG
+ALYTDVNAVIPTSAILAVTAVIVAGLFVWTVVSGRWRLSLIGTAVLVITALVVGTAYPFI
+VQEYQVKPSERTLESQYIERNIAMTREAYGLDDVEVTNYEGATDPEAGALAGEEANTANV
+RLMDPNLISQTFGQLQQFRPYYSFPTTLHVDRYEVDGQTRDTILAARDVNVDDMQSWVNR
+HTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDQDYEPRIYFGLNSPSYSVVG
+APEGAPAVERDRPQTADSQEDTAYTFSGDGGPSVGNLFNRLAYAVKFGSPELVLSSDVNE
+ASQILYDRDPAERVRKVAPYLTVDTAPYPAIVDGRVQWIVDAYTTSDQFPYSTAQQLGEV
+TVDSLSQGQNPALQGRVNYIRNSVKATVDAYDGSVSLYAWDDQDPLLQAWQNVYPSSLRP
+YSEMSAGLLDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPTREEDVKQPP
+YYMTLQMPGQDEPAFSLTSSYIPQITDGAQQRNVLYGFLSAAGDAGTGEDGVKAEGYGQL
+RLLELPRSTTVPGPGQAQANFDSNADVSRELNLLRQGASEVLNGNMITLPVAGGILYVQP
+VYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEKQAEAPAPGE
+EPTAPGTVEEELSAALEEAQDALTQGQERLAEGDWAGYGEQQKRLNEALKRATAADDALG
+GDAPAQEQAPAEASPAPSSSPSPTPSG*
+>NZ_CP033200.1_1183
+MSFGQGGGGPFGGPPRDGGGTAGGQSGPFGAFGPFGGAPRGPGDDGDRGPGGPFGGGGSS
+AARGRGRPGRPSALVLTIIAVAVLVGLFVVFTNVYTDVLWFSQLGFTEVFWTEVVAKAAL
+FLIAGLGMALAVWLAIRTAWRHRPADASAAARDSLSQAQRQLEPIRRLVFLGVPLVLGVF
+AGSTAMNGWNTVLLFLNQVPYGQADPEFGLDLMFFMATLPFLTLVVGYLISVVLVSGITG
+LLVHYLYGAVRVEEGGGVRITPAARAHIGITLAVFLLLQGVNFWLNRYRTTQSQTGNWAG
+ALYTDVNAVIPTSAILAVTAVIVAGLFVWTVVSGRWRLSLIGTAVLVITALVVGTAYPFI
+VQEYQVKPSERTLESQYIERNIAMTREAYGLDDVEVTNYEGATDTEAGALAGEEANTANV
+RLMDPNLISQTFGQLQQFRPYYAFPTTLHVDRYEVDGQTRDTILAARDVNVDDSQSWVNR
+HTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDQDYEPRIYFGLNSPSYSVVG
+APEGAPAVERDRPQTADSQEDTAYTFSGDGGPSVGNLFNRLAYAVKFGSPELVLSSDVNE
+ASQILYDRDPAERVRKVAPYLTVDTAPYPAIVDGRVQWIVDAYTTSDQFPYSTAQQLGEV
+TVDSLSQGQNPALQGRVNYIRNSVKATVDAYDGSVSLYAWDDQDPLLQAWQNVYPSSLRP
+YSEMSAGLLDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPTREEDVKQPP
+YYMTLQMPGQDEPAFSLTSSYIPQITDGAQQRNVLYGFLSAAGDAGTGEDGVKAEGYGQL
+RLLELPRSTTVPGPGQAQANFDSNADVSRELNLLRQGASEVLNGNMITLPVAGGILYVQP
+VYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEKQAEAPAPGE
+EPTAPGTVEEELSAALEEAQDALTQGQERLAEGDWAGYGEQQKRLNEALKRATAADDALG
+GDAPAQEQAPAEASPAPSSSPSPTPSG*
+>NZ_CP040019.1_1391
+MSFGQGGGGPFGGPPRDGGGSAGGSSGPFGAFGPFGGAPQGPGGDGRDGGQGGGPFGPFG
+GGAGGSSAADRPRSGRPGRPSALVLTVIAVAILVGLFVLFTNVYTEVLWFSQLGFTEVFW
+TEVLAKAALFLLGALGMALAVWLAIRTAWRHRPSDASAAGRDSLSQAQRQLEPIRRLVFL
+GVPVVLGLFAGSAAMNGWDTVLLFLNQVPYGQADPEFGLDMMFFMATLPFLSLVAGYLTS
+VVLVAGIAGVLVHYLYGSVRVEEGGGIRVAPAARVHVGVVLALFLLLQAVNFWLNRYRTA
+QSQSGSWAGALYTDVNAVIPTSAILAVTAVIVAGLFVWTVFSGKWRLSLIGTAVLVITAL
+VVGTAYPFVVQEYQVKPSERTLEAEYISRNIELTREAYGLDAVEVTNYEGVTETEAGALA
+GEEANTANVRLMDPNLISQTFGQLQQFRPYYAFPDTLHVDRYEVDGQTRDTILAARDVNV
+DDTQSWVNRHTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDEDYEPRIYFGQ
+NSPSYSVVGAPEGAPAVERDRPQTADSQDDTAYTFSGDGGPSVGGLFNRLAYAVKFGSPE
+LVLSSDVNEASQILYDRDPADRVSKVAPYLTVDTSPYPAIVDGRVQWIVDAYTTSDQFPY
+STAQQLGEVTVDSLSQGPNAALQGRVNYIRNSVKATVDAYDGSVTLYAWDDQDPLLQAWQ
+KVYPSSLRPYSEMSAALMDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPT
+RDGDVKQPPYYMTLQMPGQEEPAFSLTSNYIPQITQGSQQRNVLYGFLSAAGDAGTGEDG
+VKAEDYGTLRLLELPRSTTVPGPGQAQANFDSNATVSRELNLLRQGASEVLNGNMITLPV
+AGGVLYVQPVYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEG
+QAGDPPQGEDGAAPAPGSVQEELSSALAEAQDALTRGQERLAEGDWAGYGEQQDRLNEAL
+RRATAADDALDGDAPADGEAPAEGQPPAEGSEAPSPAPEG*
+>NZ_CP083691.1_1289
+MSFGQEGAGPFGGPPHHDGDGGAHAARRVRAGGGRPSALLLTVIAVAALVALYMLFTQVY
+TEVLWFDQLGFSEVFWTEVLTKAALFVVAGAVMALAVWLSLRTAWRHRPGTAGADGRDSL
+SRARRQLEPMRRLVWAALPAVLGLFAGSAAMNGWKTVQLFLHQVPYGKADPEFGLDLMFY
+LATLPFLTMAVGYLISVVLVAGLAGLAVHYLYGALGVGDDGRVHVSVPARVHLGVLAGLF
+LLLQAATFWLNRYRTLQSQAGNWAGAMYTDVNAAIPTSAILAVTAALVAALFVWAAFTGR
+FRLPLVGAAVLVITALVVGTAYPYVVQQYQVKPSERTLESPYIARNIEMTREAYGLDQVQ
+VANYEGTTDAQAGDLKGEEANTANVRLMDPNLISQTFGQLQQFRPYYAFPGTLHVDRYEV
+DGQTRDTILAARDVNVDPEQSWVNRHTIYTHGYGVVAADASAVGAGGRPQWMLSEIPSRG
+VLGDDSTYEPRIYFGLNSPAYSVVGAPEGAPAVERDRPQTADSTDDTAYTFQGDGGPSVG
+GLFNRLAYAVKFGSPELVLSSDVNEASQILYDRDPVDRVAKVAPYLTVDTAPYPAIVGGR
+VKWIVDAYTTSDQFPYSTAQQLGEATQDSLSEGQAAALQGRVNYIRNSVKATVDAYDGSV
+ELYAWDAEDPLLKSWQGVYPASLKPYSEMSAALLDHVRYPEDMFKVQRELLGRYHVTNPG
+DFYENNDAWSVPSDPTTDKDVKQPPYYMSLRLPGQEETAFSLTSTYIPQITDNGQQRNVL
+YGFLSADGDAGTGRDGERAPGYGTLRLLELPRSTTVPGPGQAQANFDSNAQVSQELNLLR
+QGASEVLNGNMITLPVAGGILYVQPVYVRSSGGTTYPTLRKVLVSFGDKVGFADTLDEAL
+NQVFGGDSGATTPDAGEPAQEPRGTAEEELSSALAEAQDALAEGQERLAQGDWAGYGEQQ
+TRLNEALKRATAADDAAKGAQESADPAPEG*
+>NZ_CP097650.1_1390
+MSFGQGGGGPFGGPPRDGGGTAGGQSGPFGAFGPFGGAPRGPGDDGDRGPGGPFGGGGSS
+AARGRGRPGRPSALVLTIIAVAVLVGLFVVFTNVYTDVLWFSQLGFTEVFWTEVVAKAAL
+FLIAGLGMALAVWLAIRTAWRHRPADASAAARDSLSQAQRQLEPIRRLVFLGVPLVLGVF
+AGSTAMNGWNTVLLFLNQVPYGQADPEFGLDLMFFMATLPFLTLVVGYLISVVLVSGITG
+LLVHYLYGAVRVEEGGGVRITPAARAHIGITLAVFLLLQGVNFWLNRYRTTQSQTGNWAG
+ALYTDVNAVIPTSAILAVTAVIVAGLFVWTVVSGRWRLSLIGTAVLVITALVVGTAYPFI
+VQEYQVKPSERTLESQYIERNIAMTREAYGLDDVEVTNYEGATDTEAGALAGEEANTANV
+RLMDPNLISQTFGQLQQFRPYYAFPTTLHVDRYEVDGQTRDTILAARDVNVDDSQSWVNR
+HTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDQDYEPRIYFGHNSPSYSVVG
+APEGAPAVERDRPQTADSQEDTAYTFSGDGGPSVGNLFNRLAYAVKFGSPELVLSSDVNE
+ASQILYDRDPAERVRKVAPYLTVDTAPYPAIVDGRVQWIVDAYTTSDQFPYSTAQQLGEV
+TVDSLSQGQNPALQGRVNYIRNSVKATVDAYDGSVSLYAWDDQDPLLQAWQNVYPSSLRP
+YSEMSAGLLDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPTREEDVKQPP
+YYMTLQMPGQDEPAFSLTSSYIPQITDGAQQRNVLYGFLSAAGDAGTGEDGVKAEGYGQL
+RLLELPRSTTVPGPGQAQANFDSNADVSRELNLLRQGASEVLNGNMITLPVAGGILYVQP
+VYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEKQAEVPAPGE
+KPTAPGTVEEELSAALEEAQDALTQGQERLAEGDWAGYGEQQKRLNEALKRATAADDALG
+GDAPAQDQAPAEASPAPSSSPSPTPSG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001241.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001241.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b42f9fa3f28bcf3ee69b325f5bc53de3dda9379
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001241.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1464
+MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG
+GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA
+NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL
+EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIETAYDVPVDVE
+LTVPDIGGPSAGLMFALTVIERLTPGAMTGGASIAGTGTITGDGVVGPIGGIPQKVRGAA
+EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGESPAAARTCG*
+>NZ_CP033200.1_1184
+MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG
+GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA
+NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL
+EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIETAYDVPVDVE
+LTVPDIGGPSAGLMFALTVIERLTPGAMTGGAPIAGTGTITGDGVVGPIGGIPQKVRGAA
+EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGETPAAARTCG*
+>NZ_CP040019.1_1390
+MRAVPPRTTRAYRLPASGWLALGSAGLALLLPTPYILESPGPAVDLLGERDGAEVLRVEG
+GTPDEGEGTLDMTTVMVGGPPISTTSVIDLARSLVDPAVDVVPRELMYPTGMSSEEVGAA
+NTAAMSDSQDTAAAAALHALGRPVPSTLVVHELVPGGPSEGVLRPGDEVIAAAGEPAEDL
+EDLRAAVGAAGPDPVTLTVRRDGAVTELRVPVAAAPEGAPQPWQMGALIETVVDVPLDVE
+LTVPDIGGPSAGLMFALTVLERLTPGAMTGGAPIAGTGTITPDGVVGPIGGIPQKVRGAA
+QAGATTFLAPTANCGELDGRVPEGLQVYAVDTLAQAREIVEAVGRGEPPESARTCG*
+>NZ_CP083691.1_1288
+MPYILEGPGPAIDVLGEQDGTPVLTVEGGTADPGEGRLDMTTVLVSGPPGGTTGLGDLVT
+ALADGTVDAQPRELVHPSGVSADTVAQSNAAAMTDSQDVATAAALRALGRDVPAHLAVHA
+TVPGAPAEGILREGDVILAAAGRSVTDMAGIRAAVDAAGPGDLALTLRRDGTERQVSVPV
+TAADPATGRSWQLGVLLEQRFDLPVQVEFALEDIGGPSAGMMFALAVIERLTPGDMTGGA
+RIAGTGTITADGVVGPIGGIPQKMQGAARDGADVFLAPRENCADLAGRVPAGMTVYAVDT
+LATARAVVEAVGRGERPDDVPTCS*
+>NZ_CP097650.1_1391
+MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG
+GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA
+NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL
+EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIESAYDVPVDVE
+LTVPDIGGPSAGLMFALTVIERLTPGAMTGGAPIAGTGTISGDGVVGPIGGIPQKVRGAA
+EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGESPAAARTCG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001243.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001243.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f92d6c57ecde608ce6ed82810845e5cfc11ed841
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001243.fa
@@ -0,0 +1,26 @@
+>NZ_CP042169.1_1466
+MRLVRSTARTRTVSAAWRDGRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPD
+GRPADARSDDALLAWAGRLSAAHLGGRARPVAVTWSARQRRRWGSCTPARGTIRLSTQLR
+GMPDWVVAAVLVHELAHLLESGHGPAFRRLVDRYPRYAEAMAFLEGVTFAEGRGRTAPDR
+WAEDEDAG*
+>NZ_CP033200.1_1186
+MRLVRSTARTRTVSAAWRDGRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPD
+GRPADARSDDALLAWAGRLSAAHLGGRARPVAVTWSARQRRRWGSCTPARGTIRLSTQLR
+GMPDWVVAAVLVHELAHLLESGHGPAFRRLVDRYPRYAEAMAFLEGVTFAEGRGRTAPDR
+WAEDEDAG*
+>NZ_CP040019.1_1388
+MADNGRMPPADAAVPVPAEHERGEPVPAAAAVSALARRPVRRGAVRQSTDLDWEGTPVRL
+VRSTARTRTVSAAWREGRLQVNVPARLTPAHEREWIARMVEQVARRAGAGASPGRPGAGS
+QPGSGPGAGSGGDEALMAWAQRLSAAHLGGRARPASVAWSARQRRRWGSCTPSRGTIRLS
+DRLRGMPDWVVAAVLVHELAHLLESGHGPAFRRLVAAYPRYAEAMAFLDGVAFAESRGRT
+AQDTWVDDEDAMDADAPDDGPTEDERA*
+>NZ_CP083691.1_1286
+MSPSRTVTDLDWHGTPVRLVRSARRTRTVAAVWREGRLQVSVPARLSRAEERRWIERMVD
+RAGPAPAAHPAPSASAPSTGLGSAPDPRGDADLLARADALASAHLDGAAPGGRAPRPASV
+TWSSRQRQRWGSCTPARGTIRLSAQLRGMPDWVVDAVLVHELAHLSERGHGPRFQALVGR
+LPRYTEAMAFLAGVTYATSRGLPGAYPADADVADHARGWPGGDDDVVEG*
+>NZ_CP097650.1_1393
+MPDNGRMRPVPPAPGRPPRAVPAAHRGPARESTDLDWEGTPVRLVRSTARTRTVSAAWRD
+GRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPDGRPADARSDDALLAWAGRL
+SAAHLGGRARPVSVTWSARQRRRWGSCTPGRGTIRLSTQLRGMPDWVVAAVLVHELAHLL
+ESGHGPAFRRLVDRYPRYAEAMAFLDGVTFAEGRGRTAPDRWAEDEDAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001249.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff31ea38e9ef87c2c692c42e2cca5f8dc8e0282b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001249.fa
@@ -0,0 +1,104 @@
+>NZ_CP042169.1_1472
+MTREHGVDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHNAVLVLGAPG
+TGRTTVAVEYAARRIEAGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPADVAP
+AVEARGFRREVRELVDRMSELGLEPGRLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAAERDRLAVLVVEDLHEATPAVHDLLT
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPGVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAEVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLV
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVVTAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAVL
+AADGVGVADPRRWWGLLPLSTEAALVDPEREVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGVPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLERPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR*
+>NZ_CP033200.1_1192
+MTREHGVDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHNAVLVLGAPG
+TGRTTVAVEYAARRIEAGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPDDVAP
+AVEARGFRREVRELVDRMSELGLEPGCLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAEERDRLAVLVVEDLHEATPAVHDLLS
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPEVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAAVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLL
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVATAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAAL
+AEDGVTVADPRRWWGLLPLSTEAALVDPEREVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGVPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLEHPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR*
+>NZ_CP040019.1_1382
+MTWQADEDLLLDDDAAAPERAARLVSPAAAPAERVALTLEQEAVAAMGPGHGAVLVLGAP
+GTGRTTVAVEYAARRLESGTDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVR
+TWTSYAFDLLRRARVTGPLSHLPVAPRLLTGAEQDTVIAELLEGYAAGHAEAPRWPQDVA
+AAVETRGFRREVRELVDRMSEFGVEPGRLQELGAAHARPVWEAAAVLLQDYRDRIDLGLA
+EAFDAAGLISAAVRVLTERHPEDPERDAAALAFAAAERERLRTLVVEDLQEATPAVHDLL
+AVLGRGRDVLLTAGPDTAVEGFRGARPDLVSRYPQALDPDPVPGAPEAPSSGERTRVLTQ
+GHRMAPEVQDAFLRVARRVRQRTAAVEHTRTQTAPADGPGTVRGHVVPTRAHEDQLVLER
+VLRVHHEDEVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTL
+LAAAGVLADDPEAGVEDVLDPDEVVALLTGRYGMAGALHVRRLRQDLLAAERGRGGRRSS
+DALLAAALLDPALAGPEHERHRALRRVHWMLRAGIEAARAPSASPEAVLWALWSASGRAE
+RWRSTALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGAAPEAFAVYMESQDL
+PVDTLARRAEAGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLADLL
+TLPEGGAWPTDHRTRLREVRQDELRMLAAAVSRARRQVVVTAVRSAEDAPSDFLDLVDPP
+ERLPAPARDEAGVRRLTAVPDPITAPALAGTLRRRLEEDPGQGPAAAGLAALARDGVGVA
+DPRRWWGLLPLSTDAGLADPAQDVVALSPSRVETALHNPLNWLLYHVGATAGGTLAQSVG
+TLVHSVAEHHPEGVPEQVRAELERRLPELGLPEGWITEIEHERARALVDAYIGYWSIARD
+AGRRPVAQEVRLLAELTWGGTTVRITGVVDRLEADAEGRPFIADLKTGRSAPTGPEMARQ
+PQLAAYQVAVLAGGLAQIRDDPDADPALRAALADLARPAAPAGAALVQLGAGTQKTKVQE
+QPALGPEDDWALEQVFTAARRTVGPRFLAIHEAGGRRCALPSVCPLCSEGRQVTEWPR*
+>NZ_CP083691.1_1280
+MSTTPHPSEPRTEPTPQAADADPADLAALLAEPDEEPPHAAPVPARLVRGVGQDRAGVVL
+TVEQEAVAGLGEGHGAHLVLGAPGTGRSTVAVEYAARRLEAGLDPESLLVLAPSREAAAR
+LRDALTERLAAAGHGTRAVTPVRTWASYAFDLIRRARVTGPLRGLSRPPRLLSGAEQDTV
+IAELLDTYAAGLAPAPEWPRDVAQAVDTRGFRREVRELVDRMSEFGVEPGVLQELGRRHG
+RPVWEAAAELVQDYRDRLDLGMAEAFDAAGLISTAVRLLTERFPDDPERDAAALAFAEAE
+QARLRAIVVDDLQEAGPAVHDLLVHLGRGRDVLLTASPDTTVQGFRGARPDLVSRYPAAL
+DPDAVPGASSPDPDARTHVLTAGHRMSAGVQEGWLRAARRIRQRTVGVELTRTRTVPAGE
+GGAVEGHAVPSRAHEDQLVLERVLRVHHEDGVPLDGLAVIARSGARAAALGRHLEAAGVP
+VRREAAGEVLKDEPAVAPLLTLLRAVSDQAEDPEAGVALEADEAVALLRGPYGRATALNI
+RRLRQDLLAAERARGGRRTSDELLVAAFGDPALAGEETDRHRALRRLAWMHRDGLAAARE
+PGATAETVLWAVWAASGRADRWRAAALGRAEGAEGRREARRADADLDAVVALFRIAERFV
+DQFPGAAPADFSRYMESQDLPMDTLARRAETGDAVHVLTPAGAAGREWDTVIVVGLQEGA
+WPNTALRGQLLGATDLTDLLTAAAVDGAWPTDHRTRLAEVRQDELRMLAAAVSRARRRVV
+ATAVRNEDETPSDFLDLLDPVADVAAGRPLTEVPLPLTAAALVAAARRRLEAPDLPEALV
+GLEDPAAAAVLAALAEDGVAAAAPDRWWGLAPLSTDAPLTDITAEPVRLSPSRAQTALEN
+PLNWLLYHVGAQAGGTLAQSIGVLVHSVAEHHPDGEPGAVRAELERRLPELGLPEGWTTD
+LQHARARRLVEAYIRYWSQMRAEGRRPVAQEVALHVPLAWGDERVEISGVIDRLEVDATG
+RPYVVDLKTGSSKPDTAELERLPQLAAYQVAVRARGLELLAEDPATDPALRRALSAIEAP
+AEPGGAALVQLGAATKTKATVQPQPAVTADDDWALDQVFTAARRTVGPRFLAVHRPGVRC
+ALPSVCPLCTEGRQATEWHR*
+>NZ_CP097650.1_1399
+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_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001252.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001252.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0a16fa02bba485bb0b46ccd020e000f9101edd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001252.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1475
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDVWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGLDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSLLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG*
+>NZ_CP033200.1_1195
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSMLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG*
+>NZ_CP040019.1_1379
+MTTSTRTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGREYVDL
+VCSWGPMLLGHGHPEVTDAVHAAVDRGLGFGTSTLEETALAELIAAKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRDALEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITARHGALLIW
+DEVLTGFRATATGGWGLSGQVDGWTPDIWCFGKVIGGGMPAAALAGSAEIMNHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADDAVYAAVQRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSVAFGTSGTGVRDYRDAQAQEAFRYAPFFQSMLESGVYLPPSVFEAWFVSAAHDDAAV
+QRVLDALPAAAKAAAAATPQG*
+>NZ_CP083691.1_1277
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGTEYVDL
+VCSWGPMLLGHRHPEVLEAVHAAVDRGLGFGTSTLEETALAELIASRVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAALEAVFAEHGERIAAVITEAVPCNMGVVEPAEGYNAFLREITAQHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALAGSAEIMNHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADDAVYAAVQRASDAVREGLAAALTAEGVDHSIQRAGT
+LFSVAFGTSEHGVRDYRDAQGQDVFRYAPFFQTMLESGVYLPPSVFEAWFVSAAHDDAAV
+ERVLAALPTAAKAAAAATPQG*
+>NZ_CP097650.1_1402
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSMLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001253.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001253.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37da2b38cd4a01ebc96a33a133871f3df1e956eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001253.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1476
+MSFPLHRPRRLRRSAAMRRLAAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGAVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL*
+>NZ_CP033200.1_1196
+MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL*
+>NZ_CP040019.1_1378
+MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAPEPIAIASMPGVVQHTSDT
+LKAAAAEAAELGLGGIMLFGVPETRDAVGSISLDPEGVLNQAIRDVKSEVGDALVVMSDL
+CLDEFTDHGHCGVLTEDGAVDNDATLEIYAQMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LDAAGHVDTGILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRTEALHEVALDLE
+EGADMVMVKPAMSYLDIVRDVAELADVPVSAYQISGEYAMIEAAAANGWIDRKASIVESV
+LSIRRAGADTVLTYWATELGRWMKEGSL*
+>NZ_CP083691.1_1276
+MSFPLNRPRRLRQSAAMRRLVAETRLHPNELILPAFIKEGAAEPVPIASMPGVVQHTTDT
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALREVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL*
+>NZ_CP097650.1_1403
+MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRGVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001255.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001255.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d85dd291e6a5bab208e5e0df422322843a0c5a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001255.fa
@@ -0,0 +1,38 @@
+>NZ_CP042169.1_1478
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPIADEAPAADEAPAADEAPAGDAAAGKDG
+KAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNAT
+STDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRR
+SRRAEG*
+>NZ_CP033200.1_1199
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPAVDEAPAADEAPAADAAPAGDAAPAGDA
+AAGKDGKAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALT
+KAVNATSTDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEV
+SLVRRRSRRAEG*
+>NZ_CP040019.1_1376
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDALAKEENAKASEGSGRS
+GSRRGGRGRGRGSKTTDATDTPDADVADAEAPAADAAPAGDAATGRDGKGTEAKSGAGRR
+GRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNATSTDDGWATLSLI
+GQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRRSRRAEG*
+>NZ_CP083691.1_1266
+MSEPTPASLRIAVLLDCDNVSPKYAGLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+ELAIQPVQQFAYTIGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLRESGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTHTEGVDDDEPAPSLQAEPSPKDEREAKEGPA
+TGNRRGSRGRGAKAKPAADVASEQPAEAEPAPVVEPAPDVTPAPESDEAAPQRAVRGRGR
+GAGRGSVLVDVDSAEVITAEDPTPPDVRADADDDAEPASRINLQSALVKAVNATSGDDGW
+ASLSLIGQHMSRTHVDFDPRDFGHAKLSTLVADQPYLETRTEGRSMEVTLKQRRRRAQG*
+>NZ_CP097650.1_1405
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPIADEAPAADEAPAADEAPAGDAAAGKDG
+KAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNAT
+STDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRR
+SRRAEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001256.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001256.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26baae838e35096049dea789a2fdd747c1211bdb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001256.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_1479
+MGNTLDFLRGVDRLHAFYTENVRMLAHAYDLTDEEASELLANTGFTNVSVAILRGPRVDI
+MAAATGVPQDERHDAGPAPTEDDAPDPDGGRPD*
+>NZ_CP033200.1_1200
+MGNTLDFLRGVDRLHAFYTENVRMLAHAYDLTDEEASELLANTGFTNVSVAILRGPRVDI
+MAAATGVPQDERHDAGPAPTEDDAPDPDGGRPD*
+>NZ_CP040019.1_1375
+MGNTLDFLRGVDRLHAFYTENVRMLAHAYDLTDEEASQLLSNTGFNNVAVAILREPRVDL
+MASATGVPQDEKHDAGPAPTEDDATDPDGDRPD*
+>NZ_CP083691.1_1265
+MPDSVRMANTLEFLRGVDRLHAFYTENVRMLAHAYDLSDEEASRLLAHTGFANVSVAILR
+EPRVDLLAGLGASVEDEVHTHPVVDDASAPAEEPPASGGADDPEEPPAGSAPADPDDGAR
+*
+>NZ_CP097650.1_1406
+MGNTLGFLRGVDRLHAFYTENVRMLAHAYDLTDEEASELLANTGFTNVSVAILRGPRVDI
+MAAATGVPQDERHDAGPAPSEDDAPDPDGDRPD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001257.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001257.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecf725f75d08e601af2781673145e09462fe592b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001257.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1480
+MRVLLTRQPAQAGDLEAGLAGTEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG
+DAAGPVRSDGSRWLVVTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCDAAP
+WLPPEDRSAEGLIAGLAALHPRGARAWLPQSDRARSRLADGLRAAGWDVRTGLAYRTVPY
+PAQAGRRLLDGAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFVAAGLTPLVGERVR
+LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRAAA*
+>NZ_CP033200.1_1201
+MRVLLTRQPAQAGDLEAGLAGTEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG
+DAAGPVRSDGSRWLVVTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCDAAP
+WLPPEDRSAEGLIAGLAALHPRGARAWLPQSDRARSRLADGLRAAGWDVRTGLAYRTVPY
+PAQAGRRLLDGAADEGRGDVVTPARLAEVAAGTAVVLTSSSAAEEFVAAGLTPLVGERVR
+LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRAAA*
+>NZ_CP040019.1_1374
+MRVLLTRQPAQAGDLEAGLAGAEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG
+DAAGPGRSDGSRWLVLTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCDAAP
+WLPPEDRSAEGLIAGLAALHPRGGRAWLPQSDRARPRLADGLRAAGWDVRTGLAYRTVPY
+PAQAGRRLLDAAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFLAAGLTPLVGERVR
+LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRAAA*
+>NZ_CP083691.1_1264
+MDGRPLVLTRQPAQAGTLEADLAAAGRRVAFCPLTDFELPPTPGGLRAVVEAVVGGRCAW
+LLVTSPNAVRALQAAGWTGAVGAGVRVAVTGAGTARVLADAGCAVEPWMPESASAAGILA
+EFPAAPAETGDGARRVLLPQSALATAELEEALTRRGWAVDRVEAYRTVPYPADAARRLLT
+EEPGDAGTVVPVAELAGADVVLTSPSAARALAVHPALDDPELRRTWRLVALGAPTAREAR
+RLGLRLTGQAATPDATGILAALARPVG*
+>NZ_CP097650.1_1407
+MRVLLTRQPAQAGDLEAGLAGAEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG
+DAVGPVRSDGPRWLVVTSPNTVRALRAVGWGGHVPAGARIAVTGPGTARVLTEAGCDAAP
+WLPPEDRSAEGLIAGLAALHPRGARAWLPQSDRARPRLADGLRAAGWDVRTGLAYRTVPY
+PAQAGRRLLDGAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFVAAGLTPLVGKRVR
+LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRGAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001259.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001259.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2e2eab3cc02ebba9987e9f6a13bb7657876f8ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001259.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1482
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMAMEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA*
+>NZ_CP033200.1_1203
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMALEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFIVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA*
+>NZ_CP040019.1_1372
+MSTAPENAAAASPAPEPRADAPVHAGPRAGVAPTLRAPEEAAAGVDFDVCGVMAPKEYDA
+LLLASFGGPEGQDDVIPFLRNVTRGRGIPDERLEEVATHYRANDGVSPINAQNRALKAAI
+EAELAARGLALPVYWGNRNWEPYVPDTLERMHADGHRRILTVTTSAYSCYSSCRQYREDM
+GMALRRTGLEGVVDLDKTRQYFNHPGFIEPFRDGLRADLASLREELGEDARIHVLFATHS
+IPTSDAAAAGPRGLAADLRAQAGAEPGEEGADVYSAQHLDVAREILAGVPEAADVPWSLV
+YQSRSGPPSVPWLEPDINDAMEHLAGEDAEADAAGRAVAGFVVVPLGFVSDHMEVLWDLD
+TEARQTAADLGVAFRRSPTPGTDPRFVSGLVDIVEERMGRREGRASLGCFGAWYDVCRPD
+CCSKVMRDGTVRPTTSAVDADVRGLAEHEAGTAPAGRTEES*
+>NZ_CP083691.1_1262
+MTAVPTHRVPEDARRPVHEPERAAAGVDYDACGAMAPKAYDALILASFGGPEGQEDVIPF
+LRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALISAIEAELVRRGLELPVYFGNR
+NWEPYFPDALQRAYDDGHRRILTVTTSAYSCYSSCRQYREDMGLAMERTGLEGKVDLDKT
+RQYFNHPGFVEPFAEGLRADLASLREEVGEDARVHLLFATHSIPTADAAAAGPRGLAAAL
+REQAGGEPGDVEGADAYSAQHLDVIREVLARVPEAEGVDWSLVYQSRSGAPHVPWLEPDI
+NDALEALAGPDAPADADGRALAGVVVVPVGFVSDHMEVVWDLDTEAKDTAAELGVAFRRT
+PTPGTDPRFVSGLVDIVEERLGRREGREAVGCFPAWYDVCRPDCCVKVMRDGSVRPTTSA
+VDAPVRGLAEHRGEQDGADDAGAQDS*
+>NZ_CP097650.1_1409
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMAMEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001267.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001267.fa
new file mode 100644
index 0000000000000000000000000000000000000000..906d400792934ea6a4cd87141fae12ff0c8ba541
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001267.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1491
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAQAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGRARDARLTRAQEMVRRLGADFSI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG*
+>NZ_CP033200.1_1212
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAHAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGLARDARLIRAQEMVRRLGADFPI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG*
+>NZ_CP040019.1_1363
+MSRYDLHTHSVESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWEAAAEAALAEGIAFV
+PGMEMSCMAADGTSVHVLSYLHDPADPSLLREIGTARSARLTRAQEMVHRLARDYPITWE
+LVQEHAAEGATIGRPHLADTLVTLGVVEDRSAAFAHILTGRSKYYVPHYAPDPAIAVELI
+RSAGGVPVFAHPRAVTRGRVVGVEVIEEMIDAGLAGLEADHRDNPEEERSWLREVAARHD
+LFVTGSSDYHGTGKPNLLGEFSTGEDVLAEIERQGTGAAVVRG*
+>NZ_CP083691.1_1253
+MSTARYDLHTHSTESDGTEPAADVVHAAALAGLDGLALTDHDTTAGWAAAADAARETGLL
+LVPGMEMSCMAADGTSVHLLSYLHDPADPSLLAELGASRDARLTRAQSMTDRLAEDFPIT
+WDLVREHASENATIGRPHIADALVTIGAVPDRSAAFSSILRGGSKYYVPHYAVDPVEAVR
+LVRAAGGVPVFAHPRARLRGRIVGDDVLEAMIEAGLAGLEADHRDNPEQERTWLRETATR
+HGLFVTGSSDYHGAGKPNLIGEFTTGPEVLAEIEHQGTGAAVVRG*
+>NZ_CP097650.1_1418
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAHAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGLARDARLIRAQEMVRRLGADFPI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001268.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0a017cfae8b7abdc2880de31e34b9dffcf84f9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001268.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1492
+MTDAAQHPAQTTPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMASDWA
+PSSQALPDPDASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAFAHLT
+GLGVDHEPDAVLVLEPTDPGAGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWIGPRP
+TLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAGVDLA
+AAAEADAQTAEFLSELRLVKDAWEVDRMRASVAATIAGFEDVVRALPRAVGHDRGERVVE
+GAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLYTADI
+TRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGWGLLP
+VSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEPGLYF
+KEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAALPRTPDEIEAWMARLQA*
+>NZ_CP033200.1_1213
+MTDAAQHPAQTTPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMASDWA
+PSSQALPDPDASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAFAHLT
+GLGVDHEPDAVLVLEPTDPGAGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWIGPRP
+TLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAGVDLA
+AAAEADAQTAEFLSELRLVKDAWEIERMRASVAATIAGFEDVVRALPRAVGHDRGERVVE
+GAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLYTADI
+TRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGWGLLP
+VSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEPGLYF
+KEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAVLPRTPDEIEAWMARLQA*
+>NZ_CP040019.1_1362
+MTDAAQHPAQHADQDRPQDPAATPEAGVDAEGAVSPQPLAQRVENRSQRPSSDAFRAFMG
+ADWAPSSDELPAQDASAPHAARRRAAVSARYPGERIVVPAGRLKVRSNDTDYRFRAHSAF
+AHLTGLGVDHEPDAVLVLEPTDPGAGDGGSDHAATLYFRPLAGRDTEQFYADARAGEFWI
+GPRPTLAGLAARTGLRTAGLEELESAVTKNVCADGTAVRLLREADQDMDALLAGVRAEAG
+MDAEAAASADAQVAEFLSELRLVKDAWEVERMRASVAATIAGFEDVVRALPRAVGHDRGE
+RVVEGAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGTVREGDLLLLDAGVEDDSLY
+TADITRTLPVSGSFTDVQRRIYQAVLDSADAAYAIVRPGIRFREIHAEAMRVLVERLADW
+GLLPVSAEVALSEDGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEP
+GLYFKEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAALPRTPDEIEAWMARLQA*
+>NZ_CP083691.1_1252
+MTDASAQQNDDLAPEAAADSGAALSPQPLAERVENRSQKPTSDAFRAFMASQWAPASREL
+PGPDASAPFAARRRAAVSAMFPGERIVVPAGRPKVRSNDTDYRFRAHSAFAHLTGLGVDH
+EPDAVLVLEPTDAGAGDAGTDHAATLYFRPLAGRDTEQFYSDPRAGEFWIGPRPTLAELA
+ARTGLRTAGLEELENAVTKDVAATAVRLLREADQDMDAVVAAARADAGVDAQAAGAADAA
+LAEALSELRLVKDEWEVERMRASVASTIAGFEDVVRALPRAVGHARGERVVEGAFFARAR
+EEGNDLGYDTIAASGNNATVLHWIRNTGRVREGELILVDAGVEDDSLYTADITRTLPVSG
+TYSDVQRRVYQAVLDAADAAFALVKPGIRFREIHAEAMRVLAGRLHGWGLLPVSPEEALS
+EAGQHHRRWMPHGTSHHLGLDVHDCAQARRELYLDAVLEPGMVFTIEPGLYFKAEDLAIP
+EEYRGIGVRIEDDILVTEDGAENLSAALPRTPEDVEAWMARLQG*
+>NZ_CP097650.1_1419
+MMGGMTDAAQHPAQTAPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMA
+SDWAPSSDALPDADASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAF
+AHLTGLGVDHEPDAVLVLEPADPGTGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWI
+GPRPTLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAG
+VDLTAAAEADAQTAEFLSELRLVKDAWEVERMRASVAATIAGFEDVVRALPRAVGHDRGE
+RVVEGAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLY
+TADITRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGW
+GLLPVSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEP
+GLYFKEEDLAVPEEYRGIGVRIEDDILVNEDGAENLSAALPRTPDEIEAWMARLQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001269.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001269.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8da56b31155c7fa095c8a504428be1effebfb496
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001269.fa
@@ -0,0 +1,59 @@
+>NZ_CP042169.1_1493
+MGIDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDLATAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARDPSGIVTEPSRVWLAAGPHDAVAVAD
+RPDGAVVVPLAAPDGKTLAGLQRGDEIELTDARGAHRRLEVERVSGEGVLVRADKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFA
+DATVGDRVSLDDGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L*
+>NZ_CP033200.1_1214
+MGIDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GLPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARDPSGIVTEPSRVWLAAGPHDAVATAD
+RPDGAVVVPLADPEGTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLVRAEKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEEIVLARSLEPVPAVDTPPYRIGLTLAQAFA
+DAAVGDRVSLDDGRIGARITAVSADEITLEVTQAGPRGAKLKAEKGVNFPDTHLAIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L*
+>NZ_CP040019.1_1361
+MDIDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQDALS
+DVGLSSLGRMEAGVLGHVDAVLAAARALDGEDAPSPDDDALTPARGREILARDADRLLGP
+ARPDRAARIMVTLPSEAAQDPDLVARMAEAGMDLARVNCAHDDEAAWAAMIEAVRACATP
+ERPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARTPAGLVTEPSRVWLAAAGAADAPAGA
+VVVPVTEAGAEVLAGLAAGDEVELTDARGSHHVLTVEQAGAAGALVRADKTVYWGTGLAV
+DTPRGTLTVGELAPLEQSMRVRRRDQVVLTRSLDPVPAASAPPYRIGLTLAQAFEDVAVG
+DRVSIDDGKIDAVVRAANADEITLEVTEAGPNGTKLKAEKGVNFPDTALSIPALTDEDLA
+HIPFVARHADMVNLSFVRSAEDVAQLIDALAAEDATDVDITLKIETVGAFEQLPRMLLEA
+MRWRDVGVMIARGDLAVEAGFERMAELQEEILWLCEAAHVPAIWATQILESLAKTGLPSR
+AEITDAAMAQRAEAAMLNKGPYIEEAITALGDILGRMGGHARKKRDMLRRLESWSL*
+>NZ_CP083691.1_1251
+MSTLPENAPDSRPTAESPVVAPGAAVTELIEAIDALRARIVAAEQAHAERLDRVADRHRA
+SARNLVHYVTLRGEDLRPLQDALSAVGLSSLGRMEAGVLGHLDAVRTALHPLGGRPAPDP
+ADDDPLSPAEGRALLAANAESLLGPSRPGRETRIMVTMPSEAATNAALVQGMADAGMDLA
+RVNAAHDGEAAWAAMVANIRGVARDGGRPAPRICMDLAGPKLRTGPLEPGPGVVKVKPRR
+DVDGTVLERSRVWLGEADAPEAADAVVLPLDPAGSGHSPVLSALRPGDHAMLTDARDSDR
+TLHVLAATEAGVLLACRKTVYWHTGLEVDTPRGTLVVGALPSVPQAMRVHAGDEIVLTRS
+MDPRPAVSEGPFTIGCSLPQAFQDVRPGERVLIDDGKITGEVVSNDGEAITLTVTEAGPT
+GAKLRAEKGVNFPDTDLRLPALTDEDRSHLPFAAAHADVVNMSFVRSPADVAALIDALDA
+EDARGVGVSLKIETVGAFERLPAMLLEAMRWNDVGVMIARGDLAVEAGFERMAELQEEIL
+WLCEAAHVPAVWATQILETLAKQGLPSRAEITDAAMAQRAEAAMLNKGPYIDEAIGALSD
+ILTRMGGHADKKRDMLRRLRSWSL*
+>NZ_CP097650.1_1420
+MGIDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPTRDPSGTVTEPSRVWLAAGPHDAVAAAD
+RPDGAVVVPLADPEGTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLVRAEKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFA
+DATVGDRVSLDDGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001270.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001270.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37f1e948611b0523427742f185436316be219152
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001270.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1494
+MSIMMPNPQPGAEQGLPRGELLATYATYAQAREQVDRLAATDFPVSAVSIVGKDLRVVER
+VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF
+AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAAPTPPAASQPAPAPAAEA
+EDGSVQATPAPAPSSGGSHAAPAPGGPEAPARPAPEADPAPTGLDRSYGVTLPPEEVAKL
+IEARGGHPPRPQDEPRG*
+>NZ_CP033200.1_1215
+MSFMMSNPQPGAEQGLPRGELLATYATYAQAREQVDRLAATDFPVSAVSIVGKDLRVVER
+VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF
+AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAAPTPQPAPQPAPAPAAEE
+AGGGSVQATPAAAPSSGGSHAAPAPGGPEASARPTPEADTAPTGLDRSYGVTLPPEEVAK
+LIEARGGHPPRPQDEPRG*
+>NZ_CP040019.1_1360
+MSFMMSSPPPGADRGLPRGELLATYASYADAREQVDRLAATDFPVSAVSIVGKDLRVVER
+VRGRLNYAQVALSAGVRGVFFGGLIGVFLFLLTPEGGAGQILTSMLLGLAVWLIFGVIGF
+GMRKGRHGFASSQAVVPTGYDLVVAFEHAARARTELGLGGAAATAAAAVSTSPATPAPAA
+PQAGPNQNGAGQVDAPRPDAPQADAQHAPQAGAPSSGGSHAAPDADAQPAGAEAAPAAGA
+VPTGLDRSYGVTLPPEEVAKLIQARGGQASRPQEDPRD*
+>NZ_CP083691.1_1250
+MMMSGPAAGGLPQGELLATYSTYEQAREQVDRLAEADFPVTALSIVGKDLRVVERVRGRL
+NYGRVALGAAVQGALFGAMIGAFLLLLDSSAGGMQIVTSALLGVAVWVIFGVVGFASRKG
+RHGFASTQALVPGGYDLVVAFEHAGRARQELGLGARGAATPAPAPMPVQESAPAPAPAPA
+PSGSAVSGPSGSHAAPASSAEPAPAHVDGPAQDPAAPAGLDRSYGVTLPPEEVARLIEAR
+GGRPRQDPQAPQGQPHPWDRPQS*
+>NZ_CP097650.1_1421
+MSIMMPNPQPGAEQGLPRGELLATYATYAQARDQVDRLAATDFPVSAVSIVGKDLRVVER
+VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF
+AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAAPTPPAASQPAPAPAAEA
+EDGSVQATPAPAPSSGGSHAAPAPGGPEAPARPAPEADPAPTGLDRSYGVTLPPEEVAKL
+IEARGGHPPRPQDEPRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001271.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001271.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1980f99ce724ee91faf7b098a809b71c5d6bfb52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001271.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1495
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT*
+>NZ_CP033200.1_1216
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT*
+>NZ_CP040019.1_1359
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAVPPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAADLFDRRVRLTDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLDWDEARWTGQAEPQAATSFLAAHEDLKPA
+DLADMLHEMPEKRRVEVARELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEEAEDVRRLLEYEEGTAGSVMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAVGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTSIPVVNEHHRVVGAVSVDDVLDHILPDDWRAMDHDDHDPRP
+AA*
+>NZ_CP083691.1_1249
+MNSPRIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGRGARSAATGLVIEVPGKKRVFVPM
+TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAGDLFDRRVHLTDGSGRAVVEDLGIEQQR
+NGDWLVTDYYVRRDDGRTAFGRPRGEHLLVSWDEVAWGAAAEPQGASSFVAAHDDLKPAD
+LADMLHEMTDKRRVEVANELQDERLADVLQELPDDDQVQILSHLDIERAADVLEEMDPDD
+AADLLNELPDSQQELLLELMEPEDAEDVRRLLEYEEDTVGSIMTPVPVVLPPEATVAEAM
+ATIRQQEISPALASLVIVARPPLETPTGRYLGVVHFQRLLRYPPPEAIGNIMDKDLEPVS
+DMDSVAHVTRELATYNLTSIPVVNAQHRVVGAVSVDDVLDHILPEDWRAMDPEDHPETEG
+QD*
+>NZ_CP097650.1_1422
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVARELQNERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEAV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001272.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001272.fa
new file mode 100644
index 0000000000000000000000000000000000000000..346db8f31692f302bcc5d78bee527bc7aa84d3db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001272.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1496
+MTQTARDLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF
+CAAWLGWNTFGPMEWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDRVALRED
+RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE
+IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAREAGG
+SGPAAGPADGAGPVDGGGR*
+>NZ_CP033200.1_1217
+MTQTARDLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF
+CAAWLGWNTFGPMEWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDRVALRED
+RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE
+IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAREAGG
+SGPAAGPADGAGPVDGGGR*
+>NZ_CP040019.1_1358
+MSQTSRDARPSRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF
+CAAWLGWNTFGPEDLRFDSAALGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED
+RDRAERNLADTEFLTREISGLRLAVQEVATRDFVRGELRGVQEDLRDELREALRAELREE
+IRAELRAELAEGRRERTDPGAEPRPRKQKKHKGRDRGRDERRAGDDGVDPSTTTLAVIAA
+REAAQAAQSAQAGQDAGPEAGRAVDGRDDADGAAR*
+>NZ_CP083691.1_1248
+MPQSPRDPRDTRATGLDTPMRARERVMPRLTPNPDAFGEWTEGIARFMGTPQFLLWMTLF
+CLVWVGWNSYAPEPWRFDSAALGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED
+RDRAERNLADTEFLTREISGLRIALQDMATRDYVRGELRAMNEDLVAALREVVREEVREE
+LRAEEAGPAVAPKPKEKSKKKSSRREPGRPDGTEAHTTTLAIIAAQEAADQGGAAPDAAH
+AADDAGQDAP*
+>NZ_CP097650.1_1423
+MTQTARYLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF
+CAAWLGWNTFGPMAWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED
+RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE
+IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAQEARE
+AGGSGPVTGPAGGAGPVDGGGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001273.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001273.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95bf2a214b3b7553d64a37c1efe67821138c819a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001273.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1497
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ
+IAQRVAVRPRGLAGRRLPVTPR*
+>NZ_CP033200.1_1218
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ
+IAQRVAVRPRGLAGRRLPVTPR*
+>NZ_CP040019.1_1357
+MSDLGLHVPEVRTDLERRVLDRLATVQDPEIRRPVTELGMVESVVETAPGTVEVTVLLTI
+EACPMRGTIQGDVAAAVADVPGCDAVDVRTGVMSPERRLALQDALRAARPANPFGEGSLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTASPTKLDRM
+ILPPVVRDVKVISIGMFLDEDRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQAVAGVIENMGPMTLPDGTVL
+DVFGAGGGQEVAERLERVLGSAVPLLGSVPLDPALRRGGDAGDPVVLSAPDSPAGRALAG
+VAERLAVRPRGLVGRRLPLSPR*
+>NZ_CP083691.1_1247
+MSAPALPRPEVRTPLEAAVLAALDGVVDPEIRRPITELGMVRSVAETGGGHVAVEVLLTI
+AGCPLKGTIQADVAAAVADVPGCAGVDVRLGVMTPTERAALQEALRGARPANPFAEDSLT
+RVLAVASGKGGVGKSTVTANLAVALAGRGLSVGLIDADVHGYSIPGLLGVQASPTRVGEL
+ILPPVSRGVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELVVVTTPQHAAAQVAARAGQLAAQTGQRVAGVVENMGPMALPDGTVL
+DVFGAGGGQEVADRLSGALGTSVPLLGTVPLDPALRRGGDAGEPVVVSAPESPAAAALQE
+VAARLAVRPGSLRGRGLPVSPR*
+>NZ_CP097650.1_1424
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVADVPGCGSVDVRVGVMEPERRLALQDALRAARPTNPFGKDTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLGTQVPLLGTVPLDPALRAGGDAGDPVVVSAPESPAGRALAE
+IAQRLAVRPRGLAGRPLPFTPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001276.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001276.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee6e24a92ba346b80920e53a3051c7f095a1d5fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001276.fa
@@ -0,0 +1,10 @@
+>NZ_CP042169.1_1501
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA*
+>NZ_CP033200.1_1222
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA*
+>NZ_CP040019.1_1353
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQG*
+>NZ_CP083691.1_1243
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEAKELQQCLEGVTQA*
+>NZ_CP097650.1_1428
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001284.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2e6acf941e045b32dfe8135aada2f0ff452f10c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001284.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1509
+MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAAHTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN*
+>NZ_CP033200.1_1230
+MTQTAAQQPSPRLVSGHGLATTAADGAVLDVWFPTPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLARPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN*
+>NZ_CP040019.1_1345
+MTETAAQHPSARLVSGHGLATTAADGTVLDVWFPAPVAGPLADADATLAETLRSLAADDA
+DRGTTQSVVELEADLDAAPATAEDAWLRLHALSHRLVRPNELNLDGVFGLLANVVWTNFG
+PCAVEGFELTRARLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLL
+GANSGVGISIGDDCVVEAGLYVTAGALVTVVRPGEEPRTVKAVELSGVPNLLFRRNSATG
+VVEVLPRAGRTVELNAALHAN*
+>NZ_CP083691.1_1235
+MTDTSQTSSARLVSGHGLATRAADGAVLDVWFPAPVTGPLASADASLAGTLEGLAAADAD
+RGTTQDIVALEADLDVAPASAEDAWLRLHALSHRLVRPNELNLDGVFGLLTNVVWTNFGP
+CAVEGFEATRAKLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTVM
+HEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLLG
+ANSGVGISIGDDSVVEAGLYVTAGTVVTVVEPGRKPRTVKAVELSGVTNLLFRRNSVTGG
+VEVLPRDGRTVALNAELHAN*
+>NZ_CP097650.1_1436
+MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001288.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001288.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ced540c5c527e82fb22233b157a53a26a45fb2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001288.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1515
+MTSTETRRSDLRNVAIVAHVDHGKTTLVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS
+VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLERVPAEEAGPG
+EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR
+TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGSATPFAMINLQERGTFF
+VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA*
+>NZ_CP033200.1_1236
+MTSTETRRSDLRNVAIVAHVDHGKTTMVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS
+VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLGRVPAEEAGPG
+EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR
+TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGSATPFAMINLQERGTFF
+VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA*
+>NZ_CP040019.1_1340
+MTSTDTRRSDLRNVAIVAHVDHGKTTLVDAMLRQGGAFAAHGEVAERVMDSGDLEREKGI
+TILAKNTTVFYSGPSAPEGQTVTFNVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLADEVEDLDLDS
+VLNLPVVFASGKAGRASLNQPEDGSLPDSEDLEPLFATMMEHIPAPAYTKGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLKKGQQVAWARQDGTLKTVKITELLGTKGLSREPIEEAGPG
+EIVAVAGIEDIMIGETLTDVENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDAELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTK
+TVDGKVHEPMELMTIDTPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFSVPARGLIG
+FRTQFLTDTRGAGIASSIANGYEPWAGTIEYRNNGSLVADRAGTATPFAMINLQERGSFF
+IQPGSEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSDSFEGLTPPRQLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA*
+>NZ_CP083691.1_1230
+MTSTDTRRSDLRNVAIVAHVDHGKTTLVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDASEGPL
+PQTRFVLRKALAAKLPVVLVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPELDLDS
+VLDVPVVYASGKAGRASREQPGDGALPDSEDLEPLFNVIMEHIPAPVYDESEVLQAHVTN
+LDASPFLGRLALVRIVNGTLKKGQTVAWARQDGQLKSVKITELLATKGLERVPADEAGAG
+EIVAVAGIEDIMIGETLTDLEDPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTK
+QIDGKLHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTDTRGAGIASSEAAGYEPWTGDIEYRTNGSLVADRAGTATPFAMINLQERGTFF
+IQPGAEVYEGMIVGENARADDMDVNITKEKKLTNMRAASSESFEGLTPPRTLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA*
+>NZ_CP097650.1_1442
+MTSTETRRSDLRNVAIVAHVDHGKTTMVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS
+VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLERVPAEEAGPG
+EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR
+TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGTATPFAMINLQERGTFF
+VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001290.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001290.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea4f31bc0200d1327ee83174633a6aa7c2c8ffc8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001290.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1517
+MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSLLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGGGAHRRLRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEEAGGSARISDADEDGQR*
+>NZ_CP033200.1_1238
+MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEAAGGSARISDADEDGQR*
+>NZ_CP040019.1_1338
+MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRVKAGKSYSQGALVRKRFFRHKAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGANMGILPLALVLGLVTWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRVIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISLYQNS
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAAAGRKRGLFSRRAAKTDAGAT
+TAGGLGTAPTARDGEADDLIADPDAPEHRRGGAGGPAGGVGQ*
+>NZ_CP083691.1_1228
+MTMSHSAQQNPRSTSPAVVDLAEAEDLKLQQKTGKSYSQGALIRMRFFRHKAAMVSLVVL
+AFIALMAFTSIGFAGIPGWWDESYSAASTVVDGGRPTLSVVPQFLGGEGLRWGAHPFGQT
+STGTDFFALVMRGTQQSLIIAFIVGLISTAIGALVGAASAYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGKMAGGLQLGILPLAFVLGIVSWTSLARLVRGEILSLREKEFVAAAVAMGA
+KPGRIIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSYLGFGVKSPDSSLGLLISDYQTA
+FTTRPWLFWWPGMTILAIALSVNFLGDGLRDAFDPRQSGSGRRKRGLFSRRAAVTEATPT
+TAGGLQASPASAPAGHADVVTDSRGLDAPAAWTVTDADGTSRPAGDDVDTTEGDAR*
+>NZ_CP097650.1_1444
+MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHKAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEEAGGSARISDADEDGQR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001291.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9a53adb57f28a2d609b59f9261503e939f42ca8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001291.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1518
+MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTAFMGLDQ
+PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVADLLSNAAASTLRLVVLATVLAIIIGIA
+IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG
+VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA
+AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI
+LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD
+AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL
+VTGTAAVLMNLVADVLYAVLDPRIRV*
+>NZ_CP033200.1_1239
+MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTAFMGLDQ
+PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVADLLSNAAASTLRLVVLATVLAIIIGIA
+IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG
+VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA
+AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI
+LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD
+AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL
+VTGTAAVLMNLVADVLYAVLDPRIRV*
+>NZ_CP040019.1_1337
+MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTEFMGLDQ
+PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVGDLLSSAAASTLRLVVLATVLAIIIGIA
+IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG
+VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA
+AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI
+LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD
+AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLSERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL
+VTGTAAVLMNLVADVLYAVLDPRIRV*
+>NZ_CP083691.1_1227
+MLKFILRRLGSSALVLFGASILLYVLTVNSGDPLKDLRESQASNREQLMQARIDYMGLDD
+PWYERYWNWLTGVVKYLIGAGTLGTDRSGVQVESLLGNAAASTLRLVVLATVLAIVIGVA
+IGIITAIRQYSGLDYAVTFLIFLFFSLPVFWAAVLLKEYLAIGFNNWIARPTMDWPLVIG
+LAVVLGLALQAAMGGRLVRRLLTFAATVAVIVLGGYLLFALDMWRNPRMGPLVQLLIGLA
+VAVGGTALVAGLKNRSVLKAALATVAVGVVAYYATYGVLMQSPSGWLIAGLGVIAVLVGV
+LAGRLLGGFSKGSAVSVSVVTALVMGLSILAEHMMNYWPQLLKAKPRPIATIGAETPNLT
+GHFWVLFLDKGTQLLLPTVLLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLGERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITESVFGWKGMGELFRTGLDQVDPAPVMAFFL
+VTGTAAVLMNLVADILYAVLDPRIRV*
+>NZ_CP097650.1_1445
+MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTEFMGLDQ
+PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVGDLLSNAAASTLRLVVLATVLAIIIGIA
+IGIITAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG
+VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA
+AAVGATAVISGLRNRSVLKAALVTAAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI
+LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD
+AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL
+VTGTAAVLMNLVADVLYAVLDPRIRV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001292.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001292.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c912478c8ac2993025fd1db842c7fc5418ef5e27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001292.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1519
+MKYTKLSAAAALAAGSALILSACAPGGGNAGDSSSNSASGASQGGDSGAGNVIEGDKGQK
+LTAEASGPGKADLGDVKTQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMFSSFWY
+FGTDGSIIPDKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANNDTIKA
+EGAETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAKEA
+GMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGGWQAGQ
+SITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGED
+VNVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNL
+REVFPFQDKYQEVVDAAYPKEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRRTETVA
+LIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALFAWAGSGQKASGANIYQSDGAQNQQ
+SYNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVR
+DTAAQSGALWNVEQWVRVQE*
+>NZ_CP033200.1_1240
+MKYTKLSAAAALAAGSALILSACAPGGGNAGDSSSNSASGASQGGDSGAGNVIEGDKGQK
+LTAEASGPGKADLGDVKTQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMFSSFWY
+FGTDGSIIPDKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANNDTIKA
+EGAETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAKEA
+GMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGGWQAGQ
+SITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGED
+VNVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNL
+REVFPFQDKYQEVVDAAYPKEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRRTETVA
+LIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALFAWAGSGQKASGANIYQSDGAQNQQ
+SYNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVR
+DTAAQSGALWNVEQWVRVQE*
+>NZ_CP040019.1_1336
+MKYTKLSAAAALAAGSALILSACAPGGGDDADNTASSGNGGASGSASQGGEAGAPEVTEG
+DKGQKLTAPVDGPGMADLGDVETQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMF
+SSFWYFGTDGSIIPNKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANN
+ETVKAEGSETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHI
+VAKEAGMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGG
+WQAGQSITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLE
+GLGDDVNVQTGDQLTWEHVDFNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADA
+QVMNAREVFPFQENYQEVVDAAFPEEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRR
+TETVALIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALYAWAGSGQKASGANIYQSDG
+AQNQQSYNNPEVDAAWDKLATSLDEDEQLEQVKTIERLLWEDFQAIPLYAHPGLVGHKAD
+VANVRDTAAQSGALWNVEQWVRVQE*
+>NZ_CP083691.1_1226
+MKHTKLSAAAALAFGSALVLSACAPAGPAASGSSSNGGGSSAASGSSAASGSDAAGGVTT
+GEKGEKLTAPADGPGMADLGDVKTEEGSVAYSVGKDDFLSYNGVQANTYSTYNSAIVDRL
+FSGFYYFGTDGTIVRNEEFGTFEKISDDPLKVKYTINEDATWSDGTPVTAADFIVQWAAD
+NPNIVDESGKADPKTGQKPQLFESITSEPGKYIPEAPEGDPKGKEFTVTYAEPYADWEIL
+ITTALPAHVIAKGADMSLDDLVAAAKAKDSTKLVPAAKFWNNGWDFNPGELPSADMIPSM
+GPYKIKDGGWVAGQSITLEANDKYWGTPAATKNLVIKFAAPETHVQALQNKELDVIEPQA
+TVDTVSQLEGLGDSVNIQKGDQLTWEHLDFNRGTGSTFADSKELREAFALCVPRQQIVDN
+LVKPINPDATVMNAREVFPFQDNYQEVVDAAYPKEMDQPNIEKAKELVAKSGVSKPTVRL
+GYQAGNQRRAETVKLIKASCDQAGFDVQDANSNVFFKEVMPTGDYDVALYAWSGSGQKAS
+GANIYQSDGEQNQQSYSNKTVDEAWDKLAGSLDEKEQLEQVKVIEKALWEDFQAIPLYAH
+PGVVAHQADLANVRDTVAQQGALWNVEQWKRVS*
+>NZ_CP097650.1_1446
+MKYTKLSAAAALAAGSALILSACAPGGGNADDSSSNGSGASQGGDSGAGNVVEGDKGQKL
+TAEASGPEMADLGDVETQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVVDRMFSSFWYF
+GTDGSIIPNEDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIFHWAANNDTVKAE
+GSETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAEEAG
+MSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGSYKFKDGGWQAGQS
+ITLEANPEYWGTPPATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGDDV
+NVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNLR
+EVFPFQDKYQEVVDEAYPKEMDEPNIEKAKELVEKSGVSTPTVRLGYQAGNQRRTETVAL
+IKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALYAWAGSGQKASGANIYQSDGAQNQQS
+YNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVRD
+TAAQSGALWNVEQWVRVQE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001294.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001294.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3688950e1ef283f5e58b090e88272e8c2cfb52d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001294.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1522
+MTPPGWPPRARRSPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHIHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGDQVAAVGNGGGQGHLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTADEVDGFAIPLEVAFDVVDQVLTGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRAVGDDASRMSRLV
+NDHNVGDRITVQWRTADGEVREAEAVLQPALVN*
+>NZ_CP033200.1_1243
+MTPPGWPPRARRAPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHVHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGETVAAVGNGGGQGHLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTAEEVDGFAIPLDVAFDVVDQVLSGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRPVGDDAFRMSRLV
+NDHNVGDRITVQWRTASGEVREAEAVLQPALVN*
+>NZ_CP040019.1_1331
+MSVPPGWPPRRRRSPLALAISFFGVLGALVLAVGVTLLVAGRMVDVVGAPDPVVSARESA
+PPDAGALAQELAGAHEGVAVDWDAPAHAGSELDPGLAVDHAPGILLVETVLGQRMGTGTG
+MVLTPEGLALTNYHVVEDSSEVFVVEADTGERHTATVLGRDAEHDVAVLDVHGVTDLPVA
+SVSLDPVRRGDEVAAVGNGRGQGHLTAVRGTVLGTDRSIMAASQGSDEYARLTGLIQTDA
+DVVPGYSGGPVVDDDGQVVGVTVAASDGTGAQEVDGFAIPLGVALGVVDQVLSGEETDTV
+SIGADGALGIMVAADPEAGVVVMQVDADSAAEAIGLVPGDVVLAVDGQAVEGNASRMSRL
+VNDHNVGDRITVTWRTASGEVREAEAVLQEAVVN*
+>NZ_CP083691.1_1223
+MAIAVFGVLGAVVLAVGLTLLAGGRLIAAVGAGSSSSAAAPSGPQVTTRSLDALAASLDH
+AHAGIAVPAADAPPADGSLDPGERVRRAPGVLLVETRLEAMQGTGTGMVLTSDGLALTNY
+HVVEDSTAVSVVVADTGARHAATVLGRDAKNDVAVLQIDGVSGLTTTSVSRDPVRPGEAV
+AAVGNGGGQGYLTSVGGEVLRVDQSILAATEGTDDFERLTGLIQTDADVVPGYSGGPLVD
+GEGQVVGVTVAASEGRTAAQVDGYAIPLSTAFDVVAQVLSGEETDSVSIGADGSLGISVA
+GSRDGVEVLSVDRGSAGEELGLRPGDVITAIDGRTLDGNATAMSRLVNDHEVGDRLSVQW
+RTADGEARQGEAVLQKARHN*
+>NZ_CP097650.1_1449
+MTPPGWPPRARRSPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHIHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGDQVAAVGNGGGQGYLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTADEVDGFAIPLEVAFDVVDQVLSGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRAVGDDASRMSRLV
+NDHNVGDRITVQWRTADGEVREAEAVLQPALVN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001309.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001309.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e2088f3ecc97c56149169e780e97744b344c6d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001309.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1548
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQT
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSPFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGESLSWHQRFLETGTMRQG*
+>NZ_CP033200.1_1271
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQT
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSPFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGESLSWHQRFLETGTMRQG*
+>NZ_CP040019.1_1276
+MSSRIQHAGLRAKVMSAQEAAAFIRPGTTVGMSGFTGSGYPKAVPLALAERISAAHARGE
+DFRIDLHTGASTSSEMDGALAESGGVALRTPFQSDPTMRAKINAGEVEYIDTHLSHLAQT
+VWNGFYGPMHTAVVEVSAIREDGTLVPSSSVGNNKSWLDLADEVILEVNSWQSEELEGLH
+DVYYGTALPPHRQPVMITDPADRIGQPYFECDPAKVVAVVETHGPDRNSAFKPADADSIA
+IAQHLVEFFEHEVAAGRYDERLLPLQSGVGNIANAVMAELVKSRFRGLTAFTEVVQDGML
+DALDSGTLSMASATAFSLSTEAAERFNSTVAQYKDKLILRTQEISNHPELVRRLGVLAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSVAKGGDISCIVPMVSH
+VDHTEHDVHVLVTEQGLADLRGLSPKQRARTIIAKCAHPDYRDQLQDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRHG*
+>NZ_CP083691.1_1184
+MSSRIHHPGLRAKVMSAEEAAAFITPGMTVGMSGFTGSGYPKAVPMALAERIKSAHARGE
+DFRIDLHTGASTSVEMDGALAEADGVRLRTPFNTDPTMRAKINDGSVDYIDTHLSHLAQT
+VWEGFYGPMDAAVIEVSAIREDGTLVPSSSVGNNKSWLQLADKVILEVNSWQSEDLDGIH
+DVYYDTALPPHRKPVPVNHPSDRIGRTEFVVDLDKVVAVVETHGPDRNSPFKPADADSIA
+IAQHLVEFFEHEVKAGRYDEHLLPLQSGVGNVANAVMAELVKSRFHGLTAFTEVVQDGML
+DALDSGTLAMASCTAFSLSTEVAERFNDNVLQYKDKLIIRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRQG*
+>NZ_CP097650.1_1475
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQA
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSAFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYRDPLRDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRHG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001310.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001310.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a22ead10f3848a273443cdcad5584f9c7cbdaaf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001310.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_1549
+MTKHRQPVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA
+EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP
+ALIAAALWAAGIPEREQGGRG*
+>NZ_CP033200.1_1272
+MTKHRQPVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA
+EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP
+ALIAAALWAAGIPEREQGGRG*
+>NZ_CP040019.1_1273
+MTKRRQSVPLSQTAARLGLGAALWAAGIPEREHGGRG*
+>NZ_CP083691.1_1181
+MTKRRQSVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA
+EIGLGAALLALPGQRRRTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP
+ALIAAALWAAGIPEREHGGRG*
+>NZ_CP097650.1_1476
+MTKRRQSAPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA
+EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP
+ALIAAALWAAGIPEREQGGRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001313.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001313.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48a27b3eaff8434ddaac284b45dec41c5bd6b8c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001313.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1552
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTRSAPVTVPTTYVWGTRDAALGPRAAELTAGQVAGEY
+RFVKLDADHWLPEREADAVARAILDRVR*
+>NZ_CP033200.1_1275
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTSSAPVSVPTTYVWGTRDAALGPRAAELTAGQAAGEY
+RFVALDADHWLPEREADAVARAILDRVR*
+>NZ_CP083691.1_1178
+MTGGDALWGRVDAFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDSTSWRHVEPLLHAAGLR
+TLAPDQRGYSPGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATA
+HPERVASLTVLSTPHPAALARALRGSDQLRRSWYIAAFQAPALPERILSRRLGSLLQRGQ
+VPGAEHYARRFSTPQSLRGPVNWYRANPDLVTTTRSAPVSVPTTYVWGTRDAALGPRAAE
+LTAGQVAGEYRFVALDADHWLPEREADAVARAILDRVR*
+>NZ_CP083691.1_1788
+MTIPGFALEHIPLPSGVTLRVATGGEGPAVVLLHGHPRTHATWHRVAPALADAGLRVVCP
+DLRGYGQSSAPEPSDDLHTHSDRTMAGDIALLMTHLGHDHFSVVGHDRGSYVAYRTALDF
+PERVDRMAVLDCVPILEALERADARFAEKWWHWFFFASPHAERVICADPLAWYQPDAQKM
+GQENYQDMVAAISDPQTVRSMIADYRASLHVDRDADARDRARGHQIQCPTLVAWSKHDDM
+EDLYGNPAEVWESWCAHRPESAVIDSGHHMAEDNPEQLTAVLTEFFLPS*
+>NZ_CP097650.1_1479
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTSSAPVSVPTTYVWGTRDAALGPRAAELTAGQAAGEY
+RFVALDADHWLPEREADAVARAILDRVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001316.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001316.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc8f62941c2c4d83736aebf4899fe2d2add4a101
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001316.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1561
+MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTGGRIAAVPVAAVVASPLERC
+AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQTQPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV
+GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGAGAVDERTPRIV
+A*
+>NZ_CP033200.1_1283
+MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTADRIAAVPVAAVVASPLERC
+AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATESLWATVQTQPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV
+GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGTGAVDERTPRIV
+A*
+>NZ_CP040019.1_1266
+MATVLLVRHGRTTANASGLLAGRTPGVSLDEHGREQAARTADRIAAVPVTAVVASPLERC
+AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQSRPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGMHLDMFQRLDV
+GPASVSIVSYGSSRPRVLTVNTDAGDLSWLATKGPSGDAPVGGGAGTDPVADSANGRTPR
+IDA*
+>NZ_CP083691.1_1170
+MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTADRVAAVPVAAVVASPLERC
+AQTARALLDRQSGAVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQTQPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV
+GPASVSIVSYGPSRPRVWATNTDAGDLSWLSSLGPSDDAPVGGGAGTGPGAVDEQTPRIV
+T*
+>NZ_CP097650.1_1487
+MATVLLVRHGRTTANASGLLAGRTPGVSLDDHGREQAARTADRIATLPVAAVVASPLERC
+AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATESLWATVQTQPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV
+GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGTGAVDEQTPRIV
+T*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001320.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..128be75d2fbb7bb57c6e318b1629591e04fb7cb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001320.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1577
+MARPIDPFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASIDVDVEER
+TLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVLTLTIPVA
+EQAKPRKISVTHGGAAPVAGQTVEGETAETTGE*
+>NZ_CP033200.1_1294
+MARPIDPFREMERLMTGFARTSGAASMPMNLYREGDVFVAEVELPGVDPSSIDVDVEERT
+LTVRAERKEAPAGEDRRWLTKERPAGTFARQLNLGQGLALDKIEADYSDGVLLLTIPVAE
+QAKPRKIQVKHTGSAAQVEGEAVEGEAVEGSAAEASGE*
+>NZ_CP040019.1_1249
+MARPIDPFREMERPFREMERLVNGLTRTSGTASMPMNLFREGDRFVAEVELPGVDPASID
+VDVEERTLTVRAERKESPAGEDRRWLTRERSAGTFARQLTLGEGLALDRIEADYEDGVLT
+LTIPVAEQAKPRKISVKHSGAGAGAGQTVPGETAEVEERSAEQEAAQNGGAPQA*
+>NZ_CP083691.1_1158
+MARPIDPFREMERPFREMERLVNGLTTRATGTASMPMNLYREGDAFVAEVELPGVDPASI
+DVDVEERTLTIRAERKEAAASEGRQWLTRERSSGTFARQLTLGQGLALDRIEADYRDGVL
+VLSIPVAEQAKPRKIQVKHSAADQVEGQEVAGQESVQDSAAVEAPQQPSGE*
+>NZ_CP097650.1_1506
+MARPIDPFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASIDVDVEER
+TLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVLTLTIPVA
+EQAKPRKISVTHGGTAPVAGQTVEGETAETTGE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001321.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001321.fa
new file mode 100644
index 0000000000000000000000000000000000000000..001de5bec9c38cbd2639858f56c20178f00d9453
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001321.fa
@@ -0,0 +1,23 @@
+>NZ_CP042169.1_1579
+MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGDTVDEVLFVPYGETAEAAFRAALGHLEAPQTT
+DDEGDTGR*
+>NZ_CP033200.1_1295
+MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGGTVEEVLFVPYGDTAEAAFRTALDRVERG*
+>NZ_CP040019.1_1246
+MELLIAPGDITATTADVVVNAANSTLLGGGGVDGAIHRRGGPEILAACRRLRETELPDGL
+PVGQAVATTAGRLPARWVVHTVGPVWAKTIDKSATLASCYRESLRVAAELGARSVAFPAI
+SAGVYGWPMDDAARIAVTTCREVAAQGAGSVERVLFVPFGERAEAAFRAALDAPDETGAP
+AAS*
+>NZ_CP083691.1_1153
+MKLSIAPGDITATHADAIVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPDGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLRVARELGARTVAFPAI
+SAGVYGWPMDDAARIAVETSHAMADEVGDVVEEVLFVPFGDRAEAAFRAALEHLT*
+>NZ_CP097650.1_1508
+MQLTIAPGDITATRADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAETIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGGTVDEVLFVPYGETAEAAFRAALGHLEDPQAT
+DDEGDTGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001325.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001325.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f8a44c8015db4bc181a66a7ed6e15ff65a84ef3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001325.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1583
+MEGMSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRA
+VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSP
+AVVEEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKRILLIGHDGHEEVEGTFGEAPEHT
+TVINDVAEARTVQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATS
+NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFANQVDESWFEGVA
+TVGLSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAEMKRVGDDGR
+ALGGRRRAAEA*
+>NZ_CP033200.1_1299
+MEGMSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRA
+VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSP
+AVVEEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTFGEAPEHT
+TVINDVAEAQTIQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATS
+NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFTNQVDESWFEGVA
+TVGLSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAELKRVGDESR
+SLGGRRRDAEA*
+>NZ_CP040019.1_1241
+MGGMSAPSVSARPSAVGLGMPQVPRVRRTREDVEAAAPVSGDKRVLLAAPRGYCAGVDRA
+VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVEELDEIPEGALTVFSAHGVSP
+AVVQDAERRSLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTYGEAPEHT
+TVINDVAEARAVQVADPDNLIWLSQTTLSVDETLEIVAVLRERFPNLQDPPSDDICYATS
+NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFASQVDESWFEGVS
+TVGLSSGASVPEVLIQDVLALLAEYGYGQVDEVVTAEEDIMFSLPKELRAELKRVGDDSR
+GLGGRRQTEG*
+>NZ_CP083691.1_1149
+MDGMSVPTASAPSTVGLGMPQVPRTRRSREEVEAAAPVAGDKRVLLAAPRGYCAGVDRAV
+VAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGAVFVQELDEVPAGALTVFSAHGVSPA
+VVAEAAERDLQTIDATCPLVTKVHREAVRFARQDKRILLIGHTGHEEVEGTYGEAPEHTT
+VINDVEEARTVQVDDPDNLIWLSQTTLSVDETLEIVAVLRERFPNLQDPPSDDICYATSN
+RQAAIKRISPQCDLVIIVGSANSSNSVRLKEVALEYGAARAERVDFASQVDESWFEGVAT
+VGLSSGASVPEVLVQDVLALLADYGYGQVEEVVTAEEDIIFSLPKELRAQLKQAGDEERS
+LGGRRRPAE*
+>NZ_CP097650.1_1512
+MSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRAVVA
+VEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSPAVV
+EEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTFGEAPEHTTVI
+NDVAEAQTIQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATSNRQ
+AAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFANQVDESWFEGVATVG
+LSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAEMKRVGDDGRALG
+GRRRDAEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001328.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001328.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e79d5bd0f8321284ef094c6797cd4eeabc7447a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001328.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1586
+MSEQGMEQTQDAGRPSGVEGFTSADVSDVARMSYEQARAELVETVGRLEAGGAGLEESLA
+LWERGEALADRCQAWLDGARARLDQVRGEAAPDAD*
+>NZ_CP033200.1_1302
+MSEQGMEQTQDPGRPSGVEGFTSADVSDVARMSYEQARAELMETVGRLEAGGAGLEESLA
+LWERGEALADRCQAWLDGARARLDQVRGEAAPDVD*
+>NZ_CP040019.1_1238
+MSEQQQEQTGAPVEGFTSADTSDVAGMSYEQARAELVETVTRLEAGGGRLEESLALWERG
+EALAARCQAWLDGARARLDEVRGAADSPTA*
+>NZ_CP083691.1_1146
+MSEQEQQGTAVGGFTSADTSDVARMSYEQARAELVEVVGQLEAGGAGLEESLALWERGEA
+LADRCQAWLDGARARLDQVRGEAAPDAD*
+>NZ_CP097650.1_1515
+MSEQGMEQTQDAGRPSGVEGFTSADVSDVARMSYEQARAELVETVGRLEAGGAGLEESLA
+LWERGEALADRCQAWLDGARARLDQVRGEAAPDAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001334.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001334.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c2f82bd40f73c53c5fba1e4ae4fe55591f5ed1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001334.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1593
+MSIDRAAARQAVRASGERWLRTRADALHLQRGRRLARVLDLDVMTGRAGDARVRSRTLVL
+ARDPRHPDVPAAACPPVPGERGILEDGTLWWWAPADPVLPGLTLTADPDALAALLGTAPG
+RARLTWRGYRPRDRAVLAVEATGDDGVAARTFLKVLPPARAARVARRQAAAGAAGVPVPA
+VLATPEHGVLPLASVPGLPWRALLAGPEAAGLDPARVAALLDRLPPVPEEPPGPAGPTAG
+AAGCADTDDGGPAILLEHATWAAVVLDPEAQDEVAARADRLRAALAAGDPGPRVPVHGDL
+HPGNLHVDAAGERITGVLDADDLGMGHRVDDWAVLIAHLEAGAVDLGAGGAALRAVAARF
+RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRSARRAAADAALARVGL*
+>NZ_CP033200.1_1309
+MSIDRAAARQAVRASGERWLRTRADALHLQRGRRLARVLDLDVMTGRAGDARVRSRTLVL
+ARDPRHPDVPAAACPPVPGERGFLEDGTLWWWAPADPVLPGLTLTADPDALAALLGTAPG
+RARLTWRGYRPRDRAVLAVEATGDDGVVGRTFLKVLPPARAARVARRMAAAGAAGVPVPA
+VRAAPEHGVLPLASVPGLPWRALLAGPEAAALDPARVAALLDRLPPVPEEPPGPAGPPAV
+AAGGADADDGGPAVLLEHATWAAVVLDPEAQDEAAARADRIRAALAAGDPGPRVPVHGDL
+HPGNLHVDAAGERITGVLDADDLGMGHRVDDWAVLIAHLEAGAVDLGAGGAALRAVAARF
+RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRAARRAAADAALARVGL*
+>NZ_CP040019.1_1229
+MSIGRASAPLAVRASGLRWLRTRADALHLQRGRRLARVLDVDVMEGRAGDARVRTRTLVL
+ARDPRTGPDAAPPGSARTSERGVLEDGTLWWWAAADPALPGLALTENDAGLAALLGTAPG
+RVRLTWRGYRPRERAVIALDAADAGLAGSRAYLKVLAPAAAEAVAARLSAARAAGVPVPD
+LLAAPERGTLLLGNVPGLPWGALLGDARADALDPARVAEVLDRMPAPPGEAGPAPDAAAA
+LLEHAAWAAVVLDPERQAESAARADRLRAALAAGDPGPPVPVHGDLHPGNLHVDASGGRV
+TGLVDCDGLGLGHRVDDWATLLAHLEAAAADLGPGGGAVRAVAERVRAHARTETDEVALA
+ARAAVVLAALGADPSVPRAARTARRAAADAALARVSR*
+>NZ_CP083691.1_1139
+MVLLEGPPGAGVARERVLVLRGPVEPAVAVPGPPGPPVPASGPAPRRRGRGRLPDGTRWW
+LLPHDPALPGLDLALDHERLDAWLPGLGRAGEPAWVAYRPGERAVLRVPLDAVPARPDEP
+GSSLHLKVLPPARLHGMHGRLLAARAAGLPVPPPLAPPDLGVLALGTLPGEPWRARLGAD
+APQPAPAAVAALLDALPDALAAHDDGPSRTPAWSALLAHAVRAGTLLDPGAAEELRERAR
+RLEESLAAADPGPRVPVHGDLHPDNLLLAPGTDRIVGVLDPDSLGPGHRVDDWAVLVGHL
+AVAAADAAVPGPSHDPERARRTAALAAEFTGHACGVVDEEALRARADVTALALAAAPDLP
+AAVRAARRSAR*
+>NZ_CP097650.1_1523
+MSIDRAAARQAVRASGERWLRTRADALHLQRGRWLARVLDLDVMTGRAGDARVRSRTLVL
+ARDPRHPAAPGAACPPVPGERGILEDGTLWWWAPADPVLPGLTLTADPDALVALLGTAPG
+RARLTWRGYRPRDRAVLAVEATGDDGVVARTFLKVLPPSRAARVARRMAAAGAAGVPVPA
+VRAAPEHGVLPLASVPGLPWRALLAGSEAAALDPARVAALLDRLPPVPEEPPGPAGPTAG
+VAADADADDGGPAVLLEHATWAAVVLDPEAQDEAAARADRLRAALAAGDPGPRVPVHGDL
+HPGNLHVDAAGERITGVLDADDLGTGHRVDDWAVLIAHLEAGAADLGAGGAALRAVAARF
+RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRSARRAAADAALARVGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001339.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001339.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a16ec1ad66ff58e8460368981bcb13f92f62961
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001339.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1598
+MPADGAPRRRGPRRADAPGTGPASADGREPRLPGMPRLIGQAGTSPATAPTGDVAGVESG
+PAEAERDRWLREQRPPHWG*
+>NZ_CP033200.1_1314
+MSADGAPRRRGPRRADAPGTGPAAADGREPRLPGMPRLAGQAGTSPVTAPTGDVAGVESG
+AAEAERDRWLREQRPPHWG*
+>NZ_CP040019.1_1224
+MGAEVPDPAPRRRGPRRADAPGTGPASADAPEPRLPGVGAGTDGARGAEGVRGAGGVRGA
+VGVRGAAGEPTADERDRWLLEQRPPHWG*
+>NZ_CP083691.1_1134
+MRTTPTASPEPGRRRGHRRADAAGTGPASADGPEPTLPEPTLPGPALPGAQTAGDATPSR
+PAVSRGRAVTSAAGADRPQPADELGRWLLEQRPPHWG*
+>NZ_CP097650.1_1528
+MSADGAPRRRGPRRADAPGIGPAAADGREPRLPGMPRLAGTSPATAPTGDAAGVESGPAE
+AERDRWLREQRPPHWG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001341.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001341.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc659912e47c34c180765f9956fc0cad943502cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001341.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1600
+MTQNAPHPDTPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+KPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAQTGTREYG
+STRLDSVDADSVLFAGQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIY
+GVQWHPEVGHSSHGQRVLEQFLHVGAGLGADWTVSNVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE*
+>NZ_CP033200.1_1316
+MTQNAPHPDTPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+KPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAQTGTREYG
+STRLDSVDADSVLFADQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIF
+GVQWHPEVGHSSHGQRVLEQFLHVGAGLGADWTASGVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVISEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE*
+>NZ_CP040019.1_1222
+MTENAPHSDAPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+RPAALILSGGPSSVYEPGAPTLDPALLEAGVPVLGLCYGFQSIAHALGGTVAKTGTREYG
+STRLDSVDADSVLFAGQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDAERRIY
+GVQWHPEVGHSSHGQQVLEHFLHQGAGLGSDWTASNVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMRQGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPEATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRSADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPIVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE*
+>NZ_CP083691.1_1132
+MTQNEPTRDQPAPLHDVLPTVLVMDFGAQYAQLIARRVREANVYSEVVPSSTPAQEILDR
+RPAALILSGGPSSVYEAGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVARTGTREYG
+STRLESADGGSVLLAGQDAAQVVWMSHGDAVTEAPEGFAVTAVTAGAPVAAFEDRERRIF
+GVQWHPEVGHSERGQEILANFLTEGAGLSQDWTAENVIEEQVARIREQIGDARAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMRQGESDEIERAFGEAHGGAKLVMVDAREDFL
+AALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESAHDPNAPEVRFLVQGTLYPDVVESG
+GGDGTANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRQADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVTSEDAMTADWARIPSEVLSRISNRITNEVDGINRVVLDVTSKPPGTIEWE*
+>NZ_CP097650.1_1530
+MTQNAPHPDTPTPLSDVMPTVLVLDYGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+EPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAKTGTREYG
+STRLDSVDADSVLFADQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIY
+GVQWHPEVGHSSRGQRVLEQFLHVGAGLGADWTASGVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGINRVVLDVTSKPPGTIEWE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001342.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001342.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a71edb0aee983095876af1a57e95ad9faf27209
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001342.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_1601
+MSTQHPGPEPVDPASLPDPEDITEADLPEPPPRPGREQRRFAGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFVVEKRMTRVVRDELHRFPDAAR
+RY*
+>NZ_CP033200.1_1317
+MSTQHPGPQPVDPASLPDPEDITEADLPEPPPRPGREQRRFSGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFMVEKRMTRVVRDELHRFPDAAR
+RY*
+>NZ_CP040019.1_1221
+MSHTEPVDPAALPDPEDITEADLPEAPPRPGRERRRFAGTQQQIRSATRFYVVCSWITGV
+MLLLLVAEMVFKYAWGQELFAGGTTVDGEQNILGLHPEDSVTGGVNLSLFILIAHGWMYV
+VYLLACFRLWSLMRWQPMRLLAMAGGGVVPFLSFVVEKKVTKVVRDDVHRFPDAARRY*
+>NZ_CP083691.1_1131
+MSQPHHDAGREAARAGEAPVDPATLPDPEDITEADLPAPPPRPGRAVRRFAGTRQQIVSA
+DRIYKVCAYITGVMLLLLVAEMVFKYGLHQELFAGGTTVDGEPHGFGLAPEKSVTGGVNL
+SLAILIAHGWMYVVYLLACFRLWSLMRWAPGRLLAMAGGGVVPFLSFVVERKVSGQVREE
+LAQFPDAARRY*
+>NZ_CP097650.1_1531
+MSTQHPGPQPVDPASLPDPEDITEADLPEPPPRPGREQRRFAGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFVVEKRMTRVVRDELHRFPDAAR
+RY*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001343.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001343.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0db6ed92988e9afe5ddc7d4b61d9de7ee5fdd2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001343.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1602
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTEHAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLNGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREATAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AYVAAFEMVDAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAVAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEQSR*
+>NZ_CP033200.1_1318
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTENAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLDGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREAAAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AFVAAFEMADAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAFAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEHRR*
+>NZ_CP040019.1_1220
+MLRTALKPVWLATLVLALVAAGLFVALSKWQFETAETNAPPPRTQTEQPVPLTDHVRPYE
+PLLARDADQVVTVPGEFLPDTDVLVGPRLLRGDEGFWTVSAFRVAGAPDGEVIPVVRGWS
+AGADVVDPAPQGDVTVTGRLLPPDGPLPRTAAEADTADRLLYASLAPGQLVNVWDEPSYA
+AFVAAFEVADAAGAEVGAGASEGGLEPVWVAPQPEETEVIWLNVFYAVEWILFAGFALFL
+WWRFVRDDHLRDERERELDEEWAAQWRAEELARRREEARLAKERAYAAQAAARPSTDPEE
+NRP*
+>NZ_CP083691.1_1130
+MLRTALKPKWLATLVLALVAATAFVLLSRWQFASSETAAPPPRTQTENAVPLTEHVRPGE
+PLLASQADQVVSARGEFVPGTDALVGPRLSDGREGWWTVTAFRVAGAPDGETVPVVRGWS
+EAADVVDPAPTGEVTVTGRLLPPDGPVSPADAGEDTAGRPAFSTLSPGQLVNAWDVPAYA
+AYVAAFGVTDAAGADVSAGARDGGLQPVWVPPQPEESQVVWLNVFYGVEWLLFAGFALFL
+WWRFVRDDHLRDEQEAELDAQWAARWRAEELERRRERARREKEAAARAYAAWQAGETAPD
+AAHQEPQDGPAGPRKEGQA*
+>NZ_CP097650.1_1532
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTENAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLNGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREAAAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AFVAAFEMVDAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAFAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEQSR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001345.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001345.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e83338a4fddeffb4fb64351ada8853ebffde02c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001345.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1604
+MARTRVAGLTPGHRIAETPVPKGVFVTTTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN
+ATDVIPADADPGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPREEWATRTVDTAMTRMPLVTAQEGVSRAETIRLFSQNRVEKLPLVDDAGRLTGLIT
+IKDFDKAEQYPDAAKDDEGRLRVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV
+FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPVA
+SVVHQLVGGLRQTMFYTGASTVTDLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR*
+>NZ_CP033200.1_1320
+MARTRVAGLTPGHRIAETPVPKGAFVTNTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN
+ATDVIPADADTGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPREEWATRTVDTAMTRMPLVTAQEGISRAETIRLFSQNRVEKLPLVDDAGRLTGLIT
+IKDFDKAEQYPDAAKDDEGRLLVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV
+FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPIA
+SVVHQLVGGLRQTMFYTGASTVADLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR*
+>NZ_CP040019.1_1218
+MARTRVAGLTPGHRIAETPVPKGAFVTTTSTGPSSEPVHSSADPFGFFGLTYDDVLLLPS
+ATDVIPAEADTSTQLTRNIRLNIPVVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPKATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPHEEWETRTVDTAMTRMPLITAREGISREETIRLFSQNRVEKLPLVDEAGRLTGLIT
+IKDFDKAEKYPDAAKDDEGRLRVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGAESVMLGSLLAGTAESPGDLV
+FYQGKQFKAYRGMGSLGAMQTRNGKRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPIA
+SVVHQLVGGLRQTMFYTGASTVDELKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR*
+>NZ_CP083691.1_1128
+MSTSTGPSSDPVYASEDPFGFFGLTYDDVLLLPNATDVIPADADTSTQLTRNIRLNIPVV
+SAAMDTVTEAPLAIAIARQGGMGIIHRNLSIEDQAKHVDTVKRSESGMISDPVTIGPKAT
+LAELDELCAQYRVSGLPVVAEDMTLLGIITNRDTRFIPHEEWDTRTVDTAMTRMPLITAQ
+DGISREEVLHLFSQNRVEKLPLVDDAGRLTGLITIKDFDKAEKYPDAAKDDEGRLRVGGA
+VGFFGDGWERAMTLVEAGVDALVVDTANGHTHGVLDMIARLKKEKAAAHVDVIGGQAATY
+AGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGVPQITAIYEAAKATRPAGVPLIADGGL
+QHSGDIGKALVAGADSVMLGSLLAGTAESPGDLVFYQGKQFKAYRGMGSLGAMQTRNGTR
+SFSKDRYFQADVPDEDKLIPEGIEGQVPYRGPIASVVHQLVGGLRQTMFYTGAPTIVDLK
+ENGRFVRITTAGLKESHPHDIMMTVEAPNYRSK*
+>NZ_CP097650.1_1534
+MARTRVAGLTPGHRIAETPVPKGAFVTNTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN
+ATDVIPADADTGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPREEWATRTVDTAMTRMPLVTAQEGISRAETIRLFSQNRVEKLPLVDDAGRLTGLIT
+IKDFDKAEQYPDAAKDDEGRLLVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV
+FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPVA
+SVVHQLVGGLRQTMFYTGASTVADLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001346.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001346.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9bb0a6b335741a4f6281ff99dfecb3b2fe820ed0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001346.fa
@@ -0,0 +1,46 @@
+>NZ_CP042169.1_1605
+MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTAEHPTWLGETLAT
+VGSIYISLLKAAVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG
+VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL
+QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY
+GWSTMGTLAKFVVAVYVGLALVMLVVYPLLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG
+TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIEMSLSQY
+ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ
+ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAELVGTPEPRA*
+>NZ_CP033200.1_1321
+MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTSEHPTWLGETLAT
+VGSIYISLLKATVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG
+VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL
+QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY
+GWSTMGTLAKFVVAIYVGLALVMLVVYPVLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG
+TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIDMSLSQY
+ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ
+ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAQLVGTSEPRA*
+>NZ_CP040019.1_1217
+MSTTQSSPEPAPRRRLPAWTGNFGWQIVAALVLGLVLGLVARSMGHTPDSPTWLGETLAT
+IGSVYISILKATVIPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG
+VVMQPGVGTGQSAPESYQARDVGWLDFLTSMVPANFLGLTVKSTVGEDGAVASSPTFNVL
+QILVIAIVVGIAALKVGEKAAPFLTFSRSVLAVIQKLLWWIIRLAPIGTVGLLGNAVASY
+GWSTMGTLAKFVVAIYVGLAIVMFVVYPVLARLHGLCVKQFFTGVWPAVQLGFVSRSSLG
+TLPVTQRVAERNFGVPTGYAAFAVPLGSTTKMDGCAAIYPAIAAVFVAQFYGIEMSLGQY
+ALVVLVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGLALLLAVDPIVDMGRTATNVAGQ
+ALVPALVAKQEGILDQARYDAERVDIMGEDEEEIVEARAQDRDDDQDQMVGAAARPARD*
+>NZ_CP083691.1_1127
+MTSHPSSPASGASTPARRRRLPAWTGNFGWQIAAALVLGLLLGLAARAMGHTPDSPTWLG
+ETLALIGSIYVQLLKATVVPLVFFAVVASVANLAQVTNAARLAAKTLLWFAITSFIAVLI
+GLAVGVVMQPGVGTGQSAPEGYQARTVTWLDFLTSMVPVNMLGLTVKTTAGDDGALTSTP
+SFQVLQILVIAIAVGVAALKVGEKAEPFLAFSRSVLAVIQKVLWWIIRLAPLGTVGLLGN
+AVASYGWSTMGTLVKFVVAVYVGLALVMLVVYPLLARVHGLSVKQFFTGVWPAFQMGFVS
+RSSLGTLPVTQRVAERSFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFVAQFYGIDM
+TLGQYALVVLVSVLGSAATAGTTGATVMLTLTLSTTGLPLEGMALLLAVDPIVDMGRTAV
+NVSGQALIPALVAQQEGILDRTRYDAERGDVMADEDETIVEARHDDARGASRADLTEAGS
+AR*
+>NZ_CP097650.1_1535
+MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTSEHPTWLGETLAT
+VGSIYISLLKATVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG
+VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL
+QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY
+GWSTMGTLAKFVVAIYVGLALVMLVVYPVLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG
+TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIDMSLSQY
+ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ
+ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAQLVGTPEPRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001349.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001349.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f4736d9b5094310a4b18438d96fa701bc968105
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001349.fa
@@ -0,0 +1,39 @@
+>NZ_CP042169.1_1611
+MAEPLATAPGRLPAPLGGATAAGPVDADAPRRSGAFVTAAERRRYAVVVAVLAAVAVLST
+AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVTFHTVTGNRIITPSIMG
+FEALYTAVSTVAVYVLGAAGVAVLTGVGPFLAQAALMVALTTALYSWLLSRPYGSVHLML
+LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW
+LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY
+SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG
+RL*
+>NZ_CP033200.1_1327
+MAEPLATAPGRIPAPPGGATAAGPVEADAPRRSGAFVTAADRRRYAVVVAVLAAVAVLST
+AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVTFHTVTGNRIITPSIMG
+FEALYTAVSTVAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML
+LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW
+LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY
+SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG
+RL*
+>NZ_CP040019.1_1212
+MVAVLAVVAVLSTAGILLWGNEAEPGSRAFWMIAGMRLDSLGVIAIVALCHSFATVSFHT
+VTGNRIITPSIMGFEALYTAVQTGAVYVLGAAGIGVVTGTGPFLAQAALMVVLATVLYSW
+LLSRPYGSIHLMLLVGVVLGGGLAALSTFMQRLLDPNSFDVLSARLFGNISNARSEYVAI
+AAPIVVVVCLVLWLRSRRMNVLALGADSATNLGLHHRRELMVTLLLVSVLMAMTTALVGP
+MTFLGFLVATLAYSLVDTHDHRMVLPVAALGAYAVLTLAYFVLRHVFYAGGAVTVIIELV
+GGITFLIVVMRKGRL*
+>NZ_CP083691.1_1122
+MAEPLATAPGRIPAPSGGATAAGPVDADAPRRSGAFVTAADRRRYALVVAVLAAVAVLST
+AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVSFHTVTGNRIITPSIMG
+FEALYTAVSTAAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML
+LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW
+LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY
+SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLIVVMRKG
+RL*
+>NZ_CP097650.1_1541
+MVEPLATAPGRIPAPPGGATAAGPVDADAPRRSGAFVTAADRRRYAVVVAVLAVVAVLST
+AGVLLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVSFHTVTGNRIITPSIMG
+FEALYTAVSTAAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML
+LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW
+LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY
+SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG
+RL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001353.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001353.fa
new file mode 100644
index 0000000000000000000000000000000000000000..357aee513ee47b4ade15629b714f3f1abc4a928b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001353.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1615
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFADAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDADDAVAPLRAVVLDAAARTRASLDGRAG*
+>NZ_CP033200.1_1331
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRTLHATEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAARGISLFCQGTHPFADAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDTDDAVAPLRAVVLDAAARTRASLDGRTG*
+>NZ_CP040019.1_1208
+MNLPFADSTQSTLGIEWEVALVDAATGDLRSEAPAILHELHKEAGLAEGEDHPHVTGELL
+QNTVELVTGVHEAVPTAVAELGTIAARVARAAADRGLALYCQGTHPFGEAMTQPITPKER
+YGRMVDLTQYWGRQMLIFGVHVHVGLDDPAKAMPAVNRLISRFPHLLALSASSPFWVGAD
+TGYQSQRTQLFQQLPTAGLPFQFETWAEFEACVQQMTDVGMVEDVTECRWDVRAVPRLGT
+VEMRACDGMATLEEIAAVAAYTQCLVHELSADVERGRHMEILPPWYTQENKWRASRYGMD
+ATVIVDAAGTQVPLAEHLGADLERLAPIAEELGCAAELAHARVLMEHSPADRQRAVEAEA
+LAGPPAEGESAHDAAAPLRAVVLDAAARTRESLERVGG*
+>NZ_CP083691.1_1118
+MSLPFADSAQSTLGIEWELALVDPLTGDLRSEAPGILEELRAEAGLDADADHPHVTGELL
+QNTVELVTGVHGSVPDAVADLGGIAARVQRAAADRGLALFCQGTHPFGEAMTQPITPKAR
+YGRMVDLTQYWGRQMLIFGVHVHIGLDDRAKAMPAVNRLISRLPHLLALSASSPFWVGAD
+TGYQSQRTQLFQQLPTAGLPFQFETWEGFEHCVEQMTGVGMVEDVTECRWDVRAVPRLGT
+VEMRVCDGMATLEEIGAVAAYAQCLVHELSAQVEDDEPVAILPPWYTQENKWRAARYGLE
+ATVITDDAGTQVPLAEHLAADLERLAPVAEELGCAAELAHARVLMEHSPADRQRRVAAEA
+AAGPPRTGEDPADPVAPLRAVVRDAADRTRESLRAFQG*
+>NZ_CP097650.1_1545
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFAEAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEDFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDADDAVAPLRAVVLDAAARTRTSLDGRTG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001355.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001355.fa
new file mode 100644
index 0000000000000000000000000000000000000000..157ef047ddcd19c410c4a36c0d8f28c004acc056
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001355.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1617
+MRIVVLGATGNVGTAVLHRLQAADEVSSIVGVSRRGPDRAGAPYDGVEWHRLDVAEPTAA
+GRLHDIVAGADAVVDLVWVIRPNRDRDHLRAVNVAGNERVFRAVAEAGVPHLVYASSVGA
+YGPGPKGRAVAESHPTTGVPTSHYAAQKAEVESILDRVQAEHPEMLVTRLRPGLIFQSAA
+GPEIKDYFLGDLVPARLVARLRAPVLPFPRGLRFQALTAQDVADAYWRVIAHRAGGAFNV
+AAEPVLDAHTMGTVLGARRILELPVGLFRAAAALTYRARLQPTDPGWVDMAAAVPIMDTT
+ALRAATGWSETTDAREAVRLVLDHLDGAEGLGNAGHRSHSPTE*
+>NZ_CP033200.1_1333
+MRIVVLGATGNVGTAVLHRLQAAAEVSSIVGVSRRGPDRAGAPYDGVEWHRLDVAEPTAA
+GRLREIVAGADAVVDLVWVIRPNRDRDHLRAVNVAGNERVFRAVAEAGVPHLVYASSVGA
+YGPGPKGRAVPESHPTTGVPTSHYAAQKAEVESILDRVQAEHPELLVTRLRPGLIFQSAA
+GPEIKDYFLGDLVPARLVARLRTPVLPFPRGLRFQALTAQDVADAYWRVIVHRAGGAFNV
+AADPVLDAHTMGTVLGARRILELPVGLFRAAAALSYRARLQPTDPGWVDMAAAVPIMDTT
+ALRAATGWSETTDAREAVRLVLDHLDGAEGLGNAGHRSHSPTE*
+>NZ_CP040019.1_1206
+MRIVVLGATGNVGTALLERLHAADEVTSIVGVSRRGPDRAGAPYDGVEWHRLDVAEPTAA
+GRLSEIVAGADAVVDLVWVIRPNRDRDHLRAVNVAGNERVFRAVAEARVPHLVYASSVGA
+YGPGPKGRAVPESHPATGVPTSHYAAQKAEVESILDRVQAEHPEMLVTRLRPGLIFQAGA
+GPEIKDYFLGDLVPARLVARLRAPVLPFPRGLRFQALTAQDMADAYWRVIAHRAGGAFNV
+AAEPVLDAHTMGTVLGARRILELPVGLFRAAASLTYRARLQPTDPGWVDMAAAVPIMDTT
+ALRAATGWSETTDAREAVRLVLDHLDGAEGLGNAGHRSHSPTE*
+>NZ_CP083691.1_1116
+MRIVVLGATGNVGTALLERLHRAPEATELVGVSRRGPDRAGAPYDGVEWHRMDIADAASA
+PRLTEVLRGADAVVDLVWVIRPNRDRAHLRAVNVDGNERVFRAAAAAGVPHLVYASSVGA
+YGPGPKDVRVDESHPTTGVPTSHYAAQKAEVETILDRVAAEHPRMLVSRLRPGLIFQSGA
+GPEIKDYFLGDLVPARLAARLRTPVLPFPTGLRFQALTAQDVAEAYWQVVAHRAGGAFNV
+AAEPVLDAHTMGTVLGARRILELPVAVFRAAAAVSYRARLQPTDPGWVDMAAAVPVMDTS
+ALRRATDWRPRTDARDAVRLVLDHLDGREGLGNAGHRSHSPLE*
+>NZ_CP097650.1_1547
+MRIVVLGATGNVGTAVLHRLQAADEVSSIVGVSRRGPDRAGAPYDGVEWHRLDVAEPTAA
+GRLREIVAGADAVVDLVWVIRPNRDRDHLRAVNVVGNERVFRAVAEAGVPHLVYASSVGA
+YGPGPKGRAVAESHPTTGVPTSHYAAQKAEVESILDRVQAEHPELLVTRLRPGLIFQSAA
+GPEIKDYFLGDLVPARLVARLRTPVLPFPRGLRFQALTAQDVADAYWRVIAHRAGGAFNV
+AADPVLDAHTMGTVLGARRILELPVGLFRAAAALSYRARLQPTDPGWVDMAAAVPIMDTT
+ALRAATGWSETTDAREAVRLVLDHLDGAEGLGNAGHRSHSPTE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001359.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001359.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65f4045b8bac040fe77a8397512783bae236d40e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001359.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1622
+MSPAEPDPAGDGRPAEDAHGLPPGYLLRPMTVWDIPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDVAAPGSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASSLMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKVL*
+>NZ_CP033200.1_1338
+MSPAEPAPTDDGRPAEDEHGLPPGYLLRPMTVWDIPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHDRPPTRDYRVVVRDVPAPGSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASSLMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKAL*
+>NZ_CP040019.1_1185
+MSPVEPAPGGDERPAEDEHGLPPGYLLRPMTVWDIPEVLAQEATLFPLDAWPARFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDVPAPVAPDEDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASALMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKAL*
+>NZ_CP083691.1_1112
+MSLPDATDPGDDAAPAHGLPAGFLLRPMTVWDVPEVLEHEETLFPLDAWPGHFYAEELAQ
+AGPAGALDAHGRPTTRDYRVVVRQDTGEIVGYGGIMAVGDTADVQTIGTAAAVQGRGIGA
+AQLRWMVAAARERGAESLLLEVRESNAAARRLYARHGFEPIAVRRGYYPGGEDAVVMRRA
+L*
+>NZ_CP097650.1_1552
+MSPAEPAPAGDGRPAEDGHGLPPGYLLRPMTVWDVPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDAAAPSSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGAGFLMLEVRASNAVARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKTL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001360.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001360.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1b07fb177b3498a0fd5895e8ad2bc77e412658b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001360.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1623
+MALLLAIDSSAAASVAVLRDGEELARWATDDTHAHAEVLAPAVQTVLGEAGVTGTALDAL
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHEAGVDAFRHGIEEFVVATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWESATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA*
+>NZ_CP033200.1_1339
+MALLLAIDSSAAASVAVLRDGEELAHWATDDTHAHAEVLAPAVQTVLGEAGVTGTALDAL
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHAAGVDAFRHGIEEFVVATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWETATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA*
+>NZ_CP040019.1_1184
+MALLLALDSSAAASVAVLRDGEALARWATEDTHAHAEVLAPAVRAVLAEAGVAGAGLDAV
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVRGVRSLDALAHDAAVDAFRHGAEEFVVATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPAYGAGAGLYPEALRAVPGWETATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA*
+>NZ_CP083691.1_1111
+MPLLLALDSSSAASVALLRDGEPLAAWSTADTTSHAEVLAPAVRQVLAEAGVAGGDLDGI
+AAGVGPGPFTGLRAGLATAEALGFAWDVPVHGIRSLDALAHRAGTDAFAHAVEEFVVVTD
+ARRREVYWAHYAQVGGQPTLLHGPFVTPAAEVTPLPAYGAGAGLYPEALHAVDGWEGAVP
+DAVSLGRVDELALRRGRGVLPPTPLYLRESDATVPAPRTPARPAGA*
+>NZ_CP097650.1_1553
+MALLIAIDSSAAASVAVLQDGEELARWATDDTHAHAEVLAPAVQAVLGEAGVTGTALDAL
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHEAGVDAFRHGIEEFVIATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWETATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001365.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001365.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61fe573df3c55c958a7687b222436979b6fc34cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001365.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1628
+MNERVDRGRVRRGLPRWARALCATVATLAALALAFGAGWATHAVTDPHPDDAPRVDALLV
+LYSQPRVYDAAIELAASGLTDRLFVSAYLGPDGHEKLCGGPEERDPRLAGVTVECFAPDP
+VTTQGEVIHAGERMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR
+LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA
+GAA*
+>NZ_CP033200.1_1344
+MNERVDRGRVRRGLPRWARALCATVATLAALALAFGAGWATHAVTDPHPDDAPRVDALLV
+LYSQPRVYDAAIELAASGLTDRLFVSAYLGPDGHEKLCGGPEERDPRLAGVTVECFAPDP
+VTTQGEVIHAGDRMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR
+LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA
+GAT*
+>NZ_CP040019.1_1179
+MSEGSDRARARRGARGVPRGVRALLSAAAGTATLALAFGVGWAAHAVTSPRPDDPERVDA
+LLVLYSQPRVYDAAIELAADGVADRLFVSAHLGPDGHERLCGPEERRDPRLAGVSVECFA
+PDPLTTQGEAMHAAARMRELGLEHLGVLTFHQHLERSRLLVERCWTPQEGRVSMFAFDAG
+LDRWGRVRHGAYGVLAYGKAMATPGCDQELPGVLQWPLDLAKRLRGQPVGAEAGAAGPAG
+AVSAAPAAATPAAPARGEGPA*
+>NZ_CP083691.1_1106
+MSRPAGSAPAVDGDAQAAPRGPQAGRRVQADRGRGRRRRRILGAVLAAAALVLAAAFGPG
+LMRAADMTLHPRPDDPPRVDALLVLYSQPAVYDAALELLDRGVADRVFVSAHLGPDGFEK
+FCGTPAQRDPRTRGVEVECFSPDPVTTQGEVMFAADRMRALGLRRLGVLTFDQHLERARL
+LAERCLPAADGSVSMYRFDGGYTGAEKVRQDVYGTAAFAKVALTTDCSGELPDVLQWPLD
+LVKRTAGMPVGAVAESAAGVGRAGAGVRP*
+>NZ_CP097650.1_1558
+MSAQADRGRVRRGLPRWARALCATVATLAALGLAFGAGWATHAVTEPHPDDAPRVDALLV
+LYSQPRVYDAAIELAASGVTDRLFVSAYLGPDGHEKLCGGPGERDPRLAGVSVECFAPDP
+VTTQGEVIHAADRMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR
+LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA
+GAV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001367.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001367.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2548b621231f0fbe53cdd9f5356b81d1da4b13f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001367.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1631
+MRRSRARSGILVRMCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQ
+LYHRKKAGKLANLAEELAEHPVPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLAFIHN
+GIIENYAELREELLAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAF
+TLLAVHVDHPDRVVASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITA
+DAVEISDFRGGPAEGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGA
+LMLDELRIDPEELKAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPI
+IDPHTLVVSISQSGETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEI
+AVASTKAFLAQITAAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAGKDQVKE
+LARSMADATSVLFLGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPV
+FVVMPSPLDRHSLHAKVVSNIQEVRARGARTFAVAERGDAAVRAQAEVVFEVPETQPMLM
+PLLTTVPLQIFALELATAKGYDVDQPRNLAKSVTVE*
+>NZ_CP033200.1_1346
+MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL
+AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL
+LAKGVEFLSETDTEVAAHLLADVYRHAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA
+DGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL
+KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPLDRHSL
+HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL
+ELATAKGYDVDQPRNLAKSVTVE*
+>NZ_CP040019.1_1176
+MCGIVGYIGQPSSTREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGELYHRKKAGKLANL
+AQELEEHPVPTGLVGIGHTRWATHGGPTDVNAHPHVADEGRLAMIHNGIIENYAELREEL
+LAKGAEFLSETDTEVAAHLLTDVYRNAGGQDLTRSLQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITAEGVEITDFAGSPA
+EGKRFTVDWDASAAEKGGYETFMEKEIHDQPQAVQDTLLGRMDAAGTLVLDELRIDPEEL
+KAVNKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPNTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLHAIPGKIQEILDDKEQVKELARSMADTSSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQAVFVVMPSPMDRHSL
+HAKVVSNIQEVRARGARTFVVAERGDQAVRSHAEVVIEVPETQPMLMPLLTTVPLQIFAL
+ELASAKGYDVDQPRNLAKSVTVE*
+>NZ_CP083691.1_1104
+MRMCGIVGYIGQPSSTREHDALEVLMEGLRRLEYRGYDSAGVAVVADGELYHRKKAGKLA
+NLAAELEAEPVPSAQVGIGHTRWATHGGPTDVNAHPHVADEGRLALIHNGIIENYAELRA
+ELLEKGVTFLSETDTEVAAHLLADVYRGAGEGDLTRTMQLASQRLEGAFTLLAVHVDHPD
+RVVASRRNSPLVVGVGEGENFLGSDVSGFIDFTKEAIELEQDQVVTITADAVEITDFQGA
+PAQGKAFTVDWDASAAEKGGFDTFMEKEIHDQPQAVQDTLLGRTDATGALVLDELRIDPE
+ELKAVRKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDDHTLVVSIS
+QSGETMDTLMAVRYAKEQGARTLSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQ
+ITAAYLLGLYLAQLNKKLFTGQIKDILADLAEIPGKIQEILDSSTPVRELARSMADTSSV
+LFLGRNVGFPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDEGQAVFVVMPSPLDRH
+SLHAKVVSNIQEVRARGARTFVVAERGDEAVRDHAEVVFEVPETQPVLMPLLTTVPLQIF
+ALELASAKGYDVDQPRNLAKSVTVE*
+>NZ_CP097650.1_1560
+MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL
+AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL
+LAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA
+EGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL
+KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPMDRHSL
+HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL
+ELATAKGYDVDQPRNLAKSVTVE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001370.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001370.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8f9bfa241b8e27fbd05934f0f94d3b3a1a16a25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001370.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1636
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP*
+>NZ_CP033200.1_1351
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP*
+>NZ_CP040019.1_1171
+MSSEAVPRPPRWSPFGALLAGLAVLWGAAFLAVDAPVCERHGAPVEWLPCLDRDRGDPDV
+APQR*
+>NZ_CP083691.1_1100
+MSPRRDPGRLRPLAGPAALLAALWVAAWLAVSVPVCDRGGPADWLPCVDPGRSVPAPGAP
+*
+>NZ_CP097650.1_1565
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001371.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001371.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca5e4c90e87c06159e879e6ce84a7dba8d20293b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001371.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1637
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD*
+>NZ_CP033200.1_1352
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDEHGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD*
+>NZ_CP040019.1_1170
+MSRLFGTDGVRGLANETLTVELSVQLAQAAAPVLGAEALEAGRRPVAVVARDPRISGEFI
+AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLGADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVEPRRPQGADVGRVKVFSDAEDRYVVHLLQALPHRLEGLKVVL
+DCAHGAAAGCSPEAFRDAGAEVVVIGASPDGLNINEGYGSTHLEKLQAAVLEHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVAMKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLAARVAETGRP
+LSALAAVMDRLPQVLVNVRGVDKSRAAEDVAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAEALADVVQRELRLHV*
+>NZ_CP083691.1_1099
+MSRLFGTDGVRGLANDVLTVELSVQLAQAAAPVLGADALAAGRRPVAVVARDPRISGQFI
+AAAVIAGLASSGVDVHDAGVVPTPAAAFLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDEQEDEIIQHLESEHPLRPTGAEVGRVRTFSDAEDRYVVHLLQTLPHRLDGLTVVL
+DCAHGAASGCSPDAFRDAGAQVIVIGAEPDGLNINEGVGSTHLEKLQAAVKEHGADLGIA
+HDGDADRCLAVDELGEVVDGDQIMGIMALALKDRGQLKEDTLVVTVMSNLGLKLAMRGAG
+IELVETQVGDRYVLAGMRLGEYSLGGEQSGHVIFADHATTGDGVLTGLQIAARVAETGTP
+LSQLAAVMTRLPQVLVNVRGVDKSRAAEDAAVQSAVREAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETARREAEALAEVVQRELRLHD*
+>NZ_CP097650.1_1566
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001372.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001372.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84e37aa6a9f1e3b7c72a6f16a8970275fb65e3fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001372.fa
@@ -0,0 +1,26 @@
+>NZ_CP042169.1_1639
+MAENTSPTPDPRTRGEHGTEHTAQAPFAVTRDYAAEVDEIRELGRKLGGEKKTPTPDPQA
+WREGYPYKTKLSRKSYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGGAIKRF
+NEHLNPRGARTVALEKPTEEEASQWYFQRYIQHLEFMRETPELERMLLNSGVHIIKFWFS
+VSQREQLNRFAARETDPVRRWKLSPTDLASLDKWDDYTNAKEAMFFYTHTADAPWTVVKS
+NDKKRARLEAIRHVLHTLPYPDKDERIVHRPDPQICGPANELAEYGEVSGGSFPRVR*
+>NZ_CP033200.1_1354
+MGSFSWPLTAIKRFNEHLNPRGARTVALEKPTEEEASQWYFQRYIQHLEFMRETPELERM
+LVNSGVHIIKFWFSVSQREQLNRFAARETDPVRRWKLSPTDLASLDKWDDYTNAKEAMFF
+YTHTADAPWTVVKSNDKKRARLEAIRHVLHTLPYPDKDERIVHRPDPQICGPANELAEYG
+EVSGGSFPRVR*
+>NZ_CP040019.1_1168
+MTGRSPVRCAVRSNTTSGAAAAENTSTTTETTPAGGHAMEDTADAPWTVVKSNDKKRARL
+EAIRHVLHTLPYPDKDERIVHRPVPHICAPATELFETGEDSGGSFPRVR*
+>NZ_CP083691.1_1097
+MAENTTTPPTDPSADGVLAGEHPLESGRREQPFAVTEDYAAEVDEIRELGRTLHGDSLPS
+PDPTAWREGYPYKTKLSRKTYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGG
+AIKRFNEHMNPRGARTVALEKPTEAEASQWYFQRYIQHLPSGGEIVMFDRSWYNRAGVER
+VMGYCTPQQYLEFMRETPELERMLSNSGIHIIKFWFSVSRREQLNRFAARETDPVRRWKL
+SPTDLASLDKWDDYTNAKEAMFFYTHTADAPWTVVKSNDKKRARLEAMRHVLYTLPYPNK
+DERIVHLPDPQICASADVLSEIDEADGGSFPRVR*
+>NZ_CP097650.1_1568
+MQLWVKQTGQKVLIIVEGRDAAGKGGAIKRFNEHLNPCGARTVALEKPTEEEAPQWYFQC
+YIQHLEFMRETPELERMLVNSGVHIIKFWFSVSQREQLNRFAARETDPVRRWKLSPTDLA
+SLDKWDDSTNAKEAMFFYTHTADAPWTVVKSNDEKRARLEAIRHVLHTLPYPDKDERIVH
+RPDPQICGPANELAEYGEVSGGSFPRVCGGGFSRAPPPRTPG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001380.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001380.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e104d722e4f48d784b76f84214f48d6844e8cd48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001380.fa
@@ -0,0 +1,10 @@
+>NZ_CP042169.1_1647
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG*
+>NZ_CP033200.1_1365
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG*
+>NZ_CP040019.1_1160
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG*
+>NZ_CP083691.1_1089
+MKVQPSVKRICDKCQVVRRKGRVLVICENPRHKQRQG*
+>NZ_CP097650.1_1576
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001381.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001381.fa
new file mode 100644
index 0000000000000000000000000000000000000000..edf32f3bd5c0c3835a7390667cbb5d4be47cb72c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001381.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1648
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK*
+>NZ_CP033200.1_1366
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK*
+>NZ_CP040019.1_1159
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK*
+>NZ_CP083691.1_1088
+MAKKEGVIEVEGTVTEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRVVVELSP
+YDLNRGRIVYRYK*
+>NZ_CP097650.1_1577
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001383.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001383.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bdca29d2a25c3b2519ffa256c5e0cd80b73642d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001383.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1650
+MTRMLLMGPPGSGKGTQATRIADKLGIVPISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV
+PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAEAGLSLSAVVELEVPDEE
+LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE
+RLLQAVYSVRAATGSLPVIQPGAES*
+>NZ_CP033200.1_1368
+MTRMLLMGPPGSGKGTQAARIADKLGIVPISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV
+PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAESGQSLSAVVELEVPDEE
+LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE
+RLLQAVYSVRAATGSLPVIQPGAES*
+>NZ_CP040019.1_1157
+MTRMLLMGPPGSGKGTQATRIADKLGIVAISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV
+PDDVTNRMVADRIAQPDAEHGFLLDGYPRTKGQVEALDAMLTEAGLALSAVVELEVPDAE
+LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETEAVIQEYVERGIVARVDGTGQIDDVTE
+RLLQSVYAVRAATGSLPVIAPDTES*
+>NZ_CP083691.1_1086
+MTRMLLMGPPGSGKGTQATRIADKLGIVAVSTGDIFRHNVKNMTELGKEAKRYMDAGDFV
+PDEVTNRMVADRLSQSDAETGFLLDGYPRTAGQVDALDAMLKDTGQALSAVVELEVPDAE
+LVARLLKRAEIEGRADDTEEVIQHRLDLYHRETESVIESYAERGIVARVDGTGQIDDVTE
+RVLQSVYSVRAATGTLPIITPDTQA*
+>NZ_CP097650.1_1579
+MTRMLLMGPPGSGKGTQAARIADKLGIVPISTGDIFRHNVKSMTPLGVEAKRYIDNGDFV
+PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAEAGQSLSAVVELEVPDEE
+LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE
+RLLQAVYSVRAATGSLPVIQPGAES*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001391.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001391.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7843b3cfb355cdc79799ed1ffc0b92c0b163e67e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001391.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1658
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ*
+>NZ_CP033200.1_1376
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ*
+>NZ_CP040019.1_1149
+MTEVQQTEKVAPRLKTKYREEIRATLQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVTDLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ*
+>NZ_CP083691.1_1078
+MTEVQQTEKVTPRLKTKYREEIRASLQEQFEYANVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAIADLTAITGQKPMVTKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDK*
+>NZ_CP097650.1_1587
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001395.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001395.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd850d15fc528baa744f9a176a743e6c2f9fe1a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001395.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1662
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI
+YTILRERELGIRGDVAAEAQAEKNEEAAK*
+>NZ_CP033200.1_1380
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI
+YTILRERELGIRGDVAAEAQAEKNEEAAK*
+>NZ_CP040019.1_1145
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNSSRLKAVKRDIARI
+YTILRERELGIRGDVAAEAQADNNEEAAK*
+>NZ_CP083691.1_1074
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLEDSSRLKAVKRDIARI
+YTILRERELGIRGDVETAGAEKNEEAAK*
+>NZ_CP097650.1_1591
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI
+YTILRERELGIRGDVAAEAQAEKNEEAAK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001403.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001403.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ac029fad1d1d3c02150c58eb15341d24ad17ba6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001403.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1670
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA*
+>NZ_CP033200.1_1388
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGQHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA*
+>NZ_CP040019.1_1137
+MTNTQNIKGLLGTKLGMTQVWDENNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFDKAGVTPRRHLVELRTADAAEYSLGQDLTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVSASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGVDVENNLLLIKGAVPGSKGQVVLVRSAVKGA*
+>NZ_CP083691.1_1066
+MTNTQNVKGLMGTKLGMTQVWDEDNKLIPVTVVQADANVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYTLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVSASHGAHKNHRKPGSVGGASTPARVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA*
+>NZ_CP097650.1_1599
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001406.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001406.fa
new file mode 100644
index 0000000000000000000000000000000000000000..733cc54e32cb4a6d2970d043287d8d8fc0ea80d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001406.fa
@@ -0,0 +1,13 @@
+>NZ_CP042169.1_1673
+MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER
+*
+>NZ_CP033200.1_1391
+MSDDGAAAAARLGSMPELLILIVVLAVAVVAVRWALRTFRPEIDRARRIRRANRGGELER
+*
+>NZ_CP040019.1_1134
+MPELLITLLVLAAAVVAVVWALRTFRPEIDRARRIRRANRNGELRR*
+>NZ_CP083691.1_1063
+MEWLIALVVIAAVVAGGLWARRAFAPEIERARRIRRAERGGRLER*
+>NZ_CP097650.1_1602
+MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001410.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20a279fae8d2bb6d1cd82b5e6f3150f9d620c4f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001410.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1677
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVRDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK*
+>NZ_CP033200.1_1395
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK*
+>NZ_CP040019.1_1130
+MPTIQQLVRKGRSPKVVKTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVRDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK*
+>NZ_CP083691.1_1059
+MPTIQQLVRKGRSPKVVKTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+VEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK*
+>NZ_CP097650.1_1606
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001415.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b5d6cdedc88b12072722474651b5748d5368179
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001415.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1682
+MAQRSKAYKAAKAAIGEDLYSPVEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL*
+>NZ_CP033200.1_1400
+MAQRSKAYKAAKAAIGEDLYSPVEAIRLAKETNPSKIDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL*
+>NZ_CP040019.1_1125
+MAQRSKAYKAAKAAIGEDVYSPVEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGERAEAARAAGADVVGDDDLIAKISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVTDIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVSMDPNVTSVDSSEL*
+>NZ_CP083691.1_1053
+MAQRSKAYKAAKAAIGDTVYAPAEAIALAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGERAEAARAAGADHVGDDDLIAKIADGWTDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+ANQLVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVQMDPNAAPPKDEAQA*
+>NZ_CP097650.1_1611
+MAQRSKAYKAAKAAIGEDLYSPAEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001416.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001416.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65f0853798b6c62fe635904c846c7d6cc81eba1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001416.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1683
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG*
+>NZ_CP033200.1_1401
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG*
+>NZ_CP040019.1_1124
+MAPKKKVSGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFITKTPPAAELIKKAAGVAKGSATPHTAKVGKLTQAQCEEIAQTKMEDLNA
+NDVKAAAKIIAGTARSMGITVEG*
+>NZ_CP083691.1_1052
+MAPKKKVAGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATEAQRGNVIPVEI
+TVYEDRSFTFITKTPPAVELIKKAAGVQKGSSTPHTAKVGTLTQAQCEEIAQSKMEDLNA
+NDVKAAAKIIAGTARSMGITVEG*
+>NZ_CP097650.1_1612
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001417.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001417.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43a067b963f3aa46d6827dd93c1a3c3336c7f134
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001417.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1684
+MSEQELDRQPAEESVPMSEDAVAEETAETAQDAGTPVEDALDEVAGSGDETAEATVQEAD
+LAVAEGEDAPTPVEEQSDDEPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEAR
+ILTQDMEDSIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGV
+TGFVGNDAHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPAAAESGAPAAPAIHVDF
+EVGESVTVNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI*
+>NZ_CP033200.1_1402
+MSEDAVAEETAETAQDAGTPVEDALDEAAGSGDETAEATVQEADLAVAEGEDAPTPVEEQ
+ADDEPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILTQDMEDSIYEIEVP
+MEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGNDAHHPQPLSL
+DEVYDMLAPSVIQEAARAAEKAGLAVPALVESGAPAAPAIHVDFEVGESVTVNDGPFETL
+PATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI*
+>NZ_CP040019.1_1123
+MSEQELDRQAAEESVSVQEDGAVEETVETAQDAPAPAEDAAGETAVDGEEAAEATEATAQ
+EADPAAVEQAEEEPAVDPGEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILSQDME
+DAIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGND
+AHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPASAESGAAAAPAIHVDFEVGESVT
+VNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKVI*
+>NZ_CP083691.1_1051
+MSEQELDRQDVEETAVAEDSTALEAPVEDTAAEEAEQTVQEADLAIAEGDQDAAEAPSAE
+ELDAAGQAPAQPDVEAAEQLRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARIQTQDMEDS
+IYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTSGVTGFVGNDAH
+HPQPLTLDEVYDMLAPSVVQEAVREAEKAGLVPVAVAESGAAGAPAIHVDFEVGESVTVD
+DGPFETLPATISEIKPETQQLVVLVSIFERETPVTLSFNQVTKVI*
+>NZ_CP097650.1_1613
+MSEDAVAEETAQDAGTPVEDALDEPAGSGDETAEATVQEADLAVAEGEDAPTPVEEQSDD
+EPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILTQDMEDSIYEIEVPMEE
+VVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGNDAHHPQPLSLDEV
+YDMLAPSVIQEAARAAEKAGLAVPAAAESGAPAAPAIHVDFEVGESVTVNDGPFETLPAT
+ISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001423.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001423.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0e52523988a53fae4156c60d0cd077242f50d92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001423.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1690
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL
+ARTGGTILGTSRTHPYNAEGGGPENMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFIPEGHDDPLAEAGVEA
+SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ
+RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR*
+>NZ_CP033200.1_1408
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL
+ARTGGTILGTSRTHPYDAEGGGPENMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFVPEGHDDPLAEAGVEA
+SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ
+RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR*
+>NZ_CP040019.1_1116
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKTYDMEMVGIRNGWSGLIEKDVEELPRTRVRGL
+ARNGGTILGTSRTHPYDTEGGGPENMRRNMRELGLDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLRGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMEQVAEWVKQVHDRGRSPLVVVAEGFIPEGHDDPLSEAGVED
+SGRPRLGGIGEWVTREIEAMTGVETRNTVLGHIQRGGAPTATDRVLSTRFGMGAVDLAAQ
+KRWGQMVAANGTDIISIPMSAALKGLKEVPVERYEEAKVLFGR*
+>NZ_CP083691.1_1044
+MRVGLLTSGGDCPGLNAVIRAAVLHGIKTYDMEMVGIRNGWAGIIEQDVEDLPRTRVRGL
+ARTGGTILGTSRTHPYDADGGGPENMARNLRELGIDAVVAIGGEGTLAGANRLAQDGLPV
+VGVPKTIDNDLQGTDYTFGFDTAVEIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVTQVHEKGRSPLVVVAEGFIPEGHDDPLADAGMEA
+SGRPRLGGIGEWVTREIEEMTGIETRNTVLGHIQRGGAPTARDRVLSTRFGMGAIDLAAQ
+HRWGSMVAARGTDIITIPMSAALKGLKEVPRERYDEAKVLFGR*
+>NZ_CP097650.1_1619
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL
+ARTGGTILGTSRTHPYNAEGGGPKNMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFVPEGHDDPLAEAGVEA
+SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ
+RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001429.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001429.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30a7d469dadb26957abbb5a18ed74afe07b75e92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001429.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1696
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGPDGAIDGAAVLVPEGTAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREETT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVTLY
+ASLGFELFAADAQYRRP*
+>NZ_CP033200.1_1414
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGPDGAIDGAAVLVPEGTAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREETT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVTLY
+ASLGFELFAADAQYRRP*
+>NZ_CP040019.1_1110
+MAENPVPATPTDPAAPRVSEPRPDEVDAVLALADRAQAADGHPPLSDQTRVVLARGRQRW
+WGVVREADGSVSGAAVLAPEGGEDSGSVLELVVDPEARRAGRGAALADAAAAAVRERGLE
+STTSVWAHGMLPGSDALARRHGLEPVRELRRMRLPHEALADLPQPQLADGVALRGFVPGR
+DEQAWLDANAAAFADHPEQGGLTRADLEDRMAEDWFEAEGLLLAVREEDDALLGFHWTKV
+EPQAGPGPRVGEVYAVGVTPATQGLGLGRALTLAGLHRMAGQGVDVVDLYVDADNAAAVR
+LYESLGFGLFAADAQHRRP*
+>NZ_CP083691.1_1037
+MSEQPASPALPPTPGVVSPGTPSDVDAALALADRAHRSDGHPPLNDQTRAVLARDAQRWW
+GLTRDEAGAVTGVAVLAPEGEAAGPGVVELAVDPAHRGAGLGAALAEAAADAVRERGEAR
+RTSAWAHGALPGALALARRHGLEPVRELRRMRLDPAGLGALPPTRLPEGVTLRGFVPGRD
+EDAWLALNAAAFADHPEQGSLTRADLDAREAEDWFEAAGLLLAEDAEGTPVGYHWTKVTP
+AEAGAPSEGEVYAVGISPAAQGRGLGRALTLAGLHHMAGRGVDAVDLYVDADNVPAVRLY
+ESLGFALAAADVQLRPAR*
+>NZ_CP097650.1_1625
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGTDGAIDGAAVLVPEGAAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREATT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVALY
+ASLGFELFAADAQYRRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001433.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001433.fa
new file mode 100644
index 0000000000000000000000000000000000000000..542900881a5903db8f138cec6001223bac93bc73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001433.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1700
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG
+PRHRFERWERD*
+>NZ_CP033200.1_1418
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG
+PRHRFERWERD*
+>NZ_CP040019.1_1106
+MRSDPMSRATRPTEPAIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTASEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPVLDPRWRRTAVDPAPDAWLDSASG
+PRHRFERWERD*
+>NZ_CP083691.1_1030
+MARHHDDGARPRQTIAMIWAQTPDGVIGADGTMPWHLPEDLARFKALTLGHPVIMGRRTW
+DSFPARVRPLPGRTNIVVSRTLTATPEAGEAVRAAGAVVVPDFGAALTAADEADGLDLVW
+VIGGATLYEQALDVATRAEITVVDVDAPGDTHAPALDSRWRLVAADPSPDGWLDSAAGPR
+RRDERWERD*
+>NZ_CP097650.1_1629
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPLLDARWRRTAVEPAPDAWLDSASG
+PRHRFERWERD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001436.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001436.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09aa1e9046c1d15bdefa559ab8675ebdf3e17623
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001436.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1703
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIHVLDGPLPGEGETPPAGDGARSADHEGEAVVVRIAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL*
+>NZ_CP033200.1_1421
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIHVLDGPLPGEGETPPAGDGARSADHEGEAVVVRIAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL*
+>NZ_CP040019.1_1103
+MSERLAEHTTTRVGGPARAWETARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIEVRAGDEAHGGDADDQDPAAGGDRAGEAVVVRVAAGHPWDDAVAWTVEH
+GLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVSLRAWDREAGQVVELGAEELEFDYR
+DSIIKRSMLETGAPSPRWIVLSIDLRLRRASGAAEPTAPVRYGQLASALDVAEGTHAPLA
+VVRREVLALRAAKGMVSDPQDPDTWSTGSYFTNPIVPAAVRASLPEGAPAFAAGRAADGT
+ELVKLSAAWLIDHAGFAKGFGLPDVAPREGGPDGRGADGAGLAGGRASVSTKHTLAMTNR
+GDASTEDVLTIARTVRDGVKARFGVDLHPEPMIIGTSL*
+>NZ_CP083691.1_1027
+MSERLSDHTTTRVGGPARAWVEARTEAEAVAAVRAADAAGEPLFVLGGGSNTLMADAGFE
+GTVVHMGFTGVEVLPAEGAADGAGDVVVRVAAGHVWDEAVAWTVEHGLAGVEALSGIPGS
+AGATPVQNVGAYGADVSQVLVSLRAFDRAAGQVVELSAEDLRFGYRDSVIKRSMFEDGSP
+SPRWIVLSIDLRLRRAEEGAEPTAPVRYAQLARALEVEEGADVSLAQVREHVLALRASKG
+MVSDAADHDTWSTGSYFTNPIVPATVRVTLPEGAPAFAAGTDEDGTPLVKLSAAWLIDHA
+GYGKGFGLPDAPRREGDADGSGPDGRGLAGGRAALSTKHTLAVTNRGGASTEDVLTVARA
+VRDGVKARFGVDLHHEPMIIGTRL*
+>NZ_CP097650.1_1632
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADSGFP
+GTVVRLAFEGIGVLDGPVPGEGEAPPVGDGARLADHEGEAVVVRVAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001439.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..055452d226c2041e811c90dfb8f6e0e040b299ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001439.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1706
+MSTRRPAHQPTRGTAAPRGFVSPWEHGSRLYRTLVLTGSALFLVGIVLAVVGGTTGRLAV
+SGTALGVLGAGVAVHLSAQLVRFRQAARRQGERRPGR*
+>NZ_CP033200.1_1424
+MSTRRPAHQPTRGTAAPRGFVSPWEHGSRLYRTLVLTGSALFLVGIVLAVVGGTTGRLAV
+SGTALGVLGAGVAVHLSAQLVRFRQAARRQGERRPGR*
+>NZ_CP040019.1_1100
+MSSHRPSSQRRPDRGPSTGPQRAGFVSPWENGSALYRALVLTGSALFLVGIVLAVVGATT
+SQLTVSWFALGVLGLGVVVHLSAQMVRFRQAARRQGQRPPGR*
+>NZ_CP083691.1_1024
+MPTSARRPEPSARSGGFVSPWEHGSRLYRGMVLTGSALFLIGIVLSVVGATAHVLALSWT
+ALGVLGAGVLVHLSAQLVRLREAGRRESAARSARRKGRGSGR*
+>NZ_CP097650.1_1635
+MSTRRPAHQPTRGTAAPRGFVSPWEHGSRLYRTLVLTGSALFLVGIVLAVVGGTTGRLAV
+SGTALGVLGAGVAVHLSAQLVRFRQAARRQGERRPGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001443.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001443.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b44232b3a00ff55168573970c1ebce9577ba044
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001443.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1710
+MTEQNVHEDPHATTPDTGAEDAAAHPQGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAAAGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL*
+>NZ_CP033200.1_1428
+MTEQNVHEDPHATTPDTGAEDAAAHPRGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAAAGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL*
+>NZ_CP040019.1_1096
+MTTHEQRPAGFGTRAVHAGQDLDEVYGAVVPPVHLSSTYAPVRVGELRRGYDYGRGTNPT
+RDALQTQLAALEAGVGEDGTPNALALTFASGLAAETALIMGAAEPGTTIVMGNDVYGGSY
+RLISKVLAKWGIRHAVVDMGDTAKVAAAVESAAAQGPVMVWLETPSNPLMKVSDIAAIAE
+VAHGHDALLVVDNTFATPYLQTPLALGADVVVHSTTKYIGGHSDVIGGALVIKDPELGAQ
+VQFQQFAAGAVNGPWDAYLTTRGLKTLGVRMDRHQANAQAVAEWLAGRPEVTQVLYPGLP
+DHPDHELAARQMRGFGGMVSFRLTGGAAAARTVAESTRLFQLAESLGGIESLMNYPAEMT
+HASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALEALAG*
+>NZ_CP083691.1_1020
+MTEQNAHEQPHDTAPTGPEATEGPAEGFGTRAVHAGQHLDEVYGAVVPPLHISSTYAPTA
+IGELRRGYDYGRGTNPTRDALQEQLAALEAGVDDAGTPKATGLTFASGLAAETALIMGAG
+QPGMTIVMGNDVYGGSYRLISRVLKPWGVDHAVVDMGEPEQVAAAVEQAAASGPVMVWLE
+TPSNPMMKISDVAAVAEAAHGRGAQLVVDNTFATPYLQNPIALGADVVVHSTTKYIGGHS
+DVIGGALVIPDAELAEKVKFQQFAAGAVNGPVDAYLTTRGLKTLGVRMDRHQANAQALAE
+WLTEQSAVSQVLYPGLPDHPGHELAKRQMRGFGGMVSVRFHGGAAAAKKVAESTRLFQLA
+ESLGGIESLMNYPAEMTHASVAGTELAVPDDLVRLSVGIEDASDLIADLEQAIAGLAG*
+>NZ_CP097650.1_1639
+MTEQNVHEDPHATTPDTGAEDAAAHPRGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAATGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001446.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001446.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c40ef749a775ab726050e4e77ddabbb5aeb3e043
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001446.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1713
+MTTAFEPRPHTAAAPREPDPHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWITAF
+EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLADGTWRLRD
+ADPRAWSTTYRATILGAAPEAVCTIWDVFPLPAA*
+>NZ_CP033200.1_1431
+MTTAFEPRPHAAAAPREPDPHGPGTAGSLRPGARGSVLIVTRHPDPDEAMRHAMAWITAF
+EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWRLRD
+ADPRAWSTTYRATILGAAPEAVCTIWDVFPLPAA*
+>NZ_CP040019.1_1093
+MTTAFEPRPHTGLAPREPEPHGPGTPGPLRPGVRGSVLIVSEHADPDTAMRHAMAWITAF
+EDDCGLVLDADGTELYAVGLAGELGASLRRSPGVAEDGTPTDTSEFVDAILTGGVWRLRE
+PDARAWSTAYRAAILGAAPHAVCTVWDVLPLPAA*
+>NZ_CP083691.1_1017
+MTAQHAEPTRTDRAEPHGPGTPATLRPGERGSVLVLSPAGPPEAAMGHAVAWITAFEDDC
+GLVLDRDATSLYAVSPADGLRREGDVPSDGGIAEHLDFVLAGDVWHHRGTCPPAPAGSDV
+DGWALLVHRLQREAPRGALGTVWDVFPLPAAG*
+>NZ_CP097650.1_1642
+MTTAFEPRPHTAAAPREPDPHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWITAF
+EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWRLRD
+ADPREWSTTYRAAILGAAPEAVCTIWDVFPLPAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001447.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001447.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d55ef72874471fe0cf3f27a66328e84ff270a6e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001447.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1715
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMRASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR*
+>NZ_CP033200.1_1433
+MASDSTFDIVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR*
+>NZ_CP040019.1_1091
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEASMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQEVIAMLKDFEDADLQFVNFR*
+>NZ_CP083691.1_1016
+MASDSTFDVVSKVDKQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKANSEERVK
+AVLDVFESKLVKRGISLKSLDCGEPFASGKETRMEASIKEGIDQPTAKKITKLIRDEAPK
+SVKAVIQGDELRVSSKSRDDLQETIALLKTFEDADLQFINFR*
+>NZ_CP097650.1_1644
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001448.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df9a16200a56390b239a3a8776573a4ae850086f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001448.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1716
+MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFAKAAMLLTFDDHVDLALRHGVAA
+PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD
+QSLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQAGRDR*
+>NZ_CP033200.1_1434
+MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFTKAAMLLTFEDHVDLALRHGIAA
+PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD
+QDLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQADRDR*
+>NZ_CP040019.1_1090
+MLYLIDPRGAVWSADATIGQARARARVDGRPIDDLKFARAAMLLTLDDYVDLALRHGVEA
+PRGILLDHGFVAQALAPANLKAQRANQDAMAEQLLPVERRTEDAGSLRGHRHDAAYEGAH
+QDLDRRIKKAEETARETLQKTPDEDLIRHWRRLGGDVPATIEADRKD*
+>NZ_CP083691.1_1015
+MLYLIDPRGAVWQSDVTLGRALARQKVDGRPVDDVPLKKAVLPIDEADVLDLGLRHGVAA
+PRGILLDGGWVTQVLQPSQLKRQRANQDATADQLEPVELRTETDSLRSSRHAAVVEGAHR
+DLDTRIEKAEKAAREALQAAPRRELVTHWRGMGGGLPATIQADLADAD*
+>NZ_CP097650.1_1645
+MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFTKAAMLLTFEDHVDLALRHGIAA
+PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD
+QDLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQADRDR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001451.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001451.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f1dc23cd2ecb8c34b97564d6c78c25f41738002
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001451.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1720
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDGEGLDR*
+>NZ_CP033200.1_1438
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDDEGPDR*
+>NZ_CP040019.1_1086
+MPAKPPAPVHLPAFQRLVPDLLGDAWAEDDGLSPADVEARLGQSPAAGQLGAGFMVPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDAEETVVWGLPVDNLALPDPLVW
+RRSSGAEAEEGDWQDEGGTFSEFITDLLAWTFEDPEDDDGRDER*
+>NZ_CP083691.1_1010
+MPAKPPAPVYLPGFQRLVPDLLGDTWAKDDGLAPADVEARLAESPAAEQLGTGFMVPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDEGETVVWGLPVDNLALPDPLVW
+RRDTGADAEEGDWQDEGGTFSEFITDLLVWTFEDPEDDAAEDAR*
+>NZ_CP097650.1_1649
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWAFEDPEDDDEGPDR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001461.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f6d2d6fc58278b16daff92c790896d78ea8ccf2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001461.fa
@@ -0,0 +1,49 @@
+>NZ_CP042169.1_1734
+MASRTASPPPSPAPSPAAPRGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPESLKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVVATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVAVGGAASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN*
+>NZ_CP033200.1_1452
+MASRTASPPPSPAPSPAAARGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPEALKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVAATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVTVGGGASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN*
+>NZ_CP040019.1_1071
+MGQEFRGGLATFLAMSYIVVLNPLILSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWA
+RHPFAVAAGLGVSAFVSITIATTPGLTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPE
+ALKSGIVVGIGLFIALIGLVNAGFVRRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLL
+TAVLVIRKVRGAILIGIVAATILANVLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTA
+PDLHLLGSVDLFGAFTSVGGLMASLLVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPD
+LNRVLAADALAVAVGGGASGSAHQIFVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLI
+HLVPFEAVAPALVVVGFMMCQHVVQIDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVA
+YAVIRTGQGRGREVHPLLWFVALAFVAYFGLGVVRASLGLN*
+>NZ_CP083691.1_996
+MSSRTTGATPPGTAPSNPASPAGPRSGLDRFFGISALGSSVGQEVRGGIATFLAMSYIVV
+LNPLILSGPDSTGAVLGIPRVAAATALVAAVATLAMGLWARHPFALASGLGVNAFLAITV
+ATTPGLTWPDVMGLVVIAGLVMVVLVATGFRTAVFNAVPEALKTAIVVGIGLFIALIGLV
+NAGFVRRLPDAAGTTVPVGLGTGGELAGWPVLVFIVGLLVTAILVIRNVRGAILVGIVTA
+TVLANILEAVFHIGPSVGADGSHNPTGWALVAPSLPEWAAPDLSLLGSARPFGAFEAVGG
+LMGALLVFAILLSVFFDAMGSTVGLAREAGSMDEHGNVPRLNRVLMVDALAVTGGGAASA
+SAGQIYVESGTGIGEGARTGLASVVTGLMFVATIFLTPLIHLVPFEAVAPALVVVGFMMC
+SQVVRIDWTDWGAALPAFLTFILMPFTYSIANGIGAGMIAYAVIRTGQGRAREVHPLLWV
+VAAAFVLYFGMGVFRGILGLA*
+>NZ_CP097650.1_1663
+MASRTASPPPSPAPSPAAPRGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPEALKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVAATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVTVGGGASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001462.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001462.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c28340114e93f1652c92e982194d91bd677d2a84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001462.fa
@@ -0,0 +1,70 @@
+>NZ_CP042169.1_1745
+MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVRAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQAAHWREPAFDEELYACHLSATAAES
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVGLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYAAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATARIV*
+>NZ_CP033200.1_1453
+MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REISTGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQAAHWREPAFEEELYACHLSATAAQS
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYEAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATARID*
+>NZ_CP040019.1_1060
+MPQTTSHAPVPPSVSAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLRAAIFGEIKARTVETDRSVPSRRDGWWYFARTKEGAEYPVHCRVPAADTGDLEADW
+TPPVVTPDAPLEGEQVILDGNAEAEGHPFFALGGLHISPDSTRVAYAVDHTGDERFTLRV
+REIATGEDLPDVVENIAHGVRFDRSGARVLYTVWDDSWRPYQVKAHVLGTDPAQDQLLYE
+ESDPGMWTGFTGTADRTQLLIGVGNSEVSETHVVDLPESPDAPLPAPRLLIPRAWGMLAD
+VEPVTGADGVRRLLVVHDRTVARQDAADAGADAPAPNGMLSLVAEADVADRGAWRTVVPH
+REDVKVDGVMVTLTHAALAVRRETTPRVVVAPLDSVLAGEAADWREPAFEEELYACHLAS
+TAAESPFLRLAYTSWISPARVLDVSAATGEVHLRRETEVPGYDPSLYVAERVWAPASEPS
+SVTGEPVRIPVTVIRRKDVAADGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVYAVA
+HVRGGGELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACTGGSAGGLLMGA
+VLNLAPELYRACLAVVPFVDALTSILDPELPLSALEWEEWGNPIEDPEVYAAMRDYTPYE
+NVRAVDYPTIAAVTSLHDTRVLYVEPAKWVARLRRTVTSDQATPLAEGGAPVLLRTEMDG
+GHGGASGRYQGWEDTAWEYAFLLTALGATQRVD*
+>NZ_CP083691.1_994
+MYETSLPTPPRAAARPTARTVHGETFTDDFEWMRAKTEQEVLDHLQAENAYTEAATADQA
+DLRAAIYGEIKAHTVETDQSVPARRDGWWYFVRTVEGKDYAVHCRVPAQDTGDALADWTP
+PVVPADAALPGEQVILDGNAEAAGHPFFSLGGMHISPDGALAAYAVDLAGDERYTLRVRE
+IATGTDLPDVVRNIAPGVRFDRSGTRLIYTVWDETWRPYQVRVHTLGTDAAEDAVLYEES
+DPGMWTGFDASADRTQLLIGVGNSEVSETWAVDLPVDASPLPAPRVLVPRTARMLADVEP
+FDMDGRRRLLIVHDRLADGTTAPNGMLSIVDEADVADRDAWRPVVPHADDVRVDGVLVTR
+THVGLAVRRDTTPRVLIAPLEGLREGSAPAWTEPSFDEELYMCRLAGVNLDSPFLRLSYA
+SWTTPARVLDVVAATGEVRLRREVEVPGFDREDYVAERWWAPASEPSSLTGEQVRIPLTV
+IRRRDVAQDGTAPAVVYGYGSYEMSMDPVFGVARLSLLDRGVVYVVAHVRGGGELGRAWY
+EDGKKAAKRHSFTDFVDATRFVADSGWVDPARIACTGGSAGGLLMGAVLNLAPELYRACL
+AVVPFVDALTSILDPDLPLSALEWEEWGNPIEDPEVYATMKAYTPYENVRAVDYPAIAAV
+TSLNDTRVLYVEPAKWVAQLRRTVTSDQTTPIAAGGSPILLRTEMDGGHGGASGRYQGWE
+DTAWEYAFLLTALGATARVD*
+>NZ_CP097650.1_1664
+MPQTTTHAPVPPSVAAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARETGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVTELDAVLAGQAAHWREPAFDEELYACHLSATAAES
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYAAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQARPLADGGAPVLLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATRRVV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001465.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001465.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44bcea44963632a4c04eac71662bc2876d6658b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001465.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1748
+MPATADALARATDALAAAFDGGAPVELTADGAVLPRPEARDSRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDDAGPRLISLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVTAAVAPDGPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVPAADGARAFLTEDTGILSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAALEAHPGVAAAHVAGVPDPEWGARLCAAVVPVRPAAAPDEAVLRAHVRAALGA
+AAVPKTWLLLEALPLLSTGKTDRQALAARFTAG*
+>NZ_CP033200.1_1456
+MPATADALARATDALAAAFDGGDPVELTADGAVLPRPEARDSRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDNAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVTAAVAPDGPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVTAVDGARAFLTEDTGILSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVADPEWGQRLCAAVVPADPASPVGENALRAHIRDALGA
+AAVPKTWLALDALPLLSTGKTDRQALAARFTAAG*
+>NZ_CP040019.1_1054
+MPATADALARATDALAAAFDGGDPVELTADGAVLPRPEARDPRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGIAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDHAGPRLVSLVPTQLARLLAADTDPAGRTALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAVAVAPDGPDAPPRVRLAGPMV
+AVGYLDDPARTAAHFVPAADGARAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVADPEWGQRLCAAVVPADPASPVGENALRAHIRDALGA
+AAVPKTWLALDALPLLSTGKTDRQALAARFAAAG*
+>NZ_CP083691.1_989
+MPATADALARATDALAAAFDGGAPVELTADGAVLPRPEARDPRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDDAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAVAVAPDGPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVPAADGARAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVPDPEWGARLCAAVVPAHPAAAPDEAVLRAHVRAALGA
+VAVPKTWLVLDALPLLSTGKTDRQALAARFTAG*
+>NZ_CP097650.1_1669
+MPATADALARATDALAAAFDGGAPVELTADGAALPRPEARDPRRCGDPDAVAVVRSSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDDAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAAAVAPDDPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVTAADGTRAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVPDPEWGARLCAAVVPAHEAAAPDEAVLRAHVRAALGA
+AAVPKTWLVLEALPLLSTGKTDRQALAARFTAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001467.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001467.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff1e6f5a914794b11e74c6fa7738c775d8bcaa78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001467.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1750
+MRIFFYGLVRVVLFVALWALFYYVMDLWMIFAVIAAAILAFAVSYLFLDRLRTGATEDLS
+AAWEGRPGRRGRTETADADAEDAYTEGRFRE*
+>NZ_CP033200.1_1458
+MRILYYGLLRVALFFVLWWVGLQLGLGMVMATLAAAILTFAVSYLFLGRLRRGATQDLSA
+AWEGRPGRRGRTEAADAEAEDAYTQGRFRE*
+>NZ_CP040019.1_1052
+MRILYYGLLRVALFFVLWWVGLQLGLGMVMATLAAAILTFAVSYLFLGRLRRGATQDLSA
+AWEGRPGRRGRTEAADAEAEDAYTEGRFRE*
+>NZ_CP083691.1_987
+MRLFLYGLVRVVLFFVIWALCYYVFGLGMLFSTLAAVILTFAVSYLFLTRLRLDASTDLQ
+NAWEGRPSRRGRTEAADAAAEDAYTDGRFPG*
+>NZ_CP097650.1_1671
+MRIFFYGLVRVVVFVALWALFYYVMDLGMIFGVIAATILTFAVSYLFLGRLRAGATEDLS
+AAWEGRPGRRGRTETADADAEDAYTEGRFRE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001468.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001468.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e257e7f0d08aa539892ea44c6c2266c70f0ace4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001468.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1751
+MGRFIIPAAIILAGLTLYALFEALLTPAREVRSLPKAAWVAVIVLVPLVGPLLWLLLGRA
+RPAGAGGRPAPRPTGAPDDDEAFLRSLRVQRRQVAREQDLDRREAELRAREEELRRRREQ
+GDDDADPDGDGPRA*
+>NZ_CP033200.1_1459
+MGRYIIPAAIVLVGLTLYALFEALMTPAHEVRSLPKWGWVAVVVLLPLVGPLLWLVLGRA
+RVARGTARPAPRGPGAPDDDEAFLRSLRVQRRQAEREQELDRRDAELKAREEELRRRRER
+GEEPDADDPDAPTP*
+>NZ_CP040019.1_1051
+MGRYIIPAAIVLVGLTLYALFEALMTPAHEVRSLPKWGWVAVVVLLPLVGPLLWLVLGRA
+RVARGTARPAPRGPGAPDDDEAFLRSLRVQRCQAEREQELDRRDAELKAREEELRRRRER
+GEEPDADDPDAPTP*
+>NZ_CP083691.1_986
+MARILVPTAILLVALTLFALFDALLTPAGRHRGMPKWAWIPTVLLLPLAGPLLWLFLGRP
+VPLFSGRTAAPASRPASPDDDDEFLRTLRVQRAQTERARNLDRREAELRAREEELRRRRE
+RGEDDATGEPDADA*
+>NZ_CP097650.1_1672
+MGRFIIPAAIILAGLTLYALFEALLTPAREVRSLPKAAWVAVIVLVPLVGPLLWLLLGRA
+RPAGAGGRTAPRPSGAPDDDEAFLRSLRVQRRQDAREQDLDRREAELRAREEELRRRREQ
+GDDDADPDGDGPRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001469.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001469.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd13868b311cf26cdc6870d8245fcc5f4500d2ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001469.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1754
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRAVGFFTRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL*
+>NZ_CP033200.1_1462
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFLRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL*
+>NZ_CP040019.1_1049
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLAGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL*
+>NZ_CP083691.1_983
+MQDNRFAEIALDGSLLAAAPVAFLAGLISFLSPCVLPLVPGYLGYVSGLGGAALDGARRG
+RVALGAALFVLGFTVVFMVMNILFAQVAFRILRDLSWVMQLLGVLVILMGVVFMGGLRWF
+QTERKVHVKPAAGLTGAPLLGMTFGLGWAPCIGPTLAAVFALSYTQDSSSVARAALLAFV
+YCLGLGLPFVLISFGVERGMRALGFFRRHRRGVMVFGGAVLILLGAVMVTGLWTQWMVQL
+QTWFQNEWVMPL*
+>NZ_CP097650.1_1675
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001470.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001470.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b1d9f34892a2e08dcf8d333344e0f0c2ca3c715
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001470.fa
@@ -0,0 +1,29 @@
+>NZ_CP042169.1_1757
+MSGTSPTDPHGSQNPYGTDPYGAAPQGPTPGSPDPAGASPYGQNPYGAPPAAPYGAPGQA
+GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFAITQPEGQ
+VAIQQELDRSVEQMNLPADQAEQMRTMMDGMLPALATTAAVFGVLAFLVYLWVAFAIRGG
+SRAARIVGTVLASLSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKTW
+QRFARR*
+>NZ_CP033200.1_1465
+MSGTSPTDPHGSQNPYGTDPYGAAPQGPTPGSPGPAGASPYGQNPYGAPPAAPYGAPGQA
+GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFALTQPEGQ
+AAIQQELDRSVEQMDLPADQAEQMRAMMDGMLPALATTAAVFGVVAFLVYLWVAFAIRGG
+SRAARIVGTVLAALSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKAW
+QRFARR*
+>NZ_CP040019.1_1046
+MSGTSPTDPQRGQNPYGQEAPGPSPYGENPYGAHPYGQAPYGQGGPAQGQPGQGHPNPGH
+PAPSYADQGYPAQGGWPGQQAPGPLTAPRRPGAITASFWLILAGGLVLLASTLLAAFAMT
+LPESRAMLEQQMRETYEQMGLPADQLAQMEQMTDQLLPVMSVVAAAFGVVAFLVYLLIAL
+KIRKGSRAARTVGTVLAALSVLMIVTNLMMGAFNPFDLLWVGLGVAGIVMAFRPEASEYM
+RLKAWERAGTR*
+>NZ_CP083691.1_980
+MSGTENSNPYGRPAGQSGPQWPDAAAQAPYGQAPDASAQAPYGAPPQGWGAPQQWGGQPG
+WPAAAPVPARRPGPINAAFWLIVSAGVVFLASTVLSALVATSDAGRRELEAAMTKVWGDY
+GMTPEQIREYQDMLPPMMPVMAGVMVAVGVLALLVYLLIASKIRGGSRAARTVGTVLAVL
+SVLMVLAPLASGQFSPLDLLWCLLGVAGIATAYRKEATEFMRLRAWERAARR*
+>NZ_CP097650.1_1678
+MSGTSPTDPHGSQNPYGADPYGAVPQGSTPGSPDPAGASPYGQNPYGAPPATPYGAPGQA
+GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFALTQPEGQ
+AAIQQELDRSVEQMDLPADQAEQMRAMMDGMLPALATTAAVFGVLAFLVYLWVAFAIRGG
+SRAARIVGTVLAALSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKAW
+QRFARR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001472.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001472.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce7b577074c83246cb84e0b0560012fcd5087d7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001472.fa
@@ -0,0 +1,10 @@
+>NZ_CP042169.1_1759
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK*
+>NZ_CP033200.1_1467
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK*
+>NZ_CP040019.1_1044
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK*
+>NZ_CP083691.1_978
+MGSVIKKRRKRMAKKKHRKLLRKTRHQRRNKK*
+>NZ_CP097650.1_1680
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001473.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001473.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fd62ed8f07aafef0c16423558edc2ee486ed304
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001473.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1760
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLV
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANEIGGSAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLEAFAPDVLVSQHGCDGHLTDPLADLRLSVDGQRQLAFDVGDWADRFAY
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVRSEIPAAWIEHVRALTADELTGDMS
+VHEGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD*
+>NZ_CP033200.1_1468
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLV
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANEIGGSAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLQAFAPDVLVSQHGCDGHRTDPLADLRLSVDGQRQLAFDVGDWADRFAH
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVKSEIPAAWIEHVRTLTADELTGDMS
+VHEGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD*
+>NZ_CP040019.1_1043
+MSTTSQRPAPTPAAVVWDPSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVSIIEP
+PVATDAQLALVHDPDYIAAVRRASEAASDEDAPFGLGTEDCPVFPDLHEASARIAGGTLA
+AAEAVWSGQVRRAVNFAGGMHHAARAKASGFCIYNDCALAIQRLLDLGAERVVYLDVDAH
+HGDGTQAIFYDDPRVMTISVHETGISLFPGTGFANEIGGPDAQGTAVNVAVPPRTGDAGF
+LRAVHAVVPQLLQGFDPDVIVSQHGCDGHHADPLADLRLSVDGQRQLAFDIGDWAEKFAD
+GRWVATGGGGYNPLRVVPRVWTHLTAAVLQTPIPVKAEIPQSWIEHARTLTAEELTGDMS
+LHEGDESERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRRELFPLHGLDPWFD*
+>NZ_CP083691.1_977
+MTSATSDCSQPAPSAVVWDPSLLKYRFSAQHPMAPLRLDLTHRLASSLGLLDAEHVRILQ
+PPVATDEQLATVHDPAFIAAVRAASREDAEADEPHGLGSEDCPTFPDLHESAARIAGGSL
+VAAEAVWSGEVSRAVNVAGGMHHAARAKASGFCIYNDCAVAIQRLLDLGAERVAYVDVDA
+HHGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANETGGPGAEGTAVNVALPPGTGDAG
+FLRAVHAVVPQLLGAFQPDVLVTQHGADAHRGDPLADLRLSVDGQRQLAFDLGDWADRYA
+HGRWLATGGGGYNHVRVVPRAWTHLIGAVTGQPVPSSTPVPESWLEHVRSLTPDDLEGDM
+SLFEGAEEDRYPLTMTEDADVWWRSWEVGYDPADPVDQTIMATRREVFPIHGLDPWFD*
+>NZ_CP097650.1_1681
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLA
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSVFYDDPRVLTISLHETGISLFPGTGFANEIGGAAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLEAFAPDVLVSQHGCDGHRTDPLADLRLTVDGQRQLAFDVGDWADRFAH
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVKSEIPAAWIEHVRALTADELTGDMS
+VHVGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001476.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a448a00c746783fc97f3ca6fc1467c83205479b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001476.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1763
+MKLTILGLGTMTGAILAGALDAGAVRAEDVTATTRSAASAEKAAAQHGVTVTSQERDERA
+NHAAVAEADIVLVGVKPKDMVATLTDLASSLRPETVVVSVAAGVTAATMAAVLPAGQPIV
+RTMPNTPLTVGSGVVGVAPGPGVTEEQATAVRALFEGSGLVVPVAEEQLSAVVATAGSAP
+AYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQQEGARAGALRKAVMSPNGTT
+EKAVEAFLDGGMGDLVNRAMDAAAQRDREMAEEFGA*
+>NZ_CP033200.1_1471
+MKLTILGLGTMTGAILAGALEAGAVRAEDVTATTRSAASAEKAAAQHGVTVTSQERDERA
+NHAAVAEADIVLVGVKPKGMVATLTDLAPSLRPETVVVSVAAGVTAATMAAVLPAGQPIV
+RTMPNTPLTVGSGVVGVAPGPGVTEEQTTAVRALFEGSGLVVPVAEEQLSAVVATAGSAP
+AYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQQEGARAEALRKAVMSPNGTT
+EKAVEAFLDGGMGDLVNRAMDAAAQRDKEMAEEFGA*
+>NZ_CP040019.1_1036
+MKLTILGLGTMTGAILTGAIEAGAVRAEDVRATTRSAASAERARGRHPGVEVLAAEEDAH
+ANKRAVEGADVVLLGVKPKDIAATAAEVAQALGTDTTVVSVAAGVRAETIAAALREGQPL
+VRTMPNTPLTVGSGVVGVAPARGVTDAQTQAVEALFAGSGLVVRVAEEQLAAVVAAAGSA
+PAYVFLLAESIAKHAEQLGLDRANAEAMAAATVKGAGLMLQNGIREGDQTAEDLRRGVMS
+PGGTTEQAIRTFQEGGFERLVADAMDAAARRDEEMGRELAG*
+>NZ_CP083691.1_973
+MTAQPRIAILGLGSMTGAILTGLLAASVTTPERVVATTRTAASAQAKGNRFPGVRVLSGE
+QDVDANLTAVAEADVVLLGVKPKDIVVTARQIAPALRPEAVVVSVAAGVRAETLAGALPE
+GQPLVRTMPNTPLTVGSGVVGVAPAAGVTADQRALVESLFSGSGVVVPVSEEQLPAVVAA
+SGSAPAYVFLLAEAIAAHAVELGLSAEAAEAMAAATVKGAGAMLVDAVTSGEQTAEGLRR
+AVMSPNGTTERAIAAFEDGGFAGLVADAMDAAARRDEEMGREFGA*
+>NZ_CP097650.1_1684
+MKLTILGLGTMTGAILAGALDAGAVRAEDVTATTRSAASAEKAAAQHGVTVTSQERDERA
+NHAAVAEADIVLVGVKPKDMVATLTDLAPSLRPETVVVSVAAGVTAATMAAVLPAGQPIV
+RTMPNTPLTVGSGVVGVAPGPGVTEEQATAVRALFEGSGLVVPVAEEQLSAVVATAGSAP
+AYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQQEGARAEALRKAVMSPNGTT
+EKAVEAFLDGGMGDLVNRAMDAAAQRDKEMAEEFGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001477.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001477.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9ae65c131a64d1408f875dfb0dcc53e3196f036
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001477.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_1764
+MADATAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGREAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGNDSGKDDHLVPGEGTQRVAETLRHLAAEGLAGA
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTDHHDDDGVPRPTTKETDRP*
+>NZ_CP033200.1_1472
+MPDSTAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGRKAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGDDSGKDDHLVPGEGTQPVAETLRHLATAGLAGT
+VCVEVGTRGVEYAGQREEMLAASLAFAREHLAAGGTDHHHDGGVLRPTTKEMDRP*
+>NZ_CP040019.1_1035
+MAGSTAHLAPAPRFGSDIPVTLSSSSVFPLGTQDVFATAQDLGYDGVEVMVTHNAWSQDA
+DRLKRLSARHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAPVVVAHPPFRWQ
+GTYASGFAEGIHEIMADTGVVIAVENMYPWRAHGREATMYLPHWDPMPEPYEHVCWDFSH
+AAIAREDSLEALRRLGSRVRHIHLTDGNDSGKDDHLVPGEGTQKVAESVRHLAADGFAGT
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTKDDDGAPGA*
+>NZ_CP083691.1_972
+MTGPSGAGSRPWDPHGRHLEPPLVSTAHLAPAPRFGAEIPVTLSSSSVFPLGTQDVFATA
+ADLGYDGVEVMVTHNATSQDARALARLSERTGMRIDSIHAPTLLFTQQVWGSAWSKIVRS
+VELARAVGAVTVVAHPPFRWQGSYASQFARRTAEIMEATGVVIAVENMYPWRAHGRDLTM
+YLPHWDPVPEPYEHVTWDFSHAAIAREDSLANIRGLGGRLRHVHLTDGVDGTKDAHLVPG
+EGTQNVAESLRFLGREGLAGTVCVEVGTRGVEYAGQREEKLSASLAFAREHLGQNDQSGR
+HES*
+>NZ_CP097650.1_1685
+MPDSTAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGREAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGNDSGKDDHLVPGEGTQRVAETLRHLAAEGLAGA
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTDHHDDDGVPRPTTKETDRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001483.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001483.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5b7e63ab64c9395c7afa86c3fe9c86dc333d307
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001483.fa
@@ -0,0 +1,79 @@
+>NZ_CP042169.1_1770
+MTGHLPEHDPWADPAGGWGPPGTADAAPPVDDAAPDSSGPEPQPVGEVVADVVAGLSVTA
+PGDLCPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV
+ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA
+ADQLTSWRALERDGAPGLRSAPYDGDTAPQDRIWAREHASVLMTNPDMLHVGILPHHERW
+ATFFRNLAFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA
+GHFARLIGAPAAAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA
+LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG
+RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL
+DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL
+DVLVDQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ
+AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEVEIVAVHRRLDAREGT
+LRWCLGDVQVRTQVVSFQRKALASGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT
+TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE
+RGFEQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH
+LVPADASTDGSGGGASGGSSGGATDAAPGA*
+>NZ_CP033200.1_1478
+MTGHLPEHDPWADPAGGWGPPGTADSAPPVDDAAPDFSGPEPQPVGAVLADVVAGLSVTA
+PGDLRPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV
+ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA
+ADQLTSWRALERDGAPGLRAAPYDGDTAPQDRIWAREHATVLMTNPDMLHVGILPHHERW
+AAFFRNLTFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA
+GHFARLIGAPATAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA
+LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG
+RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL
+DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL
+DVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ
+AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEIEIVAVHRRLDAREGT
+LRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT
+TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE
+RGFEQARRWVEATAGAIAACECTEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH
+LVPADASTDGSGGGASGGSADPAPGA*
+>NZ_CP040019.1_1028
+MSTPPPEPAAAGVAFDPWADPAAGWGAPDDGPSDRRDAPADVDETDHPGDEAHPWDEPAP
+LADAVADVVAGLSVSRPGDPVAGGEAADVLRGALGRHGLPEQIRHVVTLPAREARHADWP
+SEAPEALVGAFAGRGIERPWAHQVRAATVAGAGTHTVVATGTASGKSLAYQLAAGIRLSG
+DPHATVLHLSPTKALAADQLLAWRALERDGATWLRAAPYDGDTAPPDRIWAREHANVLMT
+NPDMLHVGILPHHERWARFFRHLAFVVVDESHSYRGVFGSQVGILLRRLRRVAAHWRGDR
+PEPVFIGASATSADPAGHFSRLIGAPATAVAEDASPHGAVTVAFWEPELTDRRGENGAPV
+RRSAMAASADLLTDLALQQVRTLAFIRSRRGAEAIASAARRQLEELEAGLGSRIAAYRSG
+YLPEERRALEADLRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGR
+GGQDALAFFVASDDPLDTYVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPLTP
+EAFERFGDPERVRALLDVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAE
+SGTLLGTMDSPQTHYQAHPGAVYVHQDRTYLVEELDEDAHAVIVTRAWPDFTTQARDVTE
+IEIVDVHRRLDAREGTLRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLELPARDLFTSA
+VWFQASSEELIAAGLTMDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSP
+AVFVYDGRPGGAGFAERGFAQARRWVEATAGAIAACECEAGCPSCVQSPKCGNRNSPLDK
+AGALTVLRFLLGQADHLVPVVAEGSGETDGGTDDGVGVDGEDASGSGSSGTA*
+>NZ_CP083691.1_966
+MTGGPVPWPDDDPWAARGPAEDRSARDVPTPAPGGPGWEPPQELATGDPEARAAFAAALG
+RRSLPAQIRHVTTIPARTPRSAPWPAGTPAGLVRAFAARGVQAPWEHQARGTAAALAGRH
+TVLATGTASGKSLAYQLAVGATLAADPRATVLYLAPTKALAADQLASWRALERDGAAWLR
+AAPYDGDTAPQDRIWAREHANVLLTNPDMLHVGILPHHERWAVFFRNLAYVVLDESHTYR
+GVFGSQVGILLRRLRRVVAHYRGERPETVFIGASATSAAPAEHLATLIGAAPGEVEAVTE
+DASPHGAVHVAFWEPELTDRRGENGAPVRRSATATAADLLTDLALQQVRTLAFIKSRRGA
+ETIAGAAKRQLEEVEAGLGSRIAAYRSGYLPEERRALEEALRSGRLLGMASTPALEMGID
+VAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPLDTFVVEHPGAVFDLGV
+EDTVLDPANPHLLGPQLCAAAAELPLRPEDLPWFGGPERVRELLDVLVEQGLLRRRPAGW
+FWTHTEHAASLVSLRDDGGGPMDIIDVESGALLGTMDSPQTHYQAHPGAVYVHQDRTFLV
+EDLDEDAHAVLVQRAWPDFTTQARDVTEIEIVAVHRRLDAAGSSLRWCLGDVQVTTQVIS
+FQRKALLSGEVLGEEPLDLPARDLFTSAVWFQAASEELVAAGLTMDRLPGALHAAEHAMI
+GMMPLVASNDRWDIGGVSMVLHPDTGVPTVFVYDGRPGGAGFAERGFAQARRWVEATAGA
+IAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLAERFDGLIEVPAHLPDVTA*
+>NZ_CP097650.1_1691
+MTGHLPEHDPWADPAGGWGPPGTADAAPPVDDAAPDSSGPEPQPVGEVVADVVAGLSVTA
+PGDLRPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV
+ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA
+ADQLTSWRALERDGAPGLRSAPYDGDTAPQDRVWAREHASVLMTNPDMLHVGILPHHERW
+AAFFRNLAFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA
+GHFARLIGAPARAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA
+LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG
+RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL
+DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL
+DVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ
+AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEIEIVAVHRRLDARAGT
+LRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT
+TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE
+RGFEQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH
+LVPADASSDGSGGASGGATDAAPGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001485.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001485.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e631d7c26bf76509ebebe300dbe6829531899431
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001485.fa
@@ -0,0 +1,19 @@
+>NZ_CP042169.1_1772
+MTEHPTSASPSGRRTGARTAGRPRALRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV
+QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTVEGGWVTVEVVQPGPGPL
+AWAEVLTLTAHAAAPDQRPGTPAAGPEDRS*
+>NZ_CP033200.1_1480
+MTEHPTSAPPSARRTGARTAGRPRGLRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV
+QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTVEGGWVTVEVVQPGPGPL
+AWAEALTLTAHAAAPEQRPGTPAAGPEDRS*
+>NZ_CP040019.1_1026
+MTAEYAVLLPVIAFVLAAVLLAGAAAVQQVRGQDAATAAARILARGDGEAEARRAVARMA
+GDDAALAHTADGGWVAVEVSQPGPGPLAWAEALTLTARAAAPQQHPGAAVDPDGGRT*
+>NZ_CP083691.1_964
+MADLPAEAPRPGRLRGARAGASGTVAFRDAERGEGERGAVTAEYAVLLPAAVAVLVAVLL
+AGVAAVHQVRAQDAAASAARILARGDAESLARDAVGRMAGGDAALEARTAEGWVTVTVTR
+PGPGPLAAVTLSAEAVAPVQATSPTPPGRTPGITAPTGEAAP*
+>NZ_CP097650.1_1693
+MTEHPTSASPSGRRTGARTAGWPRALRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV
+QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTIKGGWVTVEVVQPGPGPL
+AWAEALTLTAHAAAPDQRPGTPAAGPEDRS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001489.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001489.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7171e84445dfbfc9718f1dcb5293b837632d7c6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001489.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1776
+MPETPASPRPTSRDAVGTSDASLAGARDQLADLVARWGAAPADAPGHHDPVSLTTVPPEA
+VPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAERVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLGLLGWDVPWDDSRVRDARTHEILRD*
+>NZ_CP033200.1_1484
+MPETPASPHPTSRDAAGTSDASLAGAREQLADLVARWGAPPAEAPGHHDPASLTTVPPEA
+VPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAGRVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLALLGWDVPWDDSRVRDARTHRILRD*
+>NZ_CP040019.1_1022
+MAAVRDRLAALVERHGVPADQAPRDALTEIPASAVSTWGFDWPRAQRARPSAVLILFGSL
+DDVPAHHADDRVHPDVDVLLTQRAATLRTHAGQIAFPGGRVDPEDADVVATALREAEEET
+DLDPDGVEVLGVLPPVPVVVSGHVVHPVIGWWRDPSRVAVVDQAEAAAVFRMPVGDLVDP
+ANRCRVARPGGRRGETPGFLVGERLVWGFTAALLDRILTLLDWDTPWDSGRVIDAHTHAP
+LRG*
+>NZ_CP083691.1_960
+MSIPPLPPSSPSSARADLQRIVAEHGVAPVAGDDEAGLTTIPASSVRVWGFDWPQAARPR
+ASAVLILVGELDDVPAAHDGRACGVSPAVDVLLTQRAAGLRTHAGQVAFPGGGVEAQDAD
+VVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGYVVHPVIGWWRDPSRVAVVDHNEAT
+AVFRVPVADLAAPANRVRVRRPGGRRGETPGFLAGDRLVWGFTAALLSRVLELAGWDEPW
+AGAPLIDAGSRAVLEG*
+>NZ_CP097650.1_1697
+MPETPASPRPTSRDAAGTSEASLTGARDQLADLVARWGTAPADAPGHHDPASLTTIPPEA
+VPMWGFEWPRSGDPRPSAVLILFGALDDVPARHDAERVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDADVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLALLGWDVPWDDSRVRDARTHEILRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001494.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1b3effef56052ce71194e487b78bac05e96949a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001494.fa
@@ -0,0 +1,54 @@
+>NZ_CP042169.1_1782
+MSSTVSAPATAPKRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGDDPETFLMGDYLQVADDPSPSFDVVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPV
+ATTRKEL*
+>NZ_CP033200.1_1490
+MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPT
+AATRKEL*
+>NZ_CP040019.1_1015
+MSSTVSAPAAAPTRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTESVGWWQVLICVVIAVYYAAIIGWA
+IMYTWFSVDQRWGADPETFMMGEFLQVSETPNPTFDVVSGVFWPMLAVWVITLLIMGFGV
+RRGVAMASMIGIPLLVVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLKKRTNLTSSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VADVAGSGIGLAFIAFPTLISQAPVGALIGVLFFGSLVLAGFTSLISILEVVISAVKDKL
+GWGRWTATIIVVGLAGVVSMALFSTTSGLHMLDTMDAFANNFGIVGAALVSVLLVTGVLG
+SARRVTAHLNAVSSFKLGRGYVLLIGVLMPIVLAYIWLSWIMKVISEGYGGYPGDFLGVY
+GWGVAIGSVVLAVVLSLIPWSRKSNLYAEEMETEIHGDLIPHNAVPEGTTPTGAIPLVPA
+DHTRKEL*
+>NZ_CP083691.1_955
+MSTSTGATAAPSRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYEHGGGAFVIPYLVA
+LLTAGIPLLFLDYAIGHRFRGSAPMAFRRMSRWTEAIGWWQVLICAVIGVYYAAIIAWSI
+MYTWFSLDQRWGDDPEGFLFSTYLQQVKDPNPSFDIVPGVFWPMVAVWGVLLLIMGLGIR
+RGVALASMIGIPLLVVMFVVLVIISLTLPGAMQGLDALFTPNWAALKEPGVWIAAYGQIF
+FSLSVGFGIMITYASYLKKRTNLTASGLVVGFSNSGFEILAGIGVFSALGFMAQASGVQV
+SEVAGSGIGLAFIAFPTLITQAPAGALIGVLFFASLVIAGFTSLISILEVVVSAVKDKLG
+WGRWTAVLVVVGISAVISISLFSTTTGVAMLDTMDAFANNFGIVGAALVAVIAVMWIARR
+GGELVAHLNSVSSFRVGRVYRILVGVVMPVLLGWMWIEWIRENAATPYGGYPTDFLAVYG
+WGLAIGSVVLAVLLSLIPWSHKSSLHAEESVNEIDHTAPVASKES*
+>NZ_CP097650.1_1703
+MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPA
+ATTRKEL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001499.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001499.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf8759d2f5fc262c69a82359e431851e70893280
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001499.fa
@@ -0,0 +1,70 @@
+>NZ_CP042169.1_1788
+MASRTTRFPAPSSALGRLLAFVGLSAVAGLLVAALLLPVAGLAGVAAASGREMLDELPDE
+LPTEPVSVPSRILSEDGEEIAVFYEENRTPVPLDEISEHMQHAIVAIEDERFYDHDGVDA
+RGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGSKNIADKVKEIKL
+AVAVEKQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQSP
+TRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGT
+YFCDYVERQILADPTFGPDVQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESL
+GAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFNVDKQWGGGQGFQAGSTLKPFV
+ALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGGTWQFKNVIPGMLRQVRVD
+EGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSL
+AGAYAAIAANGLYCEPRAILEVTDTVGNQYDVADPQCDQVIDPDHVRELMPVLRHIAGFN
+IAEEGAGYEFGGKTGTNDNVSSTWFVGFTSELATAVWTGRYNNLKSMTGETVNGEVRNPF
+YSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFHIDDLDRGGPL
+PEAVPGF*
+>NZ_CP033200.1_1496
+MASRTTRFPAPSSAPGRLLAFVGLSALAGLLVAALLLPVAGLAGVAAASGREMLDELPDE
+LPAEPVSVPSRILSEDGEEIAVFYEENRTPVPLDKISKHMQHAIVAIEDERFYDHDGVDA
+RGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGSKNIADKVKEIKL
+AVAVEKQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQSP
+TRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGT
+YFCDYVERQILADPTFGPDVQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESL
+GAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFNVDKQWGGGQGFQAGSTLKPFV
+ALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGGTWQFKNVIPGMLRQVRVD
+EGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSL
+AGAYAAIAANGLYCEPRAILEVTDTVGNQYDVADPQCDQVIDPDHVRELMPVLRHIAGFN
+IAEEGAGYEFGGKTGTNDNVSSTWFVGFTSKLATAVWTGRYNNLKSMTGETVNGEVRNPF
+YSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFHIDDLDRGGPL
+PEAVPGF*
+>NZ_CP040019.1_1009
+MASRTSRRLPEPSSALGRLLAFLGLSALAGLLVAALLLPLAGLTGVAAASGREMLDELPD
+ELPAEPVSVPSRMISEDGEEIAVFYEEDRIPVPLDQISEHMRNAIVAVEDERFYEHDGVD
+ARGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGTKNVSDKVKEIK
+LAVAVEEQMTKDEILEGYLNIVLFSGRAYGVEAASRYVFGKSAAELESWEAATLAGMVQS
+PTRFNPARNPEEATERRNLVLGAMKKNGYLTEEEHAEAVAQPMEVVMESRPSGCLYSKFG
+SYFCDYVERQILADPAFGPDPQSRQALLDRGGLTIRTTIDSELQKAAEENLRKSVPNNES
+LGAGHALTSVQAGTGNIVTMAQNTEYAIQDELGHTSLNFNVDREWGGGQGFQAGSTLKPF
+VALTWLRNGNRMVDSVDASRNVYPTGTRFEASCRPGGYTTIGGTWQFKNVIPGMLRQVRV
+DEGLFWSVNTPTVATAYQMDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSIAPLS
+LAGAYAAIAADGLYCEPRAILEVTDTVGNQYDVAGPQCDQVVDPKHIAELMPVLRHIGAF
+NIAEEGAGYEFGGKTGTNDNVSSTWFTGFTTELATAVWTGRYNNMKSMTGETVNGEVRNP
+FYSTSINGPSWLEYNQLAKEKYPPGELPDWDGPQSEDPGAEGEHPDGTAFRIDDLDRGGP
+QPQAVPGN*
+>NZ_CP083691.1_949
+MASRSSRLPARSSALGRLLSFLGLSALAGLLVAGLMMPAAGATGIVFASGRDMLDELPDQ
+LPAEPVSMPSKIYSADGELIATFFQENRQPVPLDQISPYMRNAIVAIEDERFYQHDGVDA
+KGLVRAMVNNVSSSSTQGASTLTQQFVNNMLINSQQVRGDSRLTLSGTKQASDKVKEIKL
+AVAVEKQMSKDQILEGYLNLVLFQGRAYGIEAASQYVFGKPAKDLELWEAATLAGMVQSP
+TRFNPARNPEGTTARRNTVLKAMLKNGYISQEEHDHAVAQPLTYTMKGQSTGCLSAAFGA
+YFCDYVERQILADPTFGPDTASRQALLDRGGLTIRTTIDSNLQKKAEELTRRVIPNNESL
+GAGHSLISLRPGSGDIVTMAQNTEYSIQDELGKTTLNLNVDAKWGGGTGFAAGSTFKPFI
+GLTWLRNGGKLIDSVDGSKDRYPPDARFQASCLPGGYTTAGGGTQGWQLNNVIDGMKKRD
+RIDEGIFWSVNTPTVALAYQMDLCDIVNTLTQVGIVTARDGAPLSPAEPSFVLGKDDVSP
+MTMAGAYATLAANGKYCKPRAITEVTDTTGNQYTVPAPECRQVLDPAQVAEVTPLLRHIA
+AHNIAPDGTGYEFAGKTGTNNNMSSTWFIGYTTELATAVWAGRYTSQKTMRGETINGVVQ
+KEFYGATVNGGTWLEWNDMAKRTFVPGELPEFDGPQSEDPALEGDHPDGRFYRPEDIDRN
+GGTPTSSLGPAAGETAFSSAENAAKFESGVLTR*
+>NZ_CP097650.1_1709
+MASRTTRFPAPSSALGRLLAFVGLSAVAGLLVAALLLPVAGLAGVAAASGREMLDELPDE
+LPTEPVSVPSRILSEDGEEIAVFYEENRTPVPLDEISEHMQHAIVAIEDERFYDHDGVDA
+RGLIRAAVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGSKNIADKVKEIKL
+AVAVEEQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQSP
+TRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGA
+YFCDYVERQILADPTFGPDVQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESL
+GAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFNVDKQWGGGQGFQAGSTLKPFV
+ALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGGTWQFKNVIPNMLRQVRVD
+EGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSL
+AGAYAAIAANGLYCEPRAILEVTDTAGNQYDVADPQCDQVIDPDHVRELMPVLRHIGGFN
+IAEEGAGYEFGGKTGTNDNVSSTWFVGFTSKLATAVWTGRYNNLKSMTGETVNGEVRNPF
+YSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFTIDDLDRGGPQ
+PQAVPGF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001501.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001501.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abe3691c4742abba704f8b097f6678481141bb6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001501.fa
@@ -0,0 +1,61 @@
+>NZ_CP042169.1_1790
+MTRATSPDASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEETVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA*
+>NZ_CP033200.1_1498
+MTRATSPDASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEETVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA*
+>NZ_CP040019.1_1007
+MTRTATRPLPLREALQVVAPYLQGVRGRWVLGLLSAMAAGLVALAIPQVVQVLVNTVFAE
+AAPGTAGTADPAAGVWWAAGALALFGLAEALFIWLRRFFILPPAADVENRARISIYRRLQ
+RLPVAFHDAWASGQLLSRAQGDLALLRRWIAFGSVMLVVETVTIVVGLVLLFVMSWQLAL
+LYLVAAVPIMIRSFRFRTDFRAASRLSQDQAGDLATTVEESVHGIRVLKAFGRGPDALDG
+FRGEAETLQGTEVHKASVLAKFISLTVSLPELVLGVALGLGLYLVAVGDLTVGALAAYFA
+TTAVLARPVEGVGQLMGMTLSAKTAIDRHLEVMRVPVAVASPAGTDAAEEEATSRAVASS
+AAEDSPVVTDGLPPSSGRLAFRDVVFRYPDAPEDSRPLLAGVDLELTPGETMALVGVTGS
+GKSTLVQLVPRLLDVTAGVVEVDGTDVRAYPLDELRRRVSIAFEDATLFSDTVRANVLLG
+APAEVTADGLDSPRAQALLDLALDTAQAGFARDLPAGVDTEIGEEGLSLSGGQRQRIALA
+RAIAARPDVLVLDDPLSALDVRTEEAVTGRLREVLAGTTTLIVAHRPSTVALADRVAVLQ
+DGAIHDVGTHAELLARSAAYREIITTGAAEDRSLAGLADAAHDDAALAAATDAARPPAGA
+ARPPAGRTAGREETR*
+>NZ_CP083691.1_947
+MTRTTTAAAPLPLRDAVRGIAPYLEGVRTRWVLGLLSALAAGLVALAIPQVIRLLVNTVF
+AAPTTPGAPAAEDATASVWWAVGGLALLGAAEALFIWLRRFFILPPAADVENRARIAVYR
+RLQRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVETVTLVVGVGLLFWLSWP
+LALVYLAAALPIMWRSYGFRNDFRTASRLSQDQAGDLATTVEESVHGIRVLKAFGRGPHA
+LEGFRGEAQTLQGTEVHKAGVLASFIAFTVSLAEVMLGVALALGVWLVATGQMTVGALAA
+YFATTAVLARPVEGIGQLLGMTLSAKTAIDRHLEVMRQPVSIASPPGTDPAEEAATGASV
+GEDPDPAVADAPVDVSALPPSRGGLAFRGARFRHPDTPDDAPDLLAGVDLELVPGETMAL
+VGLTGSGKSTLLQLVPRLRDVTGGVVEVDGVDVRDYPLEELRRRVSIAFEDATLFSDTVR
+ANVLLGAPAAEVADGPDSPAAEALLELALDTAQAGFVADLPQGVDTPIGEEGLSLSGGQR
+QRLALARAIAARPDVLVLDDPLSALDVRTEEAVTARLREVLAGTTTLIVAHRPSTVALAD
+RVAVLQDGRIADVGTHADLLARSGAYRQIITTDREDAR*
+>NZ_CP097650.1_1711
+MTRATSPAASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEEAVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001510.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001510.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cee4ae635a886d2f95a19941f119e107920aa1e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001510.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1803
+MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG
+IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA
+DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE
+TALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRL
+ALEQPVEADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVESTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA
+DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRTPL*
+>NZ_CP033200.1_1510
+MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG
+IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA
+DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE
+TALELLPKIRGAYCFVFMDERTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDAAIAGRSVYESRVEMGRRL
+ALEQPVDADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFATRAELIANGAAVDQIAASIGADSLAYISEKGMIEATGQPRERLCTACFTGDYPIPLA
+DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRIPL*
+>NZ_CP040019.1_990
+MIASRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG
+IAASDGKRIGVYKDIGLVSQVFDESTLATFTGHIAVGHCRYSTTGANKWANAQPTLGATA
+GGDTVALAHNGNLVNSGELLRMVQARDGLQLRGEMKQGNTTDTALVTALLHGEEGRKLEE
+TALELLPKVRGAYCFVFMDEHTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDASIAGRSVYESRVDMGRRL
+ALEGPVDADVVIPVPESGTPAAVGYAEASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFASRAELIANGAGVAEIASSIGADSLGYISEEAMIAATGQPRERLCTACFTGTYPIELA
+DESERGKSVLETDAGSAAVTVMAPDGDATTVASTGCEPGPDADDEKLLTETDRTPL*
+>NZ_CP083691.1_933
+MISARTRRGDGRLTAALDPQEAGPQDECGVFGVWAPGEEVAKLTYYGLYALQHRGQESAG
+IAASDGKRIAVYKDMGLVSQVFDEPTLAALTGHVAVGHCRYSTTGVNKWANAQPTLGATA
+DDGTVALAHNGNLVNSAELLRMVESKEGAHTLGEIKQGNTTDTALVTALLHGEKGVSVEE
+TALELLPKVRGAYCFVFMTERTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDAAINGRSVYESRVEMGRRL
+AQEHPVDADVVIPVPESGTPAAVGYADASGIPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFATRAELIANGAGVQEIASSIGADSLAYISEEGMIAATEQPRERLCTACFTGTYPIELA
+DEKERGKAVLENGTPTAEATDVVSEDGTVTTVASTGCEPGPDSEDEKLLTQTDRTPL*
+>NZ_CP097650.1_1723
+MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG
+IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA
+DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE
+TALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRL
+ALEQPVDADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA
+DEGERGKGLLEPVAVSPASTVVLDVDGETTTVTATGCEPGPDADDEKLLTETDRTPL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001530.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001530.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fffd2e3c15241aaf47b443dd793afd5c1484e6db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001530.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_1827
+MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYRGWDGLAAAVDDDGPYP
+GVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL
+ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLILRLPSA*
+>NZ_CP033200.1_1534
+MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYRGWDGLAAAVDDDGPYP
+GVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL
+ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLILRLPSA*
+>NZ_CP040019.1_961
+MSGPGPGRPVLIGVDGRSGAGKTVLADALAARLAPFARVAVLRIESMYPGWDGLAAAVDE
+GGPYPAALRALHADGTAAWRAWDWHRGAPGEPTAIGPADVVVCEGVGALSVAARPLLDLA
+VWLELETPARRSRALARDGETYAPHWERWAAHEEAYLARHGPRAAADLVVRLPSA*
+>NZ_CP083691.1_900
+MNASTEPGTARPGGPVSAPRPALIGLDGRSGAGKTTLAAALAARLAPHARVDVLHIEEMY
+PGWDGLAAATADDGPYVRAVAALAAGRPAGWRAWDWHAGAPGEARALDPDALDVVVCEGV
+GALCPGARPLLDLAVWVDAPEDVRRTAALARDGDAYAPHWERWARQEEAYLAAADPAGAA
+DLRLST*
+>NZ_CP097650.1_1747
+MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYQGWDGLAAAVGDDGPYP
+AVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL
+ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLVLRLPSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001531.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001531.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62c94a73549d7f8f0cd59154d1e1c34af81e70ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001531.fa
@@ -0,0 +1,99 @@
+>NZ_CP042169.1_1828
+MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK
+EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVNPFEAQAQQDDA
+RTRLDEGRTELADGEQRLADGRQEIEDGRAELERRTAEADAAEQRLAEAAAQLEEGQAKL
+DAARADLEERGLDALPAEALAPLREAEQQVAEGQEQLDAGRAELEEQAERLEAGQAKLDA
+QRQELEAAQAELDARWAELEAGQAELDARAEQLAAGRAELEQARDAALAEAEAAGIPAEQ
+VTEQFADQEAQLAAAEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR
+LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED
+GRAQLAAGAERLDQAEADLADGRAELEDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV
+TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATAPSLLGPGEVVGLVVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRQELRRGTGLHESIALANGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP
+AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRDLRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERAHAPAQ
+PSVPAPDGGAHRA*
+>NZ_CP033200.1_1535
+MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK
+EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVNPFEAQAQQDDA
+RTRLDEGRTELADGEQRLADGRQEIEDGRAELERRTAEADAAEQRLAEAAAQLEEGQAKL
+DAARADLEERGLDALPAEALAPLREAEQQVAEGQEQLDAGRAELEEQAERLEAGQAKLDA
+QRQELEAAQAELDARWAELEAGQAELDARAEQLAAGRAELEQARDAALAEAEAAGIPAEQ
+VTEQFADQEAQLAAAEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR
+LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED
+GRAQLAAGAERLDQAEADLADGRAELEDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV
+TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATVSSLLGPGEVVGLVVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRHELRRGTSLHESIALATGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP
+AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRELRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERGHAPAA
+EAASAPAPEAGRTPAVDGGAHRA*
+>NZ_CP040019.1_959
+MAKLLYRLGLGAARRPLTVILAWVLALALAVGGFLAFGGTLSTNVTIPGTPTAQVTDRLQ
+DEFPEASRGMGQVVFTTEDGQPFTDAQRDAVAALLDEVAGQDAVDAVVDPFEVQAQQDDA
+RTALADGRQEIADGEQALVDGREQVDAGRAEIEEGRAQADAGEQELADAAAQLEDGQVQL
+DAARADIEARGLDALPAEALAPLREAEQQIADGQAELDAGRAEIEEQAARLAAGQAEIDA
+NREQLEAGQAELDARWGELDAAQAQLDAQREELEAGRAQLEQALAAALEQAEAAGIPAEQ
+VTAQFAEQQAQLEAGQAQLDAAQEQADAGREQLVAAQAEADAGAEQLAEAQAQADAGAEQ
+LAAGREQLEAAEAELESGREQLAAGRQQALDAAAAELDAQQARIDEGRAQHEQGVADLEA
+GRAELAAGAERLDQAEADLATGRTELEDGRVAAERGERSLALVGGYRSVSEDGSTAVGIV
+SFSQPSLDVTAEEKEAVTGALTGADIDGVAVHPSQELNATVPSILGPGEVVGLIVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSVVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRQELKRGTALHEAIALANGTSGNAVVFAGITVIIALVALNVTGIGFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGTRILSRKERARLADEGPASAAEGSAAVRRAGRRSTMSTP
+AAIASALAAIALLVLVALPFGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRELRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSVFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPI
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERGHAPAA
+EAASAPAPEAGRTPAVDGGAHRA*
+>NZ_CP083691.1_896
+MATLLHRLGLASARRPWAAILAWLIALALAVGAFLAFSGTLTTAVTIPGTPTAQVTDRLK
+EQFPDAAKGTGQVVFATEDGSAFTEAQRRAVSDALRGVEGQDAVDSVVDPFDVARQQDEA
+RTALEDGRRQIAEGEQKIAENEKALEDGRAQLAEAKDKAEAGQKELDAAAAQLDAGQEKL
+DAARADLEARGLDALPAEATAPLTEAQQKLDAGQAEYDAGVAALEEQRPALEAAEAEIAK
+QEAALEQAQARFEAGRAQAIAQAEAAGATPEQAAAAVDARLAPEREKLDAGAAQLEEARA
+RTEAGRAEFDAGEEKLAAAAAELEQGRAQLAAGREKALTAARAELDAQQQKIDAGRAEHE
+QGVRELEAGRAEIAQNEAKLADGPAQLEQARKDLAAGREKADRGQRMLTLTDGYRVVSED
+GSAALGTVAFDRPSLDVTTEQKTAVIDALADADIPGVRAIPTQALNATMPSLIGPGEVVG
+LAVAALVLVLMLGTLVGAGLPLVNALIGVGVGAAGALAFSGVVEMMSVTPVLGIMLGLAV
+GIDYALFIVNRHRLELKRGTPLHASIALANGTSGNAVVFAGITVVIALVALNVTGIPFLG
+LMGTVGAVCVAVAVLVAVTLTPALLSLAGMRILSRKERARRAAEAAPVADDAAAPSGSHA
+AAPVSRSAARAVRDARRRRRMSTPAAVATVLASAAALIVVAIPFGSMRLGLPDGASEPVG
+SDSQVSYELIADEFGEGYNGPLVVTVDLPSGLDETTAEDAQVQVGEQLKGLEHVAAVVPA
+GFNQDRTTAMFQVLPEEGPNAISTGDLVHTLRDTEPAGEASNLGVAGVTSGFIDVSEKLS
+AALPLYLGVVVGLSLLIMILVFRSILVPLIATGGFVLSVFAAMGGVVAIYQWGWLGGLFN
+VHAPGPVLSFLPTIMIGVLFGLAMDYQLFIASGMREAYAHGQPARDAVMTGLRAGRAVVT
+AAAIIMISVLGGFVFSHDAMIRPIGFGLAFGVLLDAFVVRLLLMPALMHLLGDAAWWLPK
+WLDRILPDVDVEGAGLERHGAAGEAADAAPVGADRA*
+>NZ_CP097650.1_1748
+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_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001532.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001532.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d5f87c5900a6633681fd3a8e45d1fc1cb62a258
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001532.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1829
+MPAPGPDRPGAGVYPGRMRPTAFSPAAGSPVLVLLETDADGAPAPRLADPAVPHLSVTDQ
+GVTRGDGIFETALAVADGLGTLRMRKLGAHLGRLAASAAALQLAAPEAAAWEAAVALGLR
+AFTEANDVAPGDRLAVRLTVTRGPDAAPGAVPTPTAWALLSPAPAIQDEERQRGLRVLLL
+DRGIDSQAPERSPWLLTGAKTLSYAVNMAALRYARAHGADDVVFTSADGYLLEGPTSTVL
+IVRTGEDGVRRLLTPLRQKGILAGTSQAVIFAAAHADGWELGYGPLVPADLQGAEGVWLV
+SSVRGVLPVRAVDGVEIPVDHELTGMLQAHLDADGDPGRHVSGDPVPTAG*
+>NZ_CP033200.1_1536
+MSPTPFSPSPGEPVLVLLEAGADGARLPRVADPAVPHLRVSDQGVTRGDGLFETALAVAD
+EAGVLRMRKLGAHLGRLASSAAALQLPAPSAAAWEAAVERGLQAFAAANDVAAGDRLSVR
+LTVTRGPEAAPGAVPEPSAWALLSPAPAVEDEERRTGLRVLLLDRGLDSRAPERSPWLLT
+GAKTLSYAVNMAALRHARDHGADDVVFTSADGYLLEGPTSTVLIVRTGEDGVRRLLTPLR
+QKGILAGTSQAVIFAAAHADGWELGYGPLVPADLQGAEGVWLVSSVRGVLPVRAVDGVEI
+PVDHELTGMLQAHLDADGDPGRHVSGDPVPTAG*
+>NZ_CP040019.1_958
+MLLEVGADGARLPRVADPAVPHLRVSDQGVTRGDGLFETALAVADETGVLRMRKLGAHLG
+RLASSAAALQLPAPSAAAWEAAVERGLQAFAAANDVAAGDRLSVRLTVTRGLEAAPGAVP
+EPSAWALLSPASAVEDEERRTGLRVLLLDRGLDSRAPERSPWLLTGAKTLSYAVNMAALR
+YARAHGADDVVFTSADGYLLEGPTSTVLIVRTGADGTRRLLTPLRQKGILAGTSQAVIFA
+AAGAAGWELGYGPLVPADLEGADGVWLVSSVRGVLPVRAVDGVEIPVDHALTLELQAHLD
+ADGDPGAHVAGDPAPTAG*
+>NZ_CP083691.1_895
+MPTSNPAPAAHTPAPGEPVLVLLSPDADPRLADPAAPHLSVTDQGVTRGDGLFETALAVA
+DETGTFAMRKLAAHLGRLASSADALGIAAPDPEPWRAAIEAGLAGFAAANPVAPGDRLSV
+RLTVTRGPEAPAGVEARPTAWALLTPAPRTSDAERAEGVRVLLLERGLDSAAVEGAPWLL
+TGAKTLSYAVNMAALRHAKAHGADDVVFTSADGYLLEGPTSTLLLARTGADGTRRIVTPL
+RQKGILAGTSQSVIFAAAEAAGWRLGYGPLAPADLDGADGLWLVSSVRGVLPIRAVDGQD
+VPVDAELTERLQAWLDADGDPGVHVSGDPVRDED*
+>NZ_CP097650.1_1749
+MPAPGPDRPGAGVYPGRMRPTAFSPAAGSPVLVLLETDADGAPAPRLADPAVPHLSVTDQ
+GVTRGDGIFETALAVADGLGTLRMRKLGAHLGRLAASAAALQLAAPEAAAWEAAVALGLR
+AFTEANDVAPGDRLAVRLTVTRGPDAAPGAVPTPTAWALLSPAPAIQDEERQRGLRVLLL
+DRGIDSQAPERSPWLLTGAKTLSYAVNMAALRYARAHGADDVVFTSADGYLLEGPTSTVL
+IVRTGEDGVRRLLTPLRQKGILAGTSQAVIFAAAHADGWELGYGPLVPADLQGAEGVWLV
+SSVRGVLPVRAVDGVEIPVDHELTGMLQAHLDADGDPGRHVSGDPVPTAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001533.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001533.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27a0c957d3b58623564aee16523b3555ce21645a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001533.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1830
+MNTLAQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPNDAADETLPLIEALSFAFISAG
+VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV*
+>NZ_CP033200.1_1537
+MNTLVQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPDDAADETLPLVEALSFAFISAG
+VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV*
+>NZ_CP040019.1_957
+MNTLAQKALSTGITLVGGIIGSRVVAGGWKLVTGHDAPDDAADETLPIVEALSFAFISAG
+VAAILKVAGQRGAGAALRKVTESTAHRVDNEV*
+>NZ_CP083691.1_894
+MDKVIQKVLATGITVVGGIVASRLVAGGWKLVTGHDAPSDATDETVPLVEALAFTFASAG
+IASVLKVAGQRAAAEGVRKVAQKTSSDVDNEV*
+>NZ_CP097650.1_1750
+MNTLAQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPNDAADETLPLIEALSFAFISAG
+VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001542.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a815b8b56df4a1425804eb2273fbfc5f0667f0c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001542.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1842
+MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV
+LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG
+DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTTAGRRRAVRRSPGRAVADQVRHTV
+TNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR
+RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL
+RVSKDTILVTTIVAIPAMIAVALLLA*
+>NZ_CP033200.1_1549
+MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV
+LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG
+DAALAAPALIFQLAIYTPLYVAAMDAATAREVRRRTTAGRRRAVRRSPGRAVADQVRHTV
+TNPLILGSVAGLVFSLTGWSLPGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR
+RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL
+RVSKDTILVTTIVAIPAMIAVALLLA*
+>NZ_CP040019.1_945
+MTQVLSGFVVVWVIIAVGFLVGRSGVLGEDARTVLSRTAFYIGSPALLFVTLSGADVAAV
+LGPQLWVATLSALAAAALFLAISIPVFKQRPASERIMAALSASMVNSANLGIPIAAYVLG
+DAALAAPVLIFQLAIYTPLYVAAMDVATTSEARARAAGGRPAVRRSRGQALAAQLRQTGT
+NPMILGSAAGLLFSLNDWTLPGPLMQSVELIGGLSIPAMLLAFGMSLVGSRPLERAGGRR
+ADVLLASGVKLLVHPLIAWVLAQFVLGLDAREVFVAVVLASLPTAQNVFVSAVRYDAGLR
+VAKDTILITTIVAIPAMIAVALLLA*
+>NZ_CP083691.1_883
+MIEVLSGFSVVWVIILVGLLLGRTGVLGDEAREVLSRTAFFVGNPALLFVTLSRADVGAV
+LGPQLWVACLSAFAAAVVFLGLSIPLLKGRPASERVMSGLSASLVNSANLGIPIATYVLG
+DAALAAPALIFQLAIYTPVYVAVMDWATTHEAAARASSAGAAHDAGAPAPRTVRPRNPVL
+AQLRQTATNPMILGAFGGLLLSFTGWTLPGPLMTSVELIGGLSIPAMLIAFGMSLAGSRP
+LARDSGRRADVLLASAVKLVVHPLVAWMIAQFVFGLDARRVFVAVVLASLPTAQNVYVSA
+VRYRAGETVSKDTILVTTIVAIPAMIAVALLLA*
+>NZ_CP097650.1_1762
+MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV
+LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG
+DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTTAGRRRAVRRSPGRAVADQVRHTV
+TNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR
+RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL
+RVSKDTILVTTIVAIPAMIAVALLLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001545.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001545.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eaacb3cc1454fd97573f0391bc09c02c19380b67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001545.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1847
+MSADRVRPLRRPAAPRRGRLRLVAAVAAGLLALTGCGAGDNDPAAASVPADGVHDDAGTA
+VHTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD
+RTTVQPAQCKAPLTALDFSPIALDGAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH
+IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL
+TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD*
+>NZ_CP033200.1_1554
+MSADRLPPLGRPAAPRRGRLRLAAAVAAGLLALTGCGAGDGDPAAASASADGVHGDAGTA
+APTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD
+RTTVQPAQCKAPLTALDFSPIALDEAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH
+IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL
+TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD*
+>NZ_CP040019.1_940
+MLALTGCGAGDEPAPEQPSAPADALHGDVGGAAPAPEEGAEGLGLGDRQDERMAAAAAER
+AVGFGFVRQRAAAPEEIDAAREDSRARRSDADRTTVQPAACKAPLTALDFSPISLDEGEA
+TRVDVGADTFTGTGTVEVARLTGSGRQEVERHLQTVNGLLADCREMTMTVQDGDASVDYR
+LAVSEAPLSEGTPAQSALVWERSLASADGPQLTAQVLTAVTADAVVMVSFVGQPEAGRKE
+FTLIAEEMLAAALAAG*
+>NZ_CP083691.1_879
+MSADRTRPRPAVRRLAVASSGAALAAVLLAGCASGGDAAASSGAQAAGPSSSAATGGLDL
+GDRVDQRRAEAAAARAASFGFTRQDAVGADQIAAARGDAADRAADDGRTTVEPARCQAPL
+AALDFSPILLDQEEVSRVDVGTDSFAGTGTVEVATLDGPGRQRVEEHLQTVNTLLADCRD
+MTVTTRDADGARTYRLQMSAAGLSDGSPAQSGLVWTQTPAGRDEPATAAQILTAVGPEDV
+VMVSFTGQPQAAERQFTVMAEEMLAAAGTVTR*
+>NZ_CP097650.1_1767
+MSADRVRPLRRPAAPRRGRLRLVAAVAAGLLALTGCGAGDNDPAAASVPADGVHDDAGTA
+VHTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD
+RTTVQPAQCKAPLTALDFSPIALDGAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH
+IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL
+TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001546.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001546.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50cf42737a7b802d8faca96ed34477b3901e7d27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001546.fa
@@ -0,0 +1,70 @@
+>NZ_CP042169.1_1848
+MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNVAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPATDAPSGAEPAARDSSTGPEEARDVR*
+>NZ_CP033200.1_1555
+MSAATAPARGSHPTENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVGAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHNGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLSLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLQTHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMIFHAFIGVAMTTSTGLMQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPVTDAPSGAEPVARDSSTGPEEARDVR*
+>NZ_CP040019.1_939
+MLVAAAGAGALAVAAWLTGITAVRELSDPGWITRWGVPAGELVSNLAMTMAIAAIIFAAG
+ILPPHAAGTERWHRSAAQRRADAQEGPLPEHPAFTRTLRVAAVSAGVWTVAALAVGILSY
+SDLAGIPVTAGEGFTAGLVAYVAGISVGQAWFWVTVIAAVVTTLVIAVRSHNGLFWTGIL
+AMIGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVWVGGLLVLVAISDTLVGPDGAQGR
+ARAPREQGPTPLLHTALSRYSVLAGLGLVTVALSGVVNASIRMDDPAQLTSPYGMLVVIK
+FLATLGLGLVGLMHRRWVIPRLDAGPDRPSPAPARRLLWQLIAVEAVVMAAVMGLSAVLS
+RTAPPVPEELAPDATPARILTGYELPPELTGARWITEWRLDWLWVAIIAFLALWYLRSVW
+RLHRRGDRWPVLRTLSWMVGLAVLLWATSGSPAVYGRVLFSSHMMGHMTLTMISPLFLVL
+GAPITLALRALPSRTDGSRGPREWILWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFF
+RFSLETHVGHEFMNVHFLLTGFLFALVMVGSDPLPSRPAYPLRLVLLLATMVFHAFIGVA
+MTGSAGLIQASWFGNMGRDWGPSALEDQHIGGAVMWGIGEFPTVVMAVMVAVLWYRNDRR
+NAERLDRRADRDGDAELHRWNEMYARMHGTPAAPAEPAPAAASPADPTPAASAPRPRRPG
+DPRWPLSTAHPPEDPAGPEDRAAPARWPRPPSSGCWR*
+>NZ_CP083691.1_878
+MPTSTAVPPATAQHPLGVPRPVLLGAAVVGVLALVLAAWFAGVTAPRELSDPGALTRWGV
+PVGKAVNNAAMAVTIGALIFAAGILPPHAAGTERWHRSPRQRAQDAEEGPRPEHPAFGRV
+MAVAAAAAGVWTVAALAVGVLSYSDLAGIPVSAGGSFTDGLLAYTLDISVGRAWFWVTVI
+AAVVTTLAIGVRSHTGLFWTGVLAMLGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVW
+VGGLLVLALISDTLVGPNGAQGRGASLRRQGPAPLLHTVVSRYSVLAGLGLVTVALSGVV
+NASIRMDDPAQLLSPYGTMVLTKAGAVLLLGGIGLLHRRWIIPRLDDDGAAESPPAARRL
+LWQLIAVEAVVMAAVVGVSAVLARTAPPVPEELAPDATPARILTGYELPPELTGDRWFTM
+WRWDWLWVAIIAFLAVWYVRAAWQLRRRGDRWPVLRTLSWLIGLAVLAWATSGAPAVYGM
+VLFSAHMVGHMVLTMIVPLFLVLGAPITLALRALPARTDGTRGPREWILWIVHSPWGAFI
+TNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFIFATVMVGADPLPSR
+PPYPLRLVLLLATMVFHAFIGVAMTTSTGLLQASWFGSIGRDWGPDALTDQHIGGGIMWG
+IGEFPTVLMAVTVAVLWARSDTKTAARLDRRADQDGDAELARWNQMYAAMNHPGADQDPA
+RGDRP*
+>NZ_CP097650.1_1768
+MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWMLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPATDAPSGAEPAARDSSTGPEEARDVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001557.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001557.fa
new file mode 100644
index 0000000000000000000000000000000000000000..246d1d038b6c17c5a02b156860ccdd431b0bcca8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001557.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1865
+MTTTTATPGPTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DAAGTPMLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLRED*
+>NZ_CP033200.1_1572
+MTTTTATPGPTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAATEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DVAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLREG*
+>NZ_CP040019.1_924
+MTTTPATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDAAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHTATGAPVRAADPDWCRGGAAVLTPDERI
+DVAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLAQVSAALAELGEDEAATVTPEQ
+LAPRIYPGLEGTVARVAVQTVAAHLRHLREG*
+>NZ_CP083691.1_858
+MTTTPATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVLFADDADAAVVLDPGPAEDAEGHL
+ERVRQAAEGRRIELVLVSHRHADHTGGIDAFHAGTGAPVRAADPSHCRGGGLPLTPDEEI
+VRAGVRILAWHTPGHTSDSYSFAVPESGPHGAVLTGDTILGAGTTMLDHPDGTLTDYLAS
+LARLQAAGPLTVLPAHGPVPAPLDVIARDYIDHREGRLFQLRRALDGMDPARAAMVTPSE
+LVGVIYPEVTGQVARVAEQVLAAHLAYLRRG*
+>NZ_CP097650.1_1785
+MTTTTATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DAAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLREG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001559.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001559.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd1186b51d5fe80e42617132074d54192863e2fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001559.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1868
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV
+GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA*
+>NZ_CP033200.1_1575
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVVAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEDLVGRIRNAGAVFV
+GPHAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA*
+>NZ_CP040019.1_921
+MEADRPRGPGPAAAVVVPRRCTPTPAPPTSLEDPVLSVTDLRQIDTAAADLSRIIPRADV
+DVASTVPVVAPILEQVRTGGEAALLELAERFDGVRPPALRVPAEALAAALEGLDADVRAA
+LEESIRRARLVHAAQLPQDSTVELGEGASVQNHWIPVDRVGLYVPGGRAVYPSSVVMNVV
+PAQAAGVGSLAVTSPPQADHGGLPHPTVLAACALLGVDEVYAAGGAQAVAMLAHGVRDER
+GGWLCAPVDMVTGPGNVYVAAAKRALQGIIGVDAEAGPSEIAVIADGTARADWVAADLIS
+QSEHDPLAASVLITDSEDLVRDVLAAIEAQVPGSFHEEQIRVALTGPQSGVLLVRDLDQA
+VEVSDRYATEHLEIQTRDPEAVAARIRNAGAVFVGPHAPVPLGDYSAGSNHVLPTSGTAR
+HSSGLSTVTFLRLQQRIRYTETGLKELAEGISVLAEDERLPAHGVAVRARFA*
+>NZ_CP083691.1_855
+MEADRTALDPQEEPVLSVTDLRELDTAAADLSAIVPRAEVDVAYTVPVVAPIIEQVRTGS
+EQTLLDLAERFDGVRPPALRVPAEALTAALEGLDPAVRAALEESIARARKVHAAQVPSGS
+TVELGEGAVVENRWVPVERVGLYVPGGRAVYPSSVVMNVVPAQAAGVESLVVTSPPQRDH
+GGLPHPTVLAACALLGVDEVYAAGGAQAVAMLALGVRADDGDGWLCAPVRMVTGPGNVYV
+AAAKRALQGVIGTDAEAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSADL
+LRDVLASVEAQVPGSFHEEQIRVALTGPQSGVLLVRDMEQALEVSDLYATEHLEIHTRDA
+DALAARVRNAGAVFVGPYSPVPLGDYSAGSNHVLPTSGTARFSSGLNTVTFLRSQQLIRY
+GEAGLKALADGISALAEDERLPAHGVAVRARFA*
+>NZ_CP097650.1_1788
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV
+GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001562.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001562.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d3efb4b35471c04bcde1eb9dbcfe36b71eecd04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001562.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1871
+MTLTHEPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA
+LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL
+IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDAAPPAALHRNLFHGLRAL*
+>NZ_CP033200.1_1579
+MTLTHEPHTATWDTDLSLGNLRSGLSAFPTGVVALAGLADGVPEVMVSSSFGVGISWEPA
+LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL
+IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDAAPPAALHRNLFHGLRAL*
+>NZ_CP040019.1_918
+MTLTLDDRTRVWDTDLSHHNLRSGLSAFPTGVVAVAGLAEDRREVMVSSSFGVGISWEPA
+LVAFSAQNTSRTWPRLRQAASLGISLLAADQTHLCRQLASREGDRFAGLDVHVSPNEALL
+IEGAALWLETRLHAEVPAGDHTVVMLEVTGFADHTDEVAPAALHRNLFHGLRAL*
+>NZ_CP083691.1_848
+MTLIHAPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA
+LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLAAREGDRFAGLDVHRSPHDALL
+IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDDAPPAALHRNLFHGLRAL*
+>NZ_CP097650.1_1791
+MTLTHEPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA
+LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL
+IGGSSLWLETRVHAEVPAGDHTVVLLEVTALADHTDAAPPAALHRNLFHGLRAL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001563.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df8b2807f0c0ddf1630049f815988c2739b0d679
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001563.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1872
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGNGFKELQENDRVEFETQDGPKGLQ
+AANVTKL*
+>NZ_CP033200.1_1580
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGGGFKELQENDRVEFETQDGPKGLQ
+AANVTKL*
+>NZ_CP040019.1_917
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGSGFKELQENDRVEFETQDGPKGLQ
+AANVTKI*
+>NZ_CP083691.1_847
+MAVGTVKWFNSEKGYGFIAPEDGSADVFVHFSAIQGNGFKELQENDRVEFETQQGPKGLQ
+AADVTKL*
+>NZ_CP097650.1_1792
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGGGFKELQENDRVEFETQDGPKGLQ
+AANVTKL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001569.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001569.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82d162bce101482b97eaa05fccf52db6c555421c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001569.fa
@@ -0,0 +1,37 @@
+>NZ_CP042169.1_1879
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSAAGAGGEPTTVTIMTHDSFNLPQEL
+VQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEYT
+PQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVAT
+SPVASSPGLALLAATTEKYGDDGWQDWWRGLKENGGKVADSWSDAYNSDFSGGEGKGRFP
+VVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFMLTEEVQSALPES
+MYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR*
+>NZ_CP033200.1_1587
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSASGAGGGEPTTVTIMTHDSFNLPQE
+LVQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEY
+TPQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVA
+TSPVASSPGLALLAATTEKYGDDGWQDWWRGLMENGGKVADSWSDAYNSDFSGGEGKGRF
+PVVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFMLTEEVQSALPE
+SMYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR*
+>NZ_CP040019.1_908
+MTTAPHRVRTRPRRHGALAALSVAALALTGCSVADRGGSGDQGSSSAEARTVTIMTHDSF
+SLPDELIARFEQESGHTLVTTAPGDAGSVVNQLLLAKDAPTVDGVYGIEDHSAHRLVSEG
+VIAEHVPADLPDSARDLVVDGRMTPVDQGQVCLNVDTPWFQEQGLAAPTTLEQVAAPEYA
+ELTVVTSPVSSSPGLALLAATVAEFGEDGWQDWWRTALQGGMQVDASWSDAYNTSFSGGE
+GTGTRPIVLSYSSSPAFAPDTDVVAASCTPQVEYAGVVEGAENPEGARAFVDFLLTEDVQ
+AAIPDAMYMYPVDSSVPLPEAWAEHAPLVEDPIVPDAGLLDSRREDLLKEWTALHEEAAS
+*
+>NZ_CP083691.1_841
+MSVHRTATTRRGVLAAACLSALALTGCSVSAPSTGSSSSAASSSAAPSSASGSSSTSASG
+TAAAGSKGTVTIMTHDSFALPKELIAQFEAESGYRLVTTAPGDAGAVVSQVLLSKDAPVA
+DGVYGVENHSAHRLVDQGAVQDVAPADLPASAEDLVVDGKMIPVDQGQVCFNTDPAWFTE
+HGVAEPTSIDQLRDPEYAKLTAVTSPVTSSPGLALLAATTEKYGDDGWQGWWEDLLKGGA
+KVDSTWSDAYSTDFSGGEGKGEFPVVLSYSSSPAFAPQTAVIEDSCTPQVEYAGVLTGAE
+NPEGAKAFVEFLLSKDVQAAIPENMYMYPVDDTVELPAEWAANGPLVEDPITPDPAEIDT
+EREGLLKEWTALSESAGSR*
+>NZ_CP097650.1_1799
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSAAGAGGEPTTVTIMTHDSFNLPQEL
+VQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEYT
+PQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVAT
+SPVASSPGLALLAATTEKYGDDGWQDWWQGLMENGGKIADSWSDAYNSDFSGGEGKGQFP
+VVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFLLTEEVQSALPES
+MYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001572.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001572.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c44c46be12669b0870b8a7ee94e43e3a24ae5d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001572.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1882
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL*
+>NZ_CP033200.1_1590
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAAVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRITDLAGRAEAAEAALLRHRDGADLVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVPTGPDVQRHRTDPL*
+>NZ_CP040019.1_905
+MSSPPRAGSSRGRLSATDVVDAAVGILQDFGMGDLSMRRVASVLGVQASALYWHVPDKQT
+LLARVADRIVAEAEEAVRHRGIADLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLH
+ALLTEAAPTPEEGERALALLLGGVSLRQQRAQAEALGVRVGPDVQRHRTDPL*
+>NZ_CP083691.1_838
+MSTSSARGRLSAEDVVDAAVGILQDFGMGDLSMRRVASMLGVQASALYWHVPDKQTLLAR
+VADRIVADVERACAARRVEDLAGRAEEAEAVLLRHRDGADVVLSALALGLGGLGLHRLLV
+DAAHTPEEGERALAALLGTAALRQQRNQAAALGLRLGPDVQARRTGAL*
+>NZ_CP097650.1_1802
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001573.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001573.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38eb291291259ed96fceb8118bdb30ea2fdad2de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001573.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1883
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIQLRVEDDAAG*
+>NZ_CP033200.1_1591
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWEFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSAFWSTVTVDLPPERPVIVRLGSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIRLRVEDDAAAG*
+>NZ_CP040019.1_904
+MRVVAAPLAMLPGVDHGPALRMDLHPVPGGIVYVARDLVLRELGDDVRGHVHAGMVGTAQ
+LHAFWSTVTVDLPPDRPVIVRLRSDRDAELLSLLEVLAPVEMRVVSYRLDESPVGTQRSS
+YLLPDVDPEIVARAESPRVPLEAIEATQEEEDALRRSSGVFLSRRRTDRFLRRTLPTVTH
+SLSFSDEADVADVYVDGSVLRSSRIGGAAAVGGPSMWAVQAVNGATTPLEVELEALVLGH
+VVSAWAGVPGERVTIHSDSRAALALLNAARRERLTLGGARGERVRRTLRRLLAAVDLAQA
+ADVRVETTWVKGHVGVQGNELADDLARAAARHAGVGTSEEDLRRRLDRLIDLHEEAEAEA
+GQTPARAVAAEGHRPMPPGRRPGPRL*
+>NZ_CP083691.1_837
+MDNSSTHPREGQVRSLHFDTDASSPDALLDPMWAFTGPRASRAGAPAPDGADVLARRARP
+AHPGAALVRAATSLFTLPGPPGMPHRSRSAALEAARAPAGYLSPVPHRLALPRPARPRPA
+PPRMRVRQDGVRVVARPLAMLPGVDHGRALRLDLHPVRDGIVFVSRHLELRELGDDVKGL
+VLTGVVPAARLGYFWDTVAGDLPEGRPVIVRLRSNDDAELLTLLRAIAPPWLRVVSYRLD
+ESPVGSQRSSYLLPDVDGEAVAASGAERVPLETLREAHQASAEVERASRVFLARRRVDRF
+VRRSVPDLMHSLSYTDPAEVRHVYVDGSVLRGTRTGGAAAVTRSGPWAAHALPGATIPLE
+AELEALTLGHLMAAWSGTPDERVLIHSDSRAALALLREAHRERLTLGDARGERIRRALRR
+LLAAVDLAGSAGVEVSTLWVKGHAGTHGNELADDLARSAARNTAAGVSADEMRRRMRHVV
+QLWDATTHPQA*
+>NZ_CP097650.1_1803
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIQLRVEDDAAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001574.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001574.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c39ef6c5392255aa4aa23ddae74b031b672a51a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001574.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1886
+MATPHTPDPQDARRAREATDETSGAAFDGDTPPAEGAGVGPSNPGMDVEQTGERSAGKIV
+LGLIIALVVIGVLLFILGRVAGLG*
+>NZ_CP033200.1_1594
+MATPHTPDPQDARRAREATDETSGVAFDGDTPPAEGAGVGPHNPGMDVEQTGERSAGKIV
+LGLIIALVVIGVLVFILGRVAGLG*
+>NZ_CP040019.1_901
+MAAPHTRRPHDSDPHDARRAADEHSGHTDRGGTPPAEGSGVGPTNPQMDVEQPGERSTGR
+IVLFAIIALLVIGILLFVLGRVFDLFG*
+>NZ_CP083691.1_835
+MATPHHPDQPADAHRSDHLARATDENSGHAVAGDTPPAEGLGVGPTNPGMEADKSGEGGM
+GRILLGLLIALVVIGVLLFVIGRISSIG*
+>NZ_CP097650.1_1806
+MATPHTPDPQDARRAREATDETSGAAFDGDTPPAEGAGVGPSNPGMDVEQTGERSAGKIV
+LGLIIALVVIGVLLFILGRVAGLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001575.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001575.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ed44fe74f5c9006aeb5d7846bf98cbcf588aea0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001575.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1887
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVARQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAIMSGTADLVVAGGVQSMS
+AIPLSLSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADSRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG
+RYGLQTMCEGGGQANVTVIERL*
+>NZ_CP033200.1_1595
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL*
+>NZ_CP040019.1_897
+MPEAYIIDAVRTPVGRRGKGLAQVHPLDLAAAPLREIVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSHSNRAAAEFGFADPFTGSESWAARYGNEEISQFRGAEMMARHWNLDRDVLEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG
+RYGLQTMCEGGGQANVTVIERL*
+>NZ_CP083691.1_834
+MGEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPIRELVGRQDVDSAEYDEVILGCIDQLG
+PQAMDVARSAWLAAGLSEDVPGSTIERQCGSGQQAIHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAASASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAFALRRMGLGIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL*
+>NZ_CP097650.1_1807
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001581.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001581.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16785657f64a14b73c869d4b6271e5c502d466db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001581.fa
@@ -0,0 +1,41 @@
+>NZ_CP042169.1_1908
+MTSHTDPSHPAAHPVSRRTLLGGAGLVVASAALLSTPAGTAHAATGPTPFTLGVASGDPW
+PDGVVLWTRLAVDPLALDGLGGMPDQSFRVEYQVATDEGFRKVVRSGAVTTDRAQGYAVH
+VTLTGLRPGTEYFYRFRALGHLSRVGRTVTAPARGSNPSRLTMTVASCANWEHGYFTAYG
+HMAAERPDLMVHLGDYYYEIMPYGYPVSSGVPRAHRNGESRTLAQYRARMAQYKTDPHLQ
+DAHAAAPWLVIFDDHELENNWADETPEIWDPSFLARRAAAFQAYYENMPLRASSVPRGID
+MQLYRRIHWGDLATFHLLDTRQYRSDQANLDLVKVVDADARDSRRTITGAAQEAWLREGF
+ETSVARWDLITQQVPFVQYDRTSGPLLWGDMDTWDGYVASRDRVVSAWTAAGVRNPVVLT
+GDIHEAFASDIKQDFNDLSSESVGVELITTSITSGGDGSDAAAEALAWNPHIKFNNDLRG
+YLRVDLSAQLLEARFRVVDYVSELGSSVRTRAVFGVGDGEHRLHRIA*
+>NZ_CP040019.1_877
+MPLRASSVPRGIDMQLYRRIHWGDLATFHLLGTRQYRSDQANLDLVKVVDADARDPRRTI
+TGAAQEAWLREGFETSVARWDLITQQVPFVQYDRISGPLLWGDMDSWDGYVASRDRVVSA
+WTAAGVRNPVVLTGDIHEAFASDIKRDFNDLSSESVGVELITTSITSGGDGSDAAAEALA
+WNPHIKFNNDLRGYLRVDLSAHMLEARFRVVDYVSELGSSVRTRAVFGVGDGEHRLHRIA
+*
+>NZ_CP083691.1_423
+MSSPSPTLSRRRLLGLSGASAAVLALGVNAPDAAHAEPLPQRDGLFGLGVASGYPRPDGA
+VLWTRLAPEPLAENGHGGMPLRSVPVKWEVARTADFRRIVARGTALAQPELAHSVHPRVE
+GLAPGTEHFYRFVVGPQTSPVGRFVTLPAAGAATDDYTVGLISCQAWYHGHFAAHRHLAQ
+EEDLDLTVFLGDYIYEYGITAANLWRQGAEVTPAHAVEIETLEQYRLRYALTKSDPHLQA
+LHARAAAVAIWDDHEVQNNYVGAASSTGIPEELFAHRIAVAYRAFYENLPVDIDALPEGP
+ESDIVAGLDVGALARISLLDTRQFRDAPPADAADRERENRTMLGAAQERWVTERLRTSQS
+QWNVLAGGVVLAPISDDRTDQWDGYPAARRRLLTEMKRAGNAVMLTGDIHKHVAAELRGE
+SAGLPAGPAGVELVTTSAASDGDGAKTDKYTPDWVRHDYVRHYDGRRGYLHLRFTPAQLT
+SSFWVVPWVESDDTAPKELSARFTTPAGSSRLIEA*
+>NZ_CP083691.1_816
+MAAAALISTPAGTAHAAAGPNPFTLGVASGDPWPDGFVIWTRLATMPLNRDGFGGMPDAS
+FTVEWQVSRHADFRSTVRTGTTTTSRAQGYAVHVTLTGLRAGTEFFYRFRCNGHLSRTGG
+AVTAPALGSMPGHLTATEAERLIRAAGFAPVRLGGIDESIRMEVTGELHPFGGLDGTLPT
+TANVEQLRG*
+>NZ_CP097650.1_1835
+MSSHTDPAHPTAHPVSRRTLLGGAGLVVASAALLSTPAGTAHAATGPTPFTLGVASGDPW
+PDGVVLWTRLAVDPLALDGLGGMPDQSFRVEYQVATDEGFRKVVRSGAVTTDRTQGYAVH
+VTLTGLRPGTEYFYRFRALGHLSRVGRTVTAPARGSNPSSLTMTVASCANWEHGYFTAYG
+HMAAERPDLMVHLGDYYYEIMPYGYPVSSGVPRAHRNGESRTLAQYRARMAQYKTDPHLQ
+DAHAAAPWLVIFDDHEVENNWADETPEIWDPNFLARRAAAFQAYYENMPLRASSVPRGID
+MQLYRRIHWGNLATFHLLDTRQYRSDQANLDLVKVVDADARDSRRTITGAAQEAWLREGF
+ETSVARWDLITQQVPFVQYDRSSGPVLWGDMDSWDGYVASRDRVVSAWTTAGVRNPVVLT
+GDIHEAFASDIKQDFNDLSSESVGVELITTSITSGGDGSDAAAEALAWNPHIKFNNDLRG
+YLRVDLSAQLLEARFRVVDYVSELGSSVRTRAVFGVGDGEHRLHRIA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001588.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001588.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c78096f8a4a36afd670a798f22e9d807b70e6823
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001588.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1918
+MTVPPGSPAAPSAPASRRRRRALAAALAVAVVVQLVVLYLPGEQVPQAGFAAPGLDKAIH
+VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV
+VAARSRRIGGSGASGV*
+>NZ_CP033200.1_1624
+MTVPSGSPAAPSAPASPRRRRALAAALAVAVAVQLVVLYLPGEQVPEAGFTVPGLDKAIH
+VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV
+VAARSRRIGGSGASGV*
+>NZ_CP040019.1_868
+MGDARPRVPVCPSSRRRRRALAALLAVVVVVHLVVLYLPGSDVPQTGFEVPGLDKTIHVL
+AFAAPTWAAVRLGSSWWWALPFAVHAPVSEAVQHAWVPLRTGDAWDMVADLAGVVLGAAL
+AWRAVRREVEAPGEVGEVGEAGRGDRIGGSGRPGV*
+>NZ_CP083691.1_809
+MPARSSAPAAPPPSAARRRTLALLLVIALAAHLVVLYLPGDDVPAVGFEVPGMDKAIHVA
+TFGVPALLGVLLARRVWPAAVLAVHAPLSEVLQAVQGLGRTGDPADAVADLAGVALGLLA
+ARAALRRGPTGRPIGAAPGRGV*
+>NZ_CP097650.1_1845
+MTVPSGSPAAPSAPASRRRRRAVAAALVVAVVVQLVVLYLPGEQVPEAGFAVPGLDKAIH
+VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV
+LAARSRRIGGSGASGV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001589.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001589.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0463cf04cb7e55d88287b4045146ea95c36b57f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001589.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1922
+MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE
+ETVAAAIAELLGPDARYVVPAGLEPDWLPTDSRGAGRERITEPAVGHTGERAAVRGAHDG
+EREPLNVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV
+ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR*
+>NZ_CP033200.1_1628
+MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE
+ETVAAAIAELLGPDARYVVPAGLEPDWLPADSRGAGRERITEPAVGHTGERAAVRGAHDG
+EREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV
+ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR*
+>NZ_CP040019.1_864
+MSEATPTTVPATPTPGPGGPGGEARAAILDRIRQALQDGPTPDPVERTYRRTSEAAPGDV
+VEQLVDRLVDYKAGVHREDLTTVADRVADLLGEGARYVVPPGLDPAWLPGDGQGRVRVTE
+PATADAGALGVRELDELDAVVTGSTVSCSETGTIFLTGRPEEGRRAISLVPDHHVCIVPL
+DTVVELFPEALARVEPTAAITMISGPSATSDIELERVEGVHGPRRLDVILLDR*
+>NZ_CP083691.1_798
+MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE
+ETVAAAIAELLGPDARYVVPAGLEPDWLPADSRGAGRERITEPAVGHTGERAAVRGAHDG
+EREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV
+ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR*
+>NZ_CP097650.1_1849
+MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE
+ETVAAAIAELLGPDARYVVPAGLEPDWLPADSCGAGRERITEPAVGHTGERAAVRGAHDG
+EREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV
+ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001591.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fcfa405e53faca20f43c2b4bd394226ec559043e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001591.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1924
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAGAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEARR*
+>NZ_CP033200.1_1630
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPTSAGVRRGPSARVEEARR*
+>NZ_CP040019.1_862
+MRVALFATCIVDAMYPKVALATVRILERLGHEVVFPRGQGCCAQMHVNSGYLDDALPVVK
+NHVRTFQGADYDVAVAPSGSCVASLGHQQPMVARAAGDEALARDAEEVAANTYELAALLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGDRQERLLRSVADIDYRALPDAEECC
+GFGGTFSLKNPDVSGAMAEEKIGNIERTQARLCTGGDASCLLHLGGVMSRRGTTAPDGSP
+VTTLHFAEILAATRENPLDVSGPVDLSIPAQGPARRRRQKEATR*
+>NZ_CP083691.1_796
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYVEDALPVVR
+NHVRTFMKADYDLAVAPSGSCVASLGHQQPDVARSCGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGTRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASICTGGDASCLLHLGGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEAHR*
+>NZ_CP097650.1_1851
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAGAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEARR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001592.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001592.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed918be868c3e39af70a9780143c85819c801021
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001592.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_1925
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPATHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTHFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPSITAALNSATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWMLPAAG*
+>NZ_CP033200.1_1631
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTYFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPSITAALNAATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWMLPAAG*
+>NZ_CP040019.1_861
+MDPLIQASAPVGTFTATTDAVAGSLGLSAALGTIPLLTFFVMLLLVKAKAWQAGLVSLTA
+AVLVAILAFGMPADLTLLSASQGAVFGFFPIVWIVVMALWFYQVTVLSGRFEDMRAIFDT
+VGGGDIRIQAVLIAFCFGGMLEALAGFGAPVAITATMLLALGLPPLKTAVVVLLANTAPV
+AFGAVGIPITTAGQLTDIPAAEIGAIVGHQAPFVAVLVPFFLVWIIDGFRGIRETWPALL
+TIGGTFALGIWWASTQFSYELTDVVASLLAMASAVVLLRFWRPKGAAEADARLGITPTRP
+AGDLTPGRIWMAVLPYLLVITVFGIAKLWTLGFDLPGWLASTNVRIPWPGLDGRLVTAAG
+EPITGTVYSFQWLSSPGTLLLITGLLVALIYSVFTGGGRFPLRFGDALAEIGRCFWKMRW
+SGLTIVLVLSLAYVMNFSGQTLAMGTAVAGVGAAFAFLSPVLGWLGTAVTGSDTSANALF
+ATLQQTAAEEAGLDPSLMVAANTSGGVVGKMISPQSLAIAATAVSMEGQESKILRTVLPW
+SVALLLMVCTIVFLQSNVLSWMLP*
+>NZ_CP083691.1_795
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTHFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPPITAALNSVTAKIPWPGLDGHLVNASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWLLPAAG*
+>NZ_CP097650.1_1852
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTYFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPSITAALNSATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWMLPAAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001600.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001600.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28d68a0f9a486dd9d5a131a9ab22f8a1f969ed2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001600.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1936
+MRRTDIGTVGLAGAPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSEKLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTGEDLAAARE
+VNATMRAMTESETAWDPMAFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLEHSAEPSA*
+>NZ_CP033200.1_1642
+MRRTDIGTVGLAGAPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSEKLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLAAARE
+VNATMRAMTESETAWDPVTFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLRAYLEHSAEPSA*
+>NZ_CP040019.1_849
+MSRTDIGTVGLAGTPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSENLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLSAARE
+VNATMRAMTASEKAWDPVAFTELNRRFHSILFEHHQNEHVHDLVHRGWTRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLAHQGELS*
+>NZ_CP083691.1_786
+MRRTDIGTLGLAGTPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSENLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLAAARD
+VNAAMRAMTASEKAWDPVAFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLEHSAEPSA*
+>NZ_CP097650.1_1863
+MRRTDIGTVGLAGAPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSEKLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLAAARE
+VNATMRAMTESERAWDPVAFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLEHGAEPSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001613.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001613.fa
new file mode 100644
index 0000000000000000000000000000000000000000..202f011959ba6bf3fb9f818aadc704b0f5ee274a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001613.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1954
+MSFATNDSATRHSAGVAITAEEIAAGEQKANDDVARYALALGDDALMLGQRLSWWISRAP
+EIEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA
+KTIARQLYYSFYSYELYTRLRESTDPTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES
+KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEACLTVP
+TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW*
+>NZ_CP033200.1_1676
+MSFATNDSATRHSAGVAITAEEIAAGEQKASDDVARYALALGDDALMLGQRLSWWISRAP
+ELEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA
+KTIARQLYYSFYSYELYTRLRESTDSTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES
+KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEAGLTVP
+TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW*
+>NZ_CP040019.1_816
+MSFATNDSATKHSAGVAITAEEIASGEQKASEETARYALYLGDDALMLGQRLSWWISRTP
+ELEEDIALGNIALDLVGHARFLLSYAGTAWGQSEDELAYFRDEEEFRSVRLVEAENGDFA
+KTIARQLYYSFYAFELYTRLKESTDATLAAIADKALKEVLYHQDHAALWLNRLGLGTDES
+KFRMQRGLDELWPYLPELFHDDETTRPLAEQGIAVLPSSLEEPTMTRIREAIEAAGLEVP
+TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGASW*
+>NZ_CP083691.1_752
+MSFATNDSATRHSAGVANTAEEIASGGQKASDEVARYAVYLGDDALMLGQRLSWWISRAP
+ELEEDIALGNIALDLVGHARFLLSYAGTAWDKSEDDLAYFRDEEEFRSTRLVEAENGDFG
+KTIARQLYYSVYAHGLYTRLKDSKDATLAAIADKALKEVEYHLDHAEQWVNRLGLGTEES
+NARLQRGLDELWPYLPELFHDDELTRSLAEQGIAVLPSSLEESTMARIRAAIEGADLKVP
+ETGAARGGDRSGQMSEYRGYILAEMQSLARRHPGASW*
+>NZ_CP097650.1_1893
+MSFATNDSATRHSAGVAITAEEIAAGEQKASDDVARYALALGDDALMLGQRLSWWISRAP
+ELEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA
+KTIARQLYYSFYSYELYTRLRESADPTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES
+KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEAGLTVP
+TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001618.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4dc01f51297d12aef5faccc72f7b2adde1172cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001618.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1961
+MTDFSHFSALHVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPRGAHPHVDEIAQA
+ILFESDAKFERMQAFLDRKKK*
+>NZ_CP033200.1_1682
+MDDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKCEPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPEALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA
+ILFESEAKFERMQAFLDRKKK*
+>NZ_CP040019.1_788
+MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPEALEVAAHALADRIAKQDPLAVRISKRVFHLPREAHPHVDEIAQA
+ILFESEAKFDRMQAFLDRKKK*
+>NZ_CP083691.1_746
+MADFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKREPGRFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETGLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRISKRVFHLPREAHPHVDEIAQA
+ILFESQAKFERMQAFLDRKKK*
+>NZ_CP097650.1_1899
+MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA
+ILFESEAKFERMQAFLDRKKK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001622.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001622.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d17838baf182528ad24f0f064fc6e0d72caf804a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001622.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1966
+MRCGLDGLLRDPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGIEPDPMDHVRALQ
+DLHPEGVFSHVTAARVLGLWLTGPLAADRSVHVATPRGHGTASSRAGVRSHRLRADAPVR
+IVDGVRVTAPGWIFVDLAAQAGPLEHLVALGDSMVRTAPTEARRRRLPPGVTDVAELRAA
+VEERGRVRGIRAAREALELVRPGADSPQESRLRVRLVLDGVPEPAVNPCIRLATGQRLRV
+DLVWADAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVFRPGHWELFVR
+QLRGLVAARTPPGRVPPSWI*
+>NZ_CP033200.1_1687
+MRCGLDGLLRAPTVFSTPAARETGVSAARLRRGDVVSLGWGLWGLRGVEPDPMDHLRALQ
+DLHPEGVFSHVTAARVLGLWLTGPLAADRSVHVATPRGHGTASSRAGVRSHRLRADAPVR
+IVDGVRVTAPGWIFVDLAAQAGPLDHLVALGDSMVRTAPTEARRRRLPPGVTDVAELRAA
+VEERGRVRGIRAAREALELVRPGADSPQESRLRARLVLDGVPEPAVNPCIRLATGQRLRV
+DLVWAEAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVFRPGHWELFVR
+QLRGLVAARTPPGRVPPSWI*
+>NZ_CP040019.1_781
+MRCGLDETEREPTVFSTNAAQEAGVPPGRLRRSDLEPWGRGLWRVRDAVPDVMDHLRALQ
+DLHPEGVFTHVTAARVLGLWLTGPLARDPAIHLGAPRHHGTGSRREGVRSHRLYGDVPVR
+IVDGVRVTATGWTFVDLAAAAATVETLVALGDSAVRSAPTERRRRDLPPGVTSLEELRGA
+VAERPRVKGIRLARDAVDLVRPGADSPQESRLRVGLVLDGVPEPQVNPRIVLSTGQWLRV
+DLAWPAARLVVEYDGDQHRTEQRQWREDRSRDAGLRADGWEVLRVTADVFRPAEWELFVR
+RVRARLGRDAAGRAAAG*
+>NZ_CP083691.1_741
+MPRSPAPLPPMRCGLDGLLRAPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGVEP
+DPLDHVRALQDLHPEGVFNHVTAARVLGLWLTGPLAADRSVHIATPRGHGTASSRAGIRS
+HRLRADAPVRIVDGVRVTAPGWTFVDLAAQAGPLEHLVALGDSMVRTAPTEARRRRLPPG
+VTDVAELRAAVEERGRVRGIRAAREALELVRPGVDSPPESRLRVRLVLDGVPEPAVNPCI
+RLATGQRLRVDLVWAEAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVF
+RPGHWELFVRQLRGLVAARTKPGRVPPSWI*
+>NZ_CP097650.1_1904
+MRCGLDGLLRAPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGVEPDPMDHVRALQ
+DLHPEGVFSHVTAARVLGLWLTGPLAADRSVHIATPRGHGTASSRAGIRSHRLRADAPVR
+IVDGVRVTAPGWTFVDLAAHAGPLEHLVALGDSMVRTAPTEARRRRLPPGVTDMAELRAA
+VEERGRVRGIRAAREALELVRPGADSPQESRLRVRLVLDGVPEPAVNPCIRLATGQRLRV
+DLVWADAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVFRPGHWELFVR
+QLRGLVAARTPPGRVPPSWI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001624.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001624.fa
new file mode 100644
index 0000000000000000000000000000000000000000..538551a7af64f79f7ba9e3a175fc8c8ac567fadd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001624.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1968
+MSEFTRFDQVTVLGTGVLGSQIIMQAAYHGKRVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVVEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DIVGFHVAANVSRNAGADWQRGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG*
+>NZ_CP033200.1_1689
+MSEFTRFDQVTVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DIVGFHVAANVSRNTGVDWQLGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG*
+>NZ_CP040019.1_779
+MSEFTRFEQVAVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DVVGFHVAANVSRNTGVDWQRGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG*
+>NZ_CP083691.1_2042
+MTTIQKVTVFGTGVLGSQIIMQAAYHGKDVTAYDVDDKALAQLPARWEWMRGYYQRDLPD
+FDAERFDKAVSSIRTTTDVADAVTDADVVIESIPENLELKKSVWAKIGEAVPERTVLLTN
+TSSLLPSSFADSTGHPERFLALHFANLVWKNNTGEVMATAKTAPEHFDAVLAFAGEIGLV
+PVPVRKEVPGYVLNSLLIPWLDAGAKLYQGGVSDPEDIDNVWKIATGAPKGPFEVYDVVG
+FNVAYNISRVSADPLKKAFAEETLKKGIDAGTTGLGVGEGFYRYDKDGNNLGAVESWKQE
+NRG*
+>NZ_CP097650.1_1906
+MSEFTRFEQVAVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DIVGFHVAANVSRNTGVDWQLGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001628.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001628.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7d91ec91e3bfdd0180f095eb05ac629ac682308
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001628.fa
@@ -0,0 +1,19 @@
+>NZ_CP042169.1_1972
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR*
+>NZ_CP033200.1_1693
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR*
+>NZ_CP040019.1_775
+MTLTEDHHNGFGMAHGGAVFAFADSCFALTCNDPGGDGSTITVASGVDVNFLAGTRAGQT
+LVAEGRLVAAAGRSAVYDITVTTDDGTPVAAFRGRSRTIPAPGR*
+>NZ_CP083691.1_735
+MTETPHHPALVGDRVARWLGVTLEAAEKDHARIRMTLGEEHHNAFGMAHGGVVFAFADCC
+FALTCNDPASDGSTLTVASGVDVNFLSGTRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TLVAAFRGRSRTVAVKGA*
+>NZ_CP097650.1_1910
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001630.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001630.fa
new file mode 100644
index 0000000000000000000000000000000000000000..917a6ca75e4893dc84be3ae0b5cbe06e82b80345
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001630.fa
@@ -0,0 +1,49 @@
+>NZ_CP042169.1_1978
+MGAMTSQPAPASTAHRRPLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEW
+FIHLAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVAELAATEKVTVHDVKAVEYFIADR
+LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET
+PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDA
+DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF
+AQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR
+NIGVALGHSVLALTNVTKGMGQLQVADPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGM
+DNPYERLKELTRGHRVDGARMREFVQGLGLSEGAQARLLELTPAGYTGVASELAKEFGPA
+QD*
+>NZ_CP033200.1_1697
+MTSQPAPASTAHRRPLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEWFIH
+LAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVAELAATEKVTVHDVKAVEYFIADRLEG
+LGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAETPML
+SRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDADWP
+ALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYFAQI
+PVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQRNIG
+VALGHSVLALTNVTKGMGQLQVADPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGMDNP
+YERLKELTRGHRVDGARMREFVQGLGLSEGAQARLLELTPAGYTGVASELAKEFGPAQD*
+>NZ_CP040019.1_767
+MTTQPAGPSPASTDHRRSLADSGAALGPLDGRYRAAVAPLVEHLSEAALNRNRIHVEVEW
+FIHLAEHAVLPGLTPLTDEQKAGLRAIVTDFDADSVAELAATEKVTVHDVKAVEYFIADR
+LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET
+PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAAQEYLGKINGATGTYAAHLAAAPDA
+DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF
+TQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR
+NIGVALGHSVLALTNVTKGMGQLQVAEPVLAEDLDTNWEVLGEAIQTVMRAEAIAGVPGM
+DNPYERLKELTRGHRVDGERMREFVRGLGLSDGAQARLLELTPAGYTGVAADLAREFGPA
+QG*
+>NZ_CP083691.1_732
+MGAMTSQPAPASTAHRRSLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEW
+FIHLAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVSELAATEKVTVHDVKAVEYFIADR
+LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET
+PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDA
+DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF
+AQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR
+NIGVALGHSVLALTNVTKGMGQLQVAEPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGM
+DNPYERLKELTRGHRVDGARMREFVQGLGLSEGAQARLLELTPAGYTGVASELAKEFGPA
+SAQG*
+>NZ_CP097650.1_1914
+MGAMTSQPAPASTAHRRSLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEW
+FIHLAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVAELAATEKVTVHDVKAVEYFIADR
+LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET
+PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDA
+DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF
+AQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR
+NIGVALGHSVLALTNVTKGMGQLQVAAPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGM
+DNPYERLKELTRGHRVDGARMREFVQGLGLSEAAQARLLELTPAGYTGVAAELAKEFGPA
+QG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001631.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07343de858d7ffc6cfcc64160eab3fd76cf71e8b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001631.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1979
+MLLPLLPVWLLSAAPKDPAELERDVPEPIDAHGELADAVTAAITAVDLVGVFFFAISGAV
+LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF
+DGERGHHAVMAFDAIGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP
+PAVFGGRGWYALPAILGAGTTAALGQAEVLNPLTSAAVMVLVLVLRVVSLRREWLAPGAE
+ISGETQRQRMDPHDEPPVPDIRDRKGRDGPPAAPGEDGPPANEETPGADEDVTPRGTPG*
+>NZ_CP033200.1_1698
+MLLPLLPVWLLSAAPKDPAELERDVPEPIDAHGELADAVTAAITAVDLVGVFFFAISGAV
+LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF
+DGERGHHAVMAFDAIGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP
+PAVFGGRGWYALPAILGAGTTAALGQAEVLNPLTSAAVMVLVLVLRVVSLRREWLAPGAE
+ISGETQRQRMDPHDEPPVPDIRDRKGRDGPPAAPGEDGPPANEETPGADEDVTPRGTPG*
+>NZ_CP040019.1_765
+MLLPSLPVWLLSATPKDPAELERDVPEPIDAHGELADAITAAITAVDLVGVFFFAISGAV
+LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF
+DGERGHHAVMAFDAIGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP
+PAVFGGRGWYALPAILGAGTTAALGQAELLGPLTSAAVMVLVLVLRVVSMRREWLAPGAE
+ISGETQRQRMDPHDEPPVPDIRDRKGRDGPPADPGEDGPPANEETPGAGEGVPPGTPG*
+>NZ_CP083691.1_731
+MLLPLLPVWLLSAAPKDPAELERDVPEPIDAHGELADAITAAITAVDLVGVFFFAISGAV
+LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF
+DGERGHHAVMAFDAVGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP
+PAVFGGRGWYALPAILGAGTTAALGQAELLGPLTSAAVMVLVLVLRVVSLRREWLAPGAE
+ISGETQRQRLDPHDEPPVPDIRDRKGKDGPPADPGEDGPPATEETPGADEGVPPGTPG*
+>NZ_CP097650.1_1915
+MLLPSLTVWLLSATPKDPAELERDVPEPIDAHGELAEAITAAITAVDLVGVFFFAISGAV
+LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF
+DGERGHHAVMAFDAVGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP
+PAVFGGRGWYALPAILGAGTTAALGQAEVLNPLTSAAVMVLVLVLRVVSLRREWLAPGAE
+ISGETQRQRMDPHDEPPVPDIRDRKGRDGPPAAPGEDGPPANEETPGADEDVTPRGTPG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001633.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001633.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f21efbc8d4070c1e5c279cff76c168e1110b8020
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001633.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1984
+MTGTHETARPASTTTEAAASGPLHRVGFDRAKYIELQSQHIQERRRQIGGKLYLEMGGKL
+FDDLHASRVLPGFTPDNKIAMLDRIKDETEILVCFNAKDLERNKVRADLGITYEDDVLRL
+VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHAMSTIVSEQ
+GFGANEWSETTRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLE
+HPVNAAYEAATVDLDDINLIDPFHLAEYGERVTSYNRDVEVFPLLSALLEKVTGTTPYKS
+PTDMGVNMAGAAIVDDEVCQEAAKQEIIRRYYKAQVNEALEGADDTESERVALVMSKLGL
+SSEDRPVVGAAQLVAERTGEPGAAVQLADGTLVTGKTSELLGCSAAVLLNALKVLAGIED
+DVHLLSPASIEPIQTLKTVHLGSKNPRLHTDEVLIALSVSAATDANARAAVEQLASLEGC
+DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR*
+>NZ_CP033200.1_1700
+MTGTHETARPASTTTEAAASGPLHRVGFDRAKYIELQSQHIQERRRQIGGKLYLEMGGKL
+FDDLHASRVLPGFTPDNKIAMLDRIKDETEILVCFNAKDLGRNKVRADLGITYEDDVLRL
+VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHAMSTIVSEQ
+GFGANEWSETTRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLE
+HPVNAAYEAATVDLDDINLIDPFHLAEYGERVTSYNRDVEVFPLLSALLEKVTGTTPYKS
+PTDMGVNMAGAAIVDDEVCQEAAKQEIIRRYYKAQVNEALEGADDTESERVALVMSKLGL
+SSEDRPVVGAAQLVAERTGEPGAAVQLADGTLVTGKTSELLGCSAAVLLNALKVLAGIED
+DVHLLSPASIEPIQTLKTVHLGSKNPRLHTDEVLIALSVSAATDENAKAAVEQLASLEGC
+DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR*
+>NZ_CP040019.1_762
+MTGTHETALPASTTDGRAASAPLRRIGFDRAKYIDLQSQHIQERRREIGGKLYLEMGGKL
+FDDLHASRVLPGFTPDNKIAMLERIKDETEILVCFNAKDLERNKVRADLGITYEDDVLRL
+VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHATARIVSEE
+GFGRNEWSQTTRDLVVVTAPGPGSGKLATCLSQVYHDHQRDIPSSYAKFETFPIWDLPLE
+HPVNVAYEAATADLDDINLIDPFHLAAHGEQVTSYNRDVEVFPLLAALLEKLTGTSPYRS
+PTEMGVNMAGAAIVDDEACREAARQEIIRRWYKAAVEEAANGESDEVSERIALIMSRLGL
+TSEDRPVVGASLLVAERTGEPGAAVQLADGTLVTGKTSALLGCSAAMLLNALKVLAGLSD
+EVHLLTPESIEPIQTLKTVHLGSTNPRLHTDEVLIALSVSAATDPNAKAAVEQLASLAGC
+DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR*
+>NZ_CP083691.1_729
+MTGTADMAPQKISRPLGFDREQYIALQSQHIQERRRQLGGKLYLEMGGKLFDDLHASRVL
+PGFTPDNKIAMLDRIKDETEILVCFNAKDLERNKVRADLGITYEEDVLRLVDVFRERGFL
+VEHVVVTQLEDSNHLALAFIEKLGRLGLKVARHRVIPGYPHAMATIVSEQGFGANEWSET
+TRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLEHPVNAAYEAA
+TVDLDDINLIDPFHLAEYGEKVTSYNRDVEVFPLLSALLEKVTGTTPYKSPTDMGVNMAG
+AAIVDDAVCRAAAEQEIIRRYYKAQVNEALEGADDTESERAALVMSKLGLSSEDRPVVGA
+AQLVAERTGEPGAALELADGTIVTGKTSELLGCSAAMVLNALKVLAGIDDDAHLLSPASI
+EPIQTLKTQHLGSKNPRLHTDEVLIALSVSAATDENAKAAVEQLASLEGCDVHTTTILGS
+VDEGIFRSLGMLVTSEPVFQKKGLYRKR*
+>NZ_CP097650.1_1917
+MTGTHETARPASTTTEAAASGPLHRVGFDRAKYIELQSQHIQERRRQIGGKLYLEMGGKL
+FDDLHASRVLPGFTPDNKIAMLDRIKDETEILVCFNAKDLGRNKVRADLGITYEDDVLRL
+VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHAMSTIVSEQ
+GFGANEWSETTRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLE
+HPVNAAYEAATVDLDDINLIDPFHLAEYGERVTSYNRDVEVFPLLSALLEKVTGTTPYKS
+PTDMGVNMAGAAIVDDEVCQEAAKQEIIRRYYKAQVNEALEGADDTESERVALVMSKLGL
+SSEDRPVVGAAQLVAERTGEPGAAVQLADGTLVTGKTSELLGCSAAVLLNALKVLAGIED
+DVHLLSPASIEPIQTLKTVHLGSKNPRLHTDEVLIALSVSAATDENAKAAVEQLASLEGC
+DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001638.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001638.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b12763357c784be40e23b9ac511efd28b96fe58b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001638.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_2000
+MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSRWTAGAAVVGAVTAYLVGFGLRR
+GAAMIASDLHALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMAG
+VAEAMLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR
+MAPWAWALPLLVLSFKHADDVGDALAARGID*
+>NZ_CP033200.1_1718
+MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSLWTAGAAVVGAVTAYLVGFGLRR
+GAAMIASDLRALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMTG
+VAEAVLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR
+MAPWAWALPLLVLSFKHADDVGDALAARGID*
+>NZ_CP040019.1_748
+MISLYVPGDSPLHRAPAGLKLALFAAWALAVTLAPPTPWTAGAAVGMALAAYLTGFGPRR
+GAAMLGRDLRALWVFYAFLFAAQWLFADLTAAALMVGRVLGLVLAAQVLTRTTRIAELVG
+VAEAVLAPVERIPWLGPRLARVGLRPERVGLAMGLVLASIGHLRSVAEQVRQAQASRGVR
+MAPWAWVLPLLVLSVKHADDVGDALAARGIE*
+>NZ_CP083691.1_711
+MLSLHVPGDSPLHRCPAGAKVAALAVWALVVTLAPVSALTAGASVVVGVGAYLLGFGLRR
+GVRLLAADLRGLWVFYAVLFAAQWLFTDLPTAALTTARVLGLVLAAQVLTRTTRIAEMAG
+VAEAVLGPVTRIPWLGPRLARAGVRPDRVGLAMGLVLASVGHLRGLAEQIRAAQAARGVR
+MAPWAWVLPLLVLSLKHADDVGDALAARGID*
+>NZ_CP097650.1_1935
+MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSLWTAGAAVVGAVTAYLVGFGLRR
+GAAMIASDLRALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMTG
+VAEAVLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR
+MAPWAWALPLLVLSFKHADDVGDALAARGID*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001643.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001643.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0365d366b9d6f58f237f18d2bb75cc5028268ff9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001643.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_2025
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG*
+>NZ_CP033200.1_1741
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG*
+>NZ_CP040019.1_687
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALHPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPTAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG*
+>NZ_CP083691.1_597
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASILWFTALGYGARLLARVLADPKAWRV
+VDLVIAVVMAVLAVRLIAGSGVWG*
+>NZ_CP097650.1_1964
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001649.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001649.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d925cda2a2325bd923db643cc49ada87d1f8cb0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001649.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_2031
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAAASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPATTPAVPETAAVTQEVR*
+>NZ_CP033200.1_1748
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAAASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPATTPAVPETAAVTQEVR*
+>NZ_CP040019.1_680
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLTRSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSARLAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLITDLDRA
+LAVVSAAGPAVLATTPAVPETTAVTQEVR*
+>NZ_CP083691.1_590
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALAGLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPETVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREAAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVSAAGPAVPAATPAVPETAAVTQEVR*
+>NZ_CP097650.1_1971
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAQHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTREQREAAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPAATPAVPETAAVTQEVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001653.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001653.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c8cf581528f80c4e76129291e98e3f190b10110
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001653.fa
@@ -0,0 +1,105 @@
+>NZ_CP042169.1_2042
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAP
+SPYRVQVQLQEAYDDAAEDGAGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALD
+DARRKLAEMVTTADALPAPAGRGHDGGGPAGLDAPAADGAAPPPPAGLDWRRVMEPLAGL
+HGPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRPLKRGAKGT
+WIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLA
+EAREVGVELVPLGLLTDVVLEAPVAVGLDVTAAPDGGLDVAPSLDPAPPGPGLSGVHAVG
+GIGFYRVELTDEEAVLHLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGA
+LPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRWSWLYFDPPRELGLDAGGDPLRDTR
+HEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPDYREL
+KAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHP
+AFDRLRALLSEAATLQEWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVE
+RLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDLGGILADDMGLGKTVQTLALFAHARQA
+RPEPPPFLVVAPSSVVSVWAAEAEKFTPDLDVRVLDTTTRKRGTAVADEVAGADVVVTSY
+TLLRIDAGQYGGLDWGGVVFDEAQFLKNRAAKVHTVARDLRAPFRLAITGTPMENSLSDL
+WALLDVVVPGLFPSHRRFRETYVTPIETGGDPERMAALRRRVRPFMLRRSKELVAKDLPS
+KQEQILQVELEPAHRKLYDRVLQRERRKVLGLLGDMDGNRFTIFTSLTLLRMLALAPQIV
+DDQYASVPSSKLERFLDDLTEVIGEGHRVIVFSQFTSFLRVIAEELDHLEIEHAYLDGST
+RGRADVIRGFREGEAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIG
+QERTVMVYRLVSEGTIEEKVLELQRRKAELFGALMDESDDSGAGAFTDSLTAEDIREMLG
+AEE*
+>NZ_CP033200.1_1761
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAP
+SPYRVQVQLQEAYDDAAEDGAGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALD
+DARRKLAEMVTTADALPAPAGRGHDGGGPAGLDAPAADGAAPPPPAGLDWRRVMEPLAGL
+HGPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRPLKRGAKGT
+WIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLA
+EAREVGVELVPLGLLTDVVLEAPVAVGLDVTAAPDGGLDVAPSLDPAPPGPGLSGVHAVG
+GIGFYRVELTDEEAVLHLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGA
+LPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRWSWLYFDPPRELGLDAGGDPLRDTR
+HEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPDYREL
+KAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHP
+AFDRLRALLSEAATLQEWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVE
+RLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDLGGILADDMGLGKTVQTLALFAHARQA
+RPEPPPFLVVAPSSVVSVWAAEAEKFTPDLDVRVLDTTTRKRGTAVADEVAGADVVVTSY
+TLLRIDAGQYGGLDWGGVVFDEAQFLKNRAAKVHTVARDLRAPFRLAITGTPMENSLSDL
+WALLDVVVPGLFPSHRRFRETYVTPIETGGDPERMAALRRRVRPFMLRRSKELVAKDLPS
+KQEQILQVELEPAHRKLYDRVLQRERRKVLGLLGDMDGNRFTIFTSLTLLRMLALAPQIV
+DDQYASVPSSKLERFLDDLTEVIGEGHRVIVFSQFTSFLRVIAEELDHLEIEHAYLDGST
+RGRADVIRGFREGEAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIG
+QERTVMVYRLVSEGTIEEKVLELQRRKAELFGALMDESDDSGAGAFTDSLTAEDIREMLG
+AEE*
+>NZ_CP040019.1_665
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAP
+SPYRVQVQLQEAYDDAAEAGAGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDAHQALD
+DARRKLAEMVTTADALPAPAGRGHDDAARPDAGPRGAAAGPDGESAAPEAPHSGLDWRRV
+MEPLAGLDAPRRLGAPPALAIGVELVAESSRNAFQQWGPAPAGEDQVREGRPLYVTLRPL
+KRGAKGTWIKGGLTWKNFQFGRAEFAPAQERAMRLIWRQLQAEDSYPTDAWFGLHSFDSP
+RIWQLLAEAREVGVELVPLGLLTDVVLEAPAAVGLDVARAPDGGLDVAPSLDPAPPGRGL
+AGVHAVGGIGFYRVELTDEEAVLHLIPAERPVPEAVQQLVLAGGPVRVPAVDREEFLGRI
+YPRLRGALPVTSGDASVELPEFEPPVLRLRADFRPDHELVLRWSWLYFDPPRELGLDAGG
+DPLRDTRHEDAVLRAVAELWPRAGRAEEQVLEGVAAARFSEQVLPLLQQAEHVRVDVTGH
+RPDYRELKSAPRIEVGTKATKNDWFDLGVQVSVDGHVLPFVELFTALVQGKTTLILADGS
+YLGLDHPAFDRLRALLSEAATLQEWTPENTAVSRHQVGFWEDLKELADEVEEDPEWTAAV
+GRLAAVERLPEAPEVPGLQADLRPYQEDGLRWLAFLWEQDLGGILADDMGLGKTVQTLAL
+SAHARQARPERPPFLVVAPSSVVSVWAAEAQTFTPDLDVRVLDTTVRKRGTDVAAEAAGA
+DVVVTSYTLLRIDAGQFGGIDWGGVVFDEAQFLKNRAAKVHTVARDLRAPFRLAITGTPM
+ENSLTDLWALLGVVVPGLFPSHRRFREAYVTPIETGEDPERMVALRRRVRPFMLRRSKEL
+VAKDLPPKQEQVLNVELEPAHRKLYDRVLQRERRKVLGLLGDMDGNRFTIFKSLTLLRML
+ALAPQIVDEQYASVPSSKLERFLDDLTEVIAEGHRVIVFSQFTSFLRVIAEELDHMEVAH
+AYLDGSTRGRADVIRGFREGQAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAEAQAV
+DRAHRIGQERTVMVYRLVSEGTIEEKVLELQRRKAELFGALMDESDDSGAGAFTDSLTAE
+DIRELLGAED*
+>NZ_CP083691.1_579
+MAPGVSGDPLPHLRTEAIRALVGPTSADRGFDIAAEGGVLRVTYDASRLRLTSAVRGTAP
+QPYRQAVRLQPSGETGPDGEPLLEPTAGRCQCPVGEDCKHVAAALYEITRRHADAARHAA
+REELASRVTTADRLPSPERAGAAPARPDAPAPEAGLPWRGVLESLAGLDGGPRRLAPPPD
+LAIGVELVAESSRNAFAQWGPAPAGEEHLREARLLYVIVRPLKRGAKGTWIKGGLTWKAF
+QFPRAEYDPAQERALRLIWRQLQAEDSYPTEGWFGLHAFDSPRIWQLLAEAQEAGVELVP
+QGILADVVLDAPVEVGLDVASAPDGGLEVAPSLAPAGGAGEGAPADDAAARPDAERLRDT
+HAIGSIGFYRADEEEDGTWTLHLLPAVRRVPEPVQEMVLAGRPVHVPTADREEFLGRIYP
+RLRAALDVGSADASVELPEFEPPVLRLQADFRPGHRLVLRWSWLYFDPPRELGLGHDGLR
+DPRHEEAVLRAAAQVWPRVGRAEEQELEGVGAARFSESVLPQLQRLDHVRVDVTGERPDY
+RELKAAPRIEVSTKAAQNDWFDLGVQVSVDGHVLPFVELFTALVHGKTTLMLQDGTWLGL
+DHPAFDRLRALLSEAAALQEWTPEHTTLSRHQVGFWEDLKELADEAEEDPEWTAAVGRLA
+AVERLPEAPAVPGLKAELRPYQEDGLRWLRFLHDQDLGGILADDMGLGKTVQTLALMAYA
+RAEHPDRPPFLVVAPSSVLSVWASEAAKFTPGLDVRVLDTTTRKRGTSVTEAAEGADVVV
+TSYTLLRIDAAQHADASWAGIVLDEAQFLKNRASKVHQVARDLRAPFRLAITGTPMENSL
+SDLWALLEVVVPGLFPSHRRFRETYVTPIETGEHPERMASLRRRVRPFMLRRSKELVAKD
+LPPKQEQVLRVELDAAHRKVYDRVLARERRKVLGLLGDMDGNRFTIFKSLTLLRMLALAP
+QIVDREYAAVPSSKLERFLDDLEEVLAEGHRVIVFSQFTSFLRVVAEELDAMEVEHAYLD
+GSTRNRAEVIQDFREGDAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAENQAVDRAH
+RIGQERTVMVYRMVSEGTIEEKVLELQQRKAELFGALMDESDDSGAGAFTDSLTADDIRE
+LLGAEE*
+>NZ_CP097650.1_1983
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAP
+SPYRVQVQLQEAYDDAAEDGAGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALD
+DARRKLAEMVTTADALPAPAGRGHDGGGPAGLDAPAADGAAPPPPAGLDWRRVMEPLAGL
+HGPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRPLKRGAKGT
+WIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLA
+EAREVGVELVPLGLLTDVVLEAPVAVGLDVTRAPDGGLDVAPSLDPAPPGLGLSGVHAVG
+GIGFYRVELTDEEAVLHLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGA
+LPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRWSWLYFDPPRELGLDAGGDPLRDTR
+HEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPDYREL
+KAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHP
+AFDRLRALLSEAATLQEWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVE
+RLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDLGGILADDMGLGKTVQTLALFAHARQA
+RPERPPFLVVAPSSVVSVWAAEAEKFTPDLDVRVLDTTTRKRGTAVADEVAGADVVVTSY
+TLLRIDAGQYGGLDWGGVVFDEAQFLKNRAAKVHTVARDLRAPFRLAITGTPMENSLSDL
+WALLGVVVPGLFPSHRRFRETYVTPIETGGDPERMAALRRRVRPFMLRRSKELVAKDLPS
+KQEQILQVELEPAHRKLYDRVLQRERRKVLGLLGDMDGNRFTIFTSLTLLRMLALAPQIV
+DDQYASVPSSKLERFLDDLTEVIGEGHRVIVFSQFTSFLRVIAEELDHLEIEHAYLDGST
+RGRADVIRGFREGEAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIG
+QERTVMVYRLVSEGTIEEKVLELQRRKAELFGALMDESDDSGAGAFTDSLTAEDIREMLG
+AEE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001658.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001658.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1121b5d5e22a2d833766bb9f7f8e6b4e397da612
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001658.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_2049
+MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT
+GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE
+SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR
+SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM
+AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG
+VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR
+GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV
+PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT
+YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI
+SAEVVRDELRHDARRVRPAGPGGSGT*
+>NZ_CP033200.1_1768
+MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT
+GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE
+SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR
+SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM
+AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG
+VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR
+GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV
+PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT
+YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI
+SAEVVRDELRHDARRVRPAGPGGSGT*
+>NZ_CP040019.1_658
+MSAAPNVASGAAAHDDGPRAVVIGGGFAGLATAGLLARDGHRVTLLERNDGLGGRSGRWS
+AEGFAFDTGPSWYLMPEVIDRWFRLMGASAAERLDLRRLDPGYRVYFEDHLDAPPVDVRT
+GHAEELVESLEPGAGERLRAYLDSAGRVYELAKEHFLYTDFRRPADLARPAVLRALPSLG
+PQLLGGLRAHVAARFRDPRIRQILGYPAVFLGTSPDRAPAMYHLMSHLDLRDGVQYPIGG
+FAALVDAMADLVREAGVEVVTGAEATRIEVEDAERRRRRRGRVTGVVVRQDGTERRLSAD
+VVVAAADLHHVQTALLPPAQRVAESAWDRRDPGPSGVLVCVGVRGALPQLAHHTLLFTAD
+WEDNFGRIERGEDLAADTSLYVSRTSATDPGVAPDGDESLFVLVPAPAEPGWGRGGIRVR
+EGDGWRVEREGDAQVEAVADRALDQLARWAGIEDLHERIVVRRTIGPGDFAADVHAWRGS
+MLGPGHTLAQSAMFRPSVRDADVAGLLYAGSSVRPGIGVPMCLISAEVVREELRHAARRD
+ALRAQRRGRSQDDDDGARRGRVAAS*
+>NZ_CP083691.1_574
+MTPTTPAARPAAAPSGSRRVVVIGGGFAGLATAGLLAQDGHRVTLLEKNPVLGGRSGRWS
+AEGFTFDTGPSWYLMPEVIDRWFRLMGTSADEALDLRALSPAYRVYFQEHAADDAAAPGD
+GSTPGARAPLDVVSGREESLALAEELEPGAGGRLAAYLDSAERIYALAKRRFLYTDFQDL
+TELLRPDVLRALPALAPQLLGDLRGFVARRFEDGRLRRVLGYPAVFLGTSPGKAPAMYHL
+MSHLDLADGVQYPIGGFAALVDAMAELVRAAGVEIVTAAEVTAVDVVSDPRPRGRLPRLL
+DGAPRPWEPRTPAGGRRRSGHVRGVSWRDAEGGSHRLDADAVVAAADLHHVQTALLPGDQ
+RVAERTWDRRDPGPSAVLVCVGVRGRLPELLHHTLLFTEDWDENFRRIDEGEDLQEETSL
+YVSMTSATDPGVAPEGDESLFLLVPAPAVPEWGRGGVRTPEEDRAGDAQVETVADRALAQ
+LARWAGVPDLGERIVVRRTWGPADFTADVHAWRGSLLGPGHVLRQSALFRPPVRDPRVAG
+LVYAGSSVRPGIGVPMCLISAELARDAVSGVRPGGAAPGAPAMAGR*
+>NZ_CP097650.1_1990
+MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT
+GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE
+SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR
+SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM
+AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG
+VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR
+GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV
+PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT
+YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI
+SAEVVRDELRHDARRARPAGPGGSGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001661.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001661.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6b6ba34de98528cbd1e931484208517a10fedb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001661.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_2053
+MQTPATPSPHDRPSPVARPWMAASDVPVAGPDDVERVVLLSPAGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEAGRFLLTRRALGKAAFPGVWTNGFCGHPGPGEPPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDPR*
+>NZ_CP033200.1_1772
+MQTPATPSPPDRPSPVARPWLAASDVPVAGPDDVERVVLLSPEGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEADRFLLTRRALGKAAFPGVWTNGFCGHPGPGESPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDPR*
+>NZ_CP040019.1_653
+MQTPATPSPHDRPSPVVRPWMAAPDLPIAGPDGVERVVLLSPAGEAVGTEAKAAVHRRTE
+DGGTPLHLAFSCHVYDDAGRFLLTRRALGKKAFPGVWTNGFCGHPGPGESPAQAVLRRAP
+QELGAEVSDVVEVLPDFRYRAADASGMEEHEICPVFQARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFEAR*
+>NZ_CP083691.1_570
+MQQGPSDPRTVEEVEERVVLLGADGAPIGTEAKASVHRNAADGGTPLHLAFSCHVYGPDG
+RFLLTRRALGKKAFGGVWTNGFCGHPAPGEAPAEAVLRRAPQELGVGVREVTPLLPGFRY
+RAADAGGVEEHEVCPVFRAECDGDPVPERDEVAEWCWVEVADLTAALASVPRVFSPWLVM
+QWEQGAFGPR*
+>NZ_CP097650.1_1994
+MQTPATPSPHDRPSPVVRPWMAASDVPVTGPDDVEHVVLLSPAGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEADRFLLTRRALGKAAFPGVWTNGFCGHPSPGESPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001665.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001665.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ebebdd40c11f494bd7678cf23e19303504d0976
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001665.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_2059
+MSDYQPRRPGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TIKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD*
+>NZ_CP033200.1_1779
+MSDYQPRRPGSKSTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD*
+>NZ_CP040019.1_649
+MSDYQPRRPGSNPAPARRTDRAGKPALGRPKRGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPQTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLAERQAKA
+KEIGLPAFRAKQLSVHYFERYTTDPEQMTDLPKDKREVIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVRANQVIAEGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPAPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVERLNAAGIPTTLRDTRGKEIDGACGQLAAGDEDA*
+>NZ_CP083691.1_565
+MEGMSDYTPRRPGSKPTPARQKDRAGKPALGRPRRGMIDEPEARQLAEDRERMHRAGVGH
+QLSAPPRRAAEVDADRPQVMPKTEGWQQPMGPDGRPQLQFKQPRVSQPPQHLADMTLAER
+QAKAKEIGLPAFRAKQLSVHYFEHFTTDPEQMTDLPKGKREEIAEAFFPPLLTEVRRLTT
+DRGDTVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTA
+EIVEQIVRANQVIAEGGLGGTRRDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDP
+APEGLGMSARHVTLSTVGLVPAIKKLAQEGVPLTFALSLHAPDDELRDELIPVNARWKAD
+EAIDAAYEYFLATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTP
+GSIWTASEKDVTREFVDRLNAAGIPATLRDTRGKEIDGACGQLAADDEDVAARA*
+>NZ_CP097650.1_1998
+MSDYQPRRTGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSPAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001666.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001666.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0dc336aed0d1a789e8deebb75eeff0def76876c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001666.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_2061
+MSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREVVADLKRGARI
+TTFLPALAEREATRRLQAATPAHEAMAVAA*
+>NZ_CP033200.1_1781
+MSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREVVADLKRGARI
+TTFLPALAEREATRRLQATTPAHEAMAVAA*
+>NZ_CP040019.1_647
+MSINTVHHLPAAPSPLMQRHVLKRVEETLARRFEGVATAEAVRATVREVASELKRSARMT
+MFLPALTEREAARRLQAGAPAHEPLAAAA*
+>NZ_CP083691.1_564
+MTATLTTQHHMPVHPDTTMQQRVLERIAGTLIRRFDGSVPAADVRTTVAEVTAELEAEAR
+LTTYLPALTEREALNRLEAMAAAPAHMTITHARHAA*
+>NZ_CP097650.1_2000
+MVRQPKEVLTVSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREV
+VADLKRGARITTFLPALAEREATRRLQAATPAHEAMAVAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001674.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001674.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5261ed26c5157c32e51e5e21bca5ef11023207a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001674.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_2071
+MTQTTSTPARLRARDGFVLAARHFAPTTAPQARPAGAVVIAPATGVKATYYRRYAEFLAG
+HGFHAVTFDYRGVGESREPFAVARQARWADWGALDADAVLGWARTHLPGPLLTVGHSYGG
+FGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHAAMPVVTLARGHLPGRRL
+GWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTEAA
+LDRADAYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPTFWPATLEWLRDGVAPDAAR
+*
+>NZ_CP033200.1_1791
+MTQTTSTPVRLRARDGFVLAARHFAPTTTTPPARPAGAVVIASATGVKATYYRRYAEFLA
+GHGFHAVTFDYRGVGESREPFAVARRARWADWGALDADAVLGWARTRLPGPLLTVGHSYG
+GFGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHAAMPAITLARGHFPGRR
+LGWLEDLPRGVALDWARSRRDFTASARTTAGRDELRRRLAAFTADALIVAPVDDDFGTDA
+ALDRADAYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPAFWPATLEWLRDGVAPAAA
+R*
+>NZ_CP040019.1_637
+MTQTTSTPVRLRAPDGFVLAARHFTPTTTTPPASPAGTVVIASATGVKATYYRRYAEFLA
+GHGFHAVTFDYRGVGESREPFAVARRARWADWGVLDADAVLGWARTHLPGPLLTVGHSYG
+GFGIGLADEARHVARHVAVGGQHAHWRDYRARPGRVRMWARWHAAMPAITLARGHFPGRR
+LGWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTDA
+ALDRADSYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPTFWPATLEWLRDGVVPAAA
+R*
+>NZ_CP083691.1_553
+MTQTTSTLVRLRARDGFVLAARHFAPTTTPPARPAGAVVIAPATGVKATYYRRYAEFLAG
+HGFHAVTFDYRGVGESRAPFAVARRARWADWGALDADAVLGWARTHLPGPLLTVGHSYGG
+FGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHALMPMVTLARGHFPGRRL
+GWLEDLPRGVALDWARSRRDFTASARTVAGRDELRRRLAAFTADALIVAPVDDDFGTDAA
+LDRADSYSPGRRTVRWRVRPEELGVGEIGHFGLFHARFASTFWPATLEWLRDGVAPAGAR
+*
+>NZ_CP097650.1_2010
+MTQTTSTPARLRARDGFVLAARHFAPTTAPQARPAGAVVIAPATGVKATYYRRYAEFLAG
+HGFHAVTFDYRGVGESREPFAVARQARWADWGALDADAVLGWARTHLPGPLLTVGHSYGG
+FGIGLADEARHVARHVAVGGQHAHWRDYRARPGRVRMWARWHAAMPAITLARGHFPGRRL
+GWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTDAA
+LDRADAYSPGRRTVRWRVRPEELGVTEIGHFGLLHARFAPTFWPATLEWLRDGVAPDAAR
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001675.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001675.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a2ddaa98631f17d3af34223ef0cc50afd92e57f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001675.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_2072
+MTTMKAAVVTQFGTEADVTEVERPTPGQHEALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD*
+>NZ_CP033200.1_1792
+MTTMKAAVVTQFGTEADVTEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD*
+>NZ_CP040019.1_636
+MTTMKAAVVTQFGKEADVQEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSAD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFEEMRHGKIEGRVVIDYAMQD*
+>NZ_CP083691.1_552
+MTTMKAAVVSQFGKEADVKEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWGACGHCQYCRTGWETLCEEQINGGYSMN
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFEEMRHGKIEGRVVIDYAMQD*
+>NZ_CP097650.1_2011
+MTTMKAAVVTQFGTEADVTEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001676.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001676.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67fe49918e45b6f73aa1441a8328f970c089326b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001676.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_2073
+MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+AALDAAWKAAPAWGATSPAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP
+LAIDHFRYFAGAIRAQEGRLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF*
+>NZ_CP033200.1_1793
+MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMAADDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF*
+>NZ_CP040019.1_635
+MTVYAFPGTEGAKVEFKPRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKIISYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF*
+>NZ_CP083691.1_551
+MTVYAFPGTEGAKVEFKPRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAIRETLNADLP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE
+ICTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF*
+>NZ_CP097650.1_2012
+MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADLP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASVMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMAADDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001680.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001680.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd48df35859ece0f7dc00e4ad94ccd0859a5891e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001680.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_2077
+MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLHDSGIENVVCRHEGGA
+TYMAEADGKMNVVPGVAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQ
+EFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGRPGPVVVGLPEDVIREEIDAHL
+HPQIPVASGGMTVGDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAAE
+WRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDVVTNGFTIRQNWDKK
+NFLVTIDPSLRGRSGPVSHQIVAKPDGFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAAL
+PPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNWAHRYFPTEGYRSMISARNGSM
+GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIRT
+HQERQYPGRVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALI
+HLIVEQRVKAY*
+>NZ_CP033200.1_1797
+MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLYDSGIENVVCRHEGGA
+TYMAEADGKMNVVPGVAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQ
+EFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGRPGPVVVGLPEDVIRQEIDAHL
+HPQIPVAPGGMTVEDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAAE
+WRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDVVTNGFTIRQNWDKK
+NFLVTIDPSLRGRSGPVSHQIVAKPDVFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAAL
+PPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNWAHRYFPTEGYRAMISARNGSM
+GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGAKPLVIVMDNQEYGTIRT
+HQEREYPERVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALI
+HLIVEQRVKAY*
+>NZ_CP040019.1_631
+MSQTTEAGGRLSAGHVIVKTLESHGVRRIYSVPGESYLDVLDGLHDSQIENVVCRHEGGA
+TYMAEADGKMNEVPGIAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHREKEAFQ
+EFDPHAWFGTGAKRVMVLDHADRASEIVAEAMFAATSGRPGPVVVGLPEDVIREQIDATL
+HPVIPVATGGMTVEDWKSLHSALKESKKPLFITGGNDWTDEGAQQLTQWLEGHKIPAAAE
+WRTEGTVPFSSPSYVGPIGYGRPKPTYDLLEETDLIVFIGTVPGDVVTNGFKIRQNWDKK
+NFLVTIDPSLRGRSGPVSHQIVAKPDVFVRDLVRMDLDVKPEWEEWTSRMRGEQETFAAL
+PPAEPSEGQAKMATLMANLMPKLPKDSMISLGAGEHTNWAHRYFPTEGYRAMISARNGSM
+GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIRT
+HQEREYPERVSGTQLKNPDFAGMAEAFGGLGIRVEKDADVPAAVDAALKAVQEEGRFALI
+HLIVEQRVKAY*
+>NZ_CP083691.1_547
+MSQNSEAPGRLSAGHLIVKTLESHGVRRVYSVPGESYLDVLDGLHDSAQIENVVCRHEGG
+ATYMAEADGKMNEVPGIAMVTRGPGAANAHVGLHTAWQDSTAMVLFVGLIPFEHRDREAF
+QEFDPHAWFDSGAKRVMVLDHPERASEIVAEAMFAAASGRPGPVVVGLPEDIIRVEVDAH
+LHPQIPVAPGGMTVEDWKSLHAALKESQKPLFITGGNDWTDAGAEALTSWLEDHKIPAAA
+EWRCEGTVPFSSPSYVGPIGYGRPDFTQHLLEETDLIVFVGTVPGDVVTDGFTIRQNWDK
+KNFLVTIDPSLRGRSGPVSHQIVAKPDVFVRDLVRMDLAVKPEWEAWTSRLRGQQEEFAA
+LPAAEPGDGQAKMATLMATLMPKLPKDSMISLGAGEHTNWAHRYFPTEGYRAMISARNGS
+MGYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIR
+THQEREYPERVSGTQLKNPDFAAMAEAFGGFGVRVEQDADVPAAVDAALKAVQEEGRFAL
+IHLIVEQRVKAY*
+>NZ_CP097650.1_2016
+MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLHDSGIENVVCRHEGGA
+TYMAEADGKMNVVPGVAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQ
+EFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGRPGPVVVGLPEDVIREEIDAHL
+HPQIPVAPGGMTVEDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAAE
+WRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDAVTNGFTIRQNWDKK
+NFLVTIDPSLRGRSGPVSHQIVAKPDGFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAAL
+PPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNWAHRYFPTEGYRSMISARNGSM
+GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIRT
+HQERQYPGRVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALI
+HLIVEQRVKAY*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001681.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001681.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0de0b08437ff4056b237dc5fbabd26b3284d62fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001681.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_2078
+MLSAPTLTRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+VRGRELRGRLAEVWALAAVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELVRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAEAAPATDPAGPEEAEAPEAVADEAAPADKPRQETEKEKKERKKAEKKAEKKA
+RKKAEKKARKKKSDKKKD*
+>NZ_CP033200.1_1798
+MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+VRGRELRGRLAEVWALAAGDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAESAPAADPAGPEEAEAPEAVVDSEAAADEPRRETKKEKKERRKAEKKARKKA
+EKKAGKKKSDKKKD*
+>NZ_CP040019.1_622
+MLSPRTLARLSSVAAFLNTAPGPRGGQEAPERFTAATQLPALVPELQEGEVRLRLAAAAA
+VRARELRERLTRVWALAATDESAAVERVNELLAEAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMATLALAETAMDGELARLRVCEGEDCENALVDGSRNRSKRFCDEANCANRTHVRSY
+RARLAEAAEAAPATDPAGPEEAEGTEAVVDEAAPADEPLQETEKEKKERRKAQKKARKKA
+EKKAGKKKSDKKKSDKKKD*
+>NZ_CP083691.1_545
+MLSPHTLARLASISAFLNTAPGVRGGQEAEERLTAGTQLPALVPELQEGESRLRVAAAAR
+TRAHELRARLTELWAAADAEDVPAAVAAVNELLAETGPLRLEVSDGSADLAPAQVPADAV
+ERLTAMAALALTEAALEGELTRLRVCAGEDCENTLVDASRNRSKRFCDAANCANRTHVRS
+YRARLAEAEDTQADVEAADAAPLPEVAPEADPQDATDLEAIEAAEGVESAVQEPVKKDST
+KDKKSKSEKKARRAAKKKAEKESEAAAEGKKGKREKSKKSEKHKKKAAKD*
+>NZ_CP097650.1_2017
+MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+GRGRELRGRLAEVWALAAVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAESAPAADPAGPEEAEAPEAVVDSEAAADEPRRETKKEKKERRKAEKKARKKA
+EKKAGKKKSDKKKD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001683.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001683.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce335429c53bfc20f93bed4689295f297e4b80d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001683.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_2081
+MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR
+RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE
+FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV
+RRDRGTARGL*
+>NZ_CP033200.1_1801
+MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR
+RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE
+FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV
+RRDRGTARGL*
+>NZ_CP040019.1_619
+MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAAPGLTWMKVSLALYLAFSGSAMWEYLR
+REPVPVAMRSPLSMAAAASMLGVIVLLFLGTPAGVGLAAAAALVLGGAAELVAWARHRRE
+FIPARDQLWTGLVGLLSGLGVAFGALQGFGPHALLGIAGGGAIIIGVLLLVSGLGFHHEV
+RRDRGTAKGL*
+>NZ_CP083691.1_543
+MTSPQTPLEISSEVFKPVLIRAGVALIFGLTTVFVQNPGLTWMKVAFALYLVFSGSALWE
+YLRRDPVPVGMRSPLSLAAAAWMLGTVVLVIMGSPAAVGIVVGLALLAGGAAELTAWARF
+RREFIPARDQLWTGLVGALSGLGVLVGAVQGFGPHALLGIAGGGAIIVGVLMLISGLGFH
+HEVRRDRGTAKGL*
+>NZ_CP097650.1_2020
+MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR
+RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE
+FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV
+RRDRGTARGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001686.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001686.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d951c62df629af08dde219e533b06b3c44c845d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001686.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_2084
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFVTA*
+>NZ_CP033200.1_1804
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFVTA*
+>NZ_CP040019.1_616
+MALFSQPVFINLPTTDTERIREFWTSLGAQAIEDFSDENSVCIELTESTFAMYLSPGYYT
+DFIGDREIADCMTTNSALMALTVGDAAAVDALADRAIEAGAAEVPLPVDLREEMVDSGMH
+SREIVDPDGHQWEFVTA*
+>NZ_CP083691.1_540
+MRTRWSTVLVMALFSQPVYINLPSTDTERIREFWTSMGADIDEDFSDENSVCVQLTESTF
+AMYLSPGFYTDFIGDREIADCLTTNSVLLQLTAPDRGAVDALVRAAVEAGGSEVPLPDEL
+QEDMTATGVHSRQVVDPDGHQWEFMAA*
+>NZ_CP097650.1_2023
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFITA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001688.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001688.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb46d761eda0bda854eae3e26d9d0676d0a5ea33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001688.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_2087
+MNLRTLLREALTAARTAPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPAARV
+LTVTDSGGTGFLTGATVATLAGLDSAEAALARDMPVDTVNAAIGAGGTRVAVTHVVGTVD
+RGVELTRGRLPGPGEVVVPEAKLAELGLAQPSGALESGDGRQWAVVGAFEALTPFEDLAD
+YAIAVPAAPASLVVQQVRVLAPDTAGTRAMQDSALAVIDPDPRSSQVQTARALAAGNATI
+TGELAGLGRSLLLLILGAGAFFVAIVVLADVLIRRRDLGRRRTLGIGRADLVLLVAVRTA
+APAVLGAVVGAGTGYAVVVGQGGALGLDFVAGVAVLAALTAVVASLLPAAFAAFRDPVRV
+MRTA*
+>NZ_CP033200.1_1806
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTGIGRGGARVAVTNVVGTLD
+RGIVLTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGGQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA*
+>NZ_CP040019.1_613
+MNLRTLLREALTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPAARV
+LTVTDSGGTGFLTGATVTTLAGLDAAEAALARDMPVDTVNAAIGAGGTRVAVTHVVGTLD
+RGVELTRGRLPGPGEVVVPEAKLAELGLAQPSGALESGDGRQWAVVGAFEARTPFEDLDG
+YALAVPATPASLVVQQVRVLALDTAGTRAMQDSALAVIDPDPRSSQVQPARALAAGNETI
+TGELAGLGRSLLLLILGAGAFFVAIVVLADVLIRRRDLGRRRTLGIGRADLVLLVAVRTA
+APAMRGAAVGAGAGHGLVLAQGSALGSAFVVGAAVLAVLTAVVASLLPAAFAAFRDPVRV
+MRTA*
+>NZ_CP083691.1_537
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTWIGRGGARVAVTNVVGTLD
+RGIELTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGRQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA*
+>NZ_CP097650.1_2025
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTGIGRGGARVAVTNVVGTLD
+RGIVLTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGRQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001692.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001692.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7942890d440cce10a082e669c9ed78f7563c68cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001692.fa
@@ -0,0 +1,65 @@
+>NZ_CP042169.1_2091
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLV
+AVVLNVWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALIAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPARTFVRETAPSEGTFVRE
+TAPSAASGPDVVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNLVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRSELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPEGYDTVIEHDASNVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGS
+HAELLAAKGAYHRLYMSQFKGGEDDDGAASRDDAR*
+>NZ_CP033200.1_1811
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLV
+AVVLNVWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALVAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPDGTFVWETAPSESAFVRE
+TAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGS
+HDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR*
+>NZ_CP040019.1_606
+MSGTEKHGSTAAPQGEVGELTDAEIAAFQEAGVTDEWGEGPPRKAKAFWPSAMRLLGLFA
+PERTGLILVSLMVLVAVVLNVWAPHVLGQAMDVIFGGLISRDMPAGLTREQVIEGLRGQG
+QGQAADMLSGMAFVPGQGIDFAELARLILIVLGMYVVAQLFMWLQGRVLNDLVMRIVFRL
+REDIEAKLNRLPLSYFDTRQRGDLLSRTTNDVDNVQQAMQQAFATLVYSVLTIIGIVGMM
+FWLSWQLALIALIALPVAGVMVGVIGSKSQKLFTAQWRETGRLNGHIEESFTGHELVTVF
+GRQADMAERFDERNEAMYEASFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMT
+LGAVTAFIQYSREFNQPLGQVAGMSNMLISGVASAERIFELLDEDEQDSDAEVARRASDD
+DVAEPADASVRETGASADDDVAHLPQPVAGRVEFEHVRFSYTEAKPLITDLNLVAEPGQT
+IAIVGPTGAGKTTLVNLIMRFYEVDGGRILVDGVDTRTVSREELRSHTGMVLQDAVLFGG
+TIRENIRYGRQDATDEEVVAAAKATFVDRFVHTLPEGYDTVIEQDASNVSAGERQLITIA
+RAFLAQPSLLILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVME
+HGDIVEQGNHAELLAARGAYHRLYMSQFKGGEDDGGGAASGEDAR*
+>NZ_CP083691.1_531
+MSEQLTDQEIVELQESGATDEWGGGPGRKAKAFWPSAKRLLGLFRTEKAGLALVAAMVLV
+AVVFNVWAPHVLGRAMDVLFGGVISKGMPAGVSREQVIEGLRGQGQGQAADMLSGMDFTP
+GQGIDFDALARLILTVLGMYVVAQGFMWLQGRVLNDVVMRIVFRLREQIEAKLNRLPLSH
+FDTRQRGDLLSRATNDVDNVQQAMQQAFATLVYSVLTIFGIVGMMFWLSWELALIALIAL
+PVAGVVVGVVGKKSQALFTAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAERFDERND
+AMYEASFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQVAGMSNMLISGVASAERIFELLDEPEEEPDDVVAARADDDVAHLPQPVAGRVEFE
+HVRFSYTEAKPLITDLNLVAEPGQTIAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVD
+TRRVPRQELRAATGMVLQDAVLFGGTIRENIRYGRLEATDEEVLAAAKATYVDRFVHTLP
+DGYDTVIEQDASNISAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQQAMAALR
+NDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGSHEELLAARGAYHRLYTSQFRGGEDEH
+HDDGAPASR*
+>NZ_CP097650.1_2030
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLAVVAVMVLV
+AVVFNVWAPRVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALVAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPDGTFVWETAPSESAFVRE
+TAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGS
+HDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001695.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001695.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2324f707126a8a5e0f161878129cdca4cc9213f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001695.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_2094
+MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT
+VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT
+VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT
+TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA
+IELVRMRSEVSAAWTEMRRSTDPR*
+>NZ_CP033200.1_1819
+MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT
+VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT
+VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT
+TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA
+IELVRMRSEVSAAWTEMRRSTDPR*
+>NZ_CP040019.1_596
+MKPAGALALEFRADSFDHPGGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+SVPVDHRAVVQARVVHTDGADVHVQTRLLLPEVKDESGDPVVATSSLVVYSAEEDGARVT
+VPAWVPSTPGQIERDEQASRSTVARRAVERGMARLPFPSPGQAPEEMSTLAFLAPASEAT
+VGGTMNAGAILRWLDEAAAVCAARWTGHESVVAVFGGGVRFVRNILVGDLVRVDALLVNT
+TERSMQVALRVYAGRPTGVQPRLVAHSIAVMVDVSAEDKAQPVRQYVPESEGARSLQEAA
+VQLVRLRSEVGAAWTETRRSPESR*
+>NZ_CP083691.1_520
+MMRSGALSLDFRADSFDHPSGLVDAGTAIGWIDKVGYAVAASWSGTYVRARYMGTMQFRH
+PVPVDMRVTVQGRVVRTHGAAVHVQLRLLLPEVLDDDGRPVVSTSTLSVYYAEEDGQMLQ
+VPEWTPSTPDQIERDERARVSSVERRGIEQVMARLPFPEPGQEHEEMTTLAFIAPMAEAS
+VGGTVAAGAVMRWLDEAAGVCAARWTGHENVVAVFAGGVRFVRPVKVGDLVRVDALLVHT
+SERSMHVALRVHAGPRHQRDHRLVAHSIAVMVDVTREGRAESVRPYAPGSPAAHRLEESA
+VELVRLRSEAGAVWSDPS*
+>NZ_CP097650.1_2038
+MRPPGALALEFRADSFDHPTGLVDAGTVVSWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEDGVPVT
+VPAWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT
+VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT
+TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEGQAQPVRQYVPESESARRLQETA
+IELVRMRSEVSAAWTETRRSTDPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001699.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2fadc5569383c38b1487d69542b29781a17f4b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001699.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_2101
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTAFGVAPGDLGGAIGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPHMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR*
+>NZ_CP033200.1_1826
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTVFGVAPGDLGGAVGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPQMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR*
+>NZ_CP040019.1_585
+MQVLLALTPILLTLALLLTRLPAWVAPAAGGVLAAALAPTVFGVDPGVLAAEVGRGVPTV
+VEILAIIAGGITLSRVMEHSGAHARLALWLSAGNGPTLATALLMVHGIIPFLETVTGFGV
+SLIVGVPLLLGLGFTAFRSALLAVLALTIGPWGSMAPGTLMGARLYDLDFQAVGVTAALF
+NLPASLVAGAATVLLLRGAQGMRGDGEPARTVPWLAVGLLSGAAQWALILGANLSVGTAP
+AGAVGTFVLTVAWLLVIRRGRLTPGPGRDVVPYVTLMAGTVFGTTVEDALGLTGVLSVVG
+TPALWSFVAVGAGVALLGLGPHARRTVPGEAARLWVGTAIPNALYVAFGLTLSAGGVSQA
+LAGALSGMGPAYLAAIPVIGAFSGFVTASNTGAMALMGPLQMDTGAALGVPPTWTNGLHN
+AAAGWGIIAGPARIQVAHAMAVGAQTPEMPGWAVSRRALLAVLLPAMVVGIALMSLLGLA
+VLPRV*
+>NZ_CP083691.1_507
+MQVLLALAPILLTLGLLMTRLPAWAAPAAGSVAAVVLGLTVFGVDPAVLGAAVGHGVPTV
+LEILAIIAGGITLSRVMEHSGAHARLGGWLSAGNGPTLATALLMVHGVIPFLETVTGFGV
+SLVVGVPLLLGLGFTAYRAALLSVLSLTIGVWGSMAPGTLMGARLAGLDVQEVGVTAAVF
+NLPASLVAGVATVLAVRGARGLRDDSAPARLAPWLGVALASGTAQWALILGANLLVGTAP
+AGAVATFALTLAWLLVIRRGRLTPGPGRDVVPYVTLMAGTVLGTTAEDALGLTGPLSVVG
+TPALWSFVAVGVGLRLLDLDAAARRTVPRESLRLWRGTAVPNALYVAFGLVLSAGGASPA
+LAGALSGLGESYLAAMPFIGAFAGFVTASNTGAMALVGPLQMDTGAALGVPPAWSNGLHN
+AAAGWGIIAGPARIQVAHGMAAPAQTPDMPGRAVSPRGLVAALLPASLAGVAGMSLMGWL
+LLPR*
+>NZ_CP097650.1_2045
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTAFGVAPGDLGGAIGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPQMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001700.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001700.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33b730bc4859bd548757a3f8b33f6b21410d5882
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001700.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_2102
+MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA
+QVDALRALLGAERPDRWGVNLFVPDAVNTAIPAAARTEAARSARAAAVAAYRAGLTADGA
+ADLPAVADVVPDPDAERADFEAMLVAAEEQAWPLVSFTFGLPAADVFARLAAAGVPAGAT
+VTDAAEARAALEHGAAFLVVQGHRAGGHRGTSDPAAEPTRAELPTVLAAVRDVVGTGAAS
+AAPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA
+DDGRARTALTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAVGDLERVH
+LWAGTEAHRVREAPAADVLASLTP*
+>NZ_CP033200.1_1827
+MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA
+QVDALRALLGAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARAAAVAAYRADLTADGA
+ADLPTAADVVPDPDAERADFDALLTAAEEQAWPLVSFTFGLPAADVFARLAAAGIPAGAT
+VTDATEARAALEHGAAFLVVQGHRAGGHRGTSDPAAEPPRAELPAVLPAVRDVVGTGATS
+AVPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA
+DDGRARTGLTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAAGDLERVH
+LWAGTEAHRVREAPAVDVLASLTP*
+>NZ_CP040019.1_584
+MSAAQLPDDVVRARLIPPARVLAAPMAGGPSTPELVAAVVRAGGSGFLAGGMRTAAQVRE
+QVDALRGLLGGGDGSVDGSDAARRWGVNLFVPDAVNTAIPAADRTERARAERRAAVAAYR
+ERLAAEGERAAGGAAAEGAGGAPTLPSPDDVTPDPARERAEFAAMLTAAEEQAWPLVSFT
+FGLPEPAVFARLAAAGIPAGVTVTDADEARSARAHGAAFLVVQGHRAGGHRGTLDPAADP
+VERELPSVLAQVRAVVGTRVPVVAAGGVGAAAHVRSLLAAGADAVAAGTAFLLAAEAGTS
+VAHRAGIRRCAAGEGFVGPDGAARTVLTRAYTGRWARTLATDFAAAHPDAPAAYPELNAL
+TTGLRAAAATAGDLERVHLWAGTQAHTAREAGAADVVAGLTP*
+>NZ_CP083691.1_506
+MSSTTVPSVPAPVPAPLDPPVPVLAAPMAGGPSTPELAAAVIRAGGGAFLAGGMRSAAQV
+REQVDGLRALLTAPEEAGRFGVNLFVPDAVNTAVAASARGGAARIARAQAVASYRERLAP
+LAADLGAELPSVLTVTPDPDAERAAFEDMLAAAEEQSWPAVSFTFGLPAPDVFARLDAAG
+IPAGVTVTSPAEAMAAVASGARFLVVQGPKAGGHRATLDPQGRPGITDLRTLVFAVRHAL
+GPAAVPLVAAGGITDGAQVRPLLEAGAVAVAAGTAFLLTPEAGTSAAHRTALRQASAGVA
+FAHPDDGAASTALTRAYTGRWARGLVTPFMDEHHDAPAAYPEVNGLTGPLRRAAAEEGDL
+EHVHLWAGTGAHRVEEVGAAEVLASLAPRAEP*
+>NZ_CP097650.1_2046
+MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA
+QVDALRALLGAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARTAAVAAYRAGLTADGA
+AGLPTAADVVPDPDAERADFDALLTAAEEQAWPLVSFTFGLPAADVFARLAAAGIPAGAT
+VTDATEARAALDHGAAFLVVQGHRAGGHRGTSDPAAEPTRAEMPTVLAAVRDVVGTGAAS
+AAPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA
+DDGRARTGLTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAAGDLERVH
+LWAGTEAHRVREAPAADVLASLAP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001707.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001707.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5962d10ab73f0ea445441dcd40324e55c6d1fac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001707.fa
@@ -0,0 +1,33 @@
+>NZ_CP042169.1_2114
+MATPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV
+PVRPTAAGERMLRLARQTLALEDETLAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA
+TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE
+LHRDARGRVDFGSLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG
+LGWGMLPSVQIPPGVLEGRHPDLETIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP
+SAGDTAD*
+>NZ_CP033200.1_1840
+MATPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV
+PVRPTAAGERMLRLARQTLVLEDETLAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA
+TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE
+LHRDARGRVDFGTLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG
+LGWGMLPSVQIPPGVLEGRHPDLEPIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP
+SAGDTAD*
+>NZ_CP040019.1_566
+MNSDHLRALVSAVDHGTFDAAADALRISGSAFSQRVKALERQVGQVLLARTVPVRPTPAG
+ERMLRLARHTLALEEEALASLGRGDGGRVPVRVAINADSLDTWWELVLREAATWDDVVLQ
+LRTEDQEHTAALLRDGTVVAAVTDDPTPVSGCTSTPLGTMRYHAVCASFLLEMHRDERGR
+LDLATLPRVDYGLRDGLQRTVLRRAARGRAAFDPPHHLVPSVQSYLRAVELGLGWGMLPS
+AQLPPGVLEGRHPDLEPVPSLGTVDLTLHWQRWSAGTAALDRLTDAVLRAAPSVADAAD*
+>NZ_CP083691.1_492
+MNSDHLRALAAAVDEGTFDAAAAWLGISGSALSQRIKALEGQTGQVLLTRTVPVRPTEAG
+ERMLRLARQTLPLEEEALAALGRGTGRRAPLRVGVNADSLETWWTPVLREAATWDDVVLH
+LHAEDQGHTPELLRQGTVVAVVTDDPTPVTGCTVTRIGTMRYHAVAASFLLDLHRDAHGR
+VDVATMPVVDYGPRDGLQRTMLERAARGRVSVPRPPHHLVPSVGAYASAVGMGLGWGMLP
+TGQVPPELAAGSHPDLELVPELGTAEVPLYWQRWSAGTPALDRLTAAVTAAAPAG*
+>NZ_CP097650.1_2060
+MTTPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV
+PVRPTAAGERLLRLARQTLALEDEALAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA
+TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE
+LHRDARGRVDFGSLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG
+LGWGMLPSVQIPPGVLEGRHPDLEPIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP
+SAGDTAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001708.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001708.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86be8a447115a31647636f5bfb92811db7a14ebe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001708.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_2117
+MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA
+GRPDLAILDVMLPDMDGLDVLDRLRAHWSEMPAMFLTAKDATEDRVAGLAAGSDDYVTKP
+FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF
+LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR
+PA*
+>NZ_CP033200.1_1843
+MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA
+GRPDLAILDVMLPDMDGLDVLDRLRAHWSEMPAMFLTAKDATEDRVAGLAAGSDDYVTKP
+FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF
+LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR
+PA*
+>NZ_CP040019.1_563
+MSRIQSTTSPSSMAELKKVLPELSHPDGSPVRVLVVDDEPMIADLLSMGLSLCGWDVVVA
+HDGASAVEQGTARRPDLAILDVMLPDMDGLEVLERLRAHWPEVPAMFLTAKDATEDRVAG
+LASGGDDYVTKPFSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGQVI
+DLTATQYNLLKFLMANVRTVLSKERILQEVWGYDFGGRANIVELYISYLRKKIDADRDPM
+IHTIRGAGYVIRPA*
+>NZ_CP083691.1_490
+MTSAEHTVSPASMAELRESLPDLTHQDGSPVRVLVADAEGLEADLLSMGYSLLGWETVVA
+KDTAAAVQEGTARRPDLALLDAGLPDGGGLEVLARLRAHWAEMPAIVLASPAEAEDRIAA
+LLAGADDVVAKPFAVEEILLRSHHLVRRAGLNASTGEELVVGDLVMNTRTHEVTRGGDLI
+ELTATQFNLLKFLMANVRTVLSKDRILQDVWGYDFGGRANIVELYISYLRKRIDAGREPM
+IHTVRGAGYVIRPAEG*
+>NZ_CP097650.1_2063
+MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA
+GRPDLAILDVMLPDMDGLDVLERLRAHWSEMPAMFLTAKDATEDRVAGLAAGGDDYVTKP
+FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF
+LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR
+PA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001713.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001713.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d05d492a079824d0f7439009ab49e7ff5d081450
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001713.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_2123
+MSADGMIVAHTRVVSVEQPCRGFRRIVLAGPDLEAASGDLLGLLPPGVADLHALYRGARP
+RRDAYVKLLIPPPGGTSADPDLSAGFRAGFLAIPEEERGWMRTYTVRSAGLVRLDGRQVP
+SLTVDVVLHGDPDDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSGWRQTGAHRVL
+AVGDETAVPALVSVAEELADPFGGFDGEADLVLELPHDGQAADLIAERLAVPEPWDWRAV
+TELTDRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPVAPPAASVEREWTVAA
+LEADERPEAYVFLAGESAMVRALRRLSVGPGGVPKKHVSFMGYWREGQAES*
+>NZ_CP033200.1_1849
+MSADGMIVAHTRVVSVEQPCRGLRRIVLAGPDLEAASGDLLGLLPPGVADLHALYRGARP
+RRDAYVKLLIPPPGGTSADPDLSAGFRAGFLAIPEEERGWMRTYTVRSAGLVRLDGRQVP
+SLTVDVVLHGDPDDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSGWRQTGAHRVL
+AVGDETAVPALVSVAEELADPFGGFDGEADLVLELPHDGQAADLIAERLAVPEPWDWRAV
+TELTDRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPVAPPAASVEREWTVAA
+LEADERPEAYVFLAGESAMVRALRRLSVGPGGVPKKHVSFMGYWRQGQAES*
+>NZ_CP040019.1_557
+MSEGMFVAHTRVVSVEQPCRGFRRIVLAGPDLERASPDLMGLLPPGTADLHALYRGSRPR
+RDAYVKVLIPPPGGVSADPDLSAGFRAGFLAIPEAERGWMRTYTVRSAGPVRLDGRPVPS
+LTVDVVLHGDADDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSAWRQTGARRVLA
+VGDETAVPALVSVAEELADPFGGFDGVADLVLELPHDGQVADLIAERLAVPEPWDWRQVT
+ELADRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPVAPPAASADREWSVAAL
+AEDERPEAYVFLAGESAMVRALRRLTVGPGGVPKAHVSFMGYWRQGQAES*
+>NZ_CP083691.1_484
+MSTEAMFVAHTRVVSTSQPCRGFRRIVLAGEDLEHASADLLGTLPPGVPDLHAIYRGSRP
+RRDAYVKVLVPPPGGVSADPDLSAGFRAGFTAVPEDERGWMRTYTVRSAGRTRVDGREVP
+ALTIDVVLHGDPDDAADPHQGPGLRWARTVAAGESVNVLVPTGEAPAWAGWRDTGARRVL
+AVGDATAAPALLSVAEELADPFGGFDGEADLVLELPADAELADLIAERLAVPEPWDESRP
+LDVAEHGRVRLHVGRTAPGRPVGAWAQARLGALLGLSGTARAGVVGVDGVVEAPPAEGAA
+REWTLADLEPVTGVDRPDTYVFLAGESGMVRALRRLAVDGGDIPKKNVSFMGYWRQGQAE
+S*
+>NZ_CP097650.1_2069
+MSADGMFVAHTRVVSVEQPCRGFRRIVLAGPDLEAASRDLLGLLPPGVADLHALYRGARP
+RRDAYVKLLIPPPGGTSADPDLSAGFRAGFLAIPEEERGWMRTYTVRSAGLVRLDGRQVP
+SLTVDVVLHGDPDDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSGWRQTGAHRVL
+AVGDETAVPALVSVAEELADPFGGFDGEADLVLELPHDGQAADLIAERLAVPEPWDWRAV
+TELADRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPVAPPAASVEREWTVAA
+LEADERPEAYVFLAGESAMVRALRRLSVGPGGVPKKHVSFMGYWREGQAES*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001720.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001720.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb82b516a81c022431ede7b4f60c39d372e75c58
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001720.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_2133
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG*
+>NZ_CP033200.1_1859
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG*
+>NZ_CP040019.1_541
+MSIPATEVEARWNEASEPFTAVVRAVRDWDAATPCEGWDALDLLDHVVGAERDFAARQGR
+EVPLFDGSRQQTANQWTKHSAALSALAGDEEFIMKPMHTALGEMTVGEAMIRFHAFDLIV
+HRWDLARSQGVDERFTDAEMDCIEESLDLFGDAAYTPGILAQPVPVADDADRQARLLGRL
+GRRA*
+>NZ_CP083691.1_468
+MSTQTDVEQYWMDCVEPFTDVVRAVEDWDASTPCKGWSAQDLLDHVVVAERDFAARQGRE
+IPVFDGSRNELWTQWVKHASAVTALAGDETFIMQSLHTATGDMTVGEALLHFHGFDLLVH
+RWDLARSQGRDEQWTDEEMDRIERALDSFGEQAYQPGILADPVPVADDAPRQVRLLGRLG
+RRA*
+>NZ_CP097650.1_2079
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAALSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001723.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001723.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4dc479f117e5529b9acbd2b05315b0d424d2dc9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001723.fa
@@ -0,0 +1,75 @@
+>NZ_CP042169.1_2139
+MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR
+GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPQQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGTASAEDGASRLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGAASAQDGAGRLADGLDQAREGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVVPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA
+EDGAGARIADAQTALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDGGLAQLQDGAGELRAGLGTLDDGAHELASGLSDGADRVPALTEDERDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLVLQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGPDQRF
+WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA*
+>NZ_CP033200.1_1864
+MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR
+GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPRQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGTASAEDGASQLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGAASAQDGAGRLADGLDQARGGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVIPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA
+EDGAGARIADAQAALAELAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDGGLAQLQDGAGELRAGLGTLDDGAHELASGLSDGVDRVPALTEDERDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLVLQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGPDQRF
+WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA*
+>NZ_CP040019.1_533
+MLFRYELRRFRRGLPLLALLFILLVPAIYGALYLSANWDPYGAMNRLPVAIVNEDEPVQR
+GDTTLRTGADMTARLKEDHAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPQQAQITLRRDDANGFVIGSVTASSQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGSASAVDGASQLEDGIVQAHDGSGRLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGATSAQDGAGRLADGLDQAREGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVVPGLDRVIERQDAVAADVAAVDEDVQRVAEVAGTA
+GDGAGARIADAQAALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDDGLAQLQDGAGELHTGLRTLDDGAHELASGLSDGVDRVPALTEDQRDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGHRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLILQLASTGGTYPAEVLPGFFRALHPFMPMSYSIEAFRNAISGGLDQHF
+WVPVVVLMGVGAAALALDVLVVRRRRRFRMKDLHPALQA*
+>NZ_CP083691.1_462
+MLFRYELRRFRGVLPTIALLFIVLVPTIYGALYLSANWDPYGNLSSLPVAIVNEDRPVES
+DGKTLTTGADITEELVDQHTFDWHETTRDDAEAGLRDGRYYLVMEIPEGLSADLVSANTS
+DPQQAHITLRRNDANGFVIGSVTSSSQSKIENAVDKAAVEAYFKAVFENLATIRQGMADA
+RDGAGRLADGAGQADDGAAQLADGIVQAHDGSGQLAQGASDAQDGAGQLADGAGQLKDGA
+DQLAAGATSAKDGAVQLQTGIGQAREGSQKLADGAGQIAAKVPDLRDGATALSNGLTQLD
+TGSADLADGAHQVADGTQQLYDTVIPGLDAVIERQDKVASDVATVNQDVQTLNDAVATAG
+SGAGGDIDTASEQLQALAESNPDIAVAPEYAALQQSLTDAKEKAGSATSTAQDVADRSAA
+VNSRVQGFVSEDVAGNAKADITKLNDGAHAVAEGADTLHAGIGQANTGAQALADGVGRFA
+DALDQLAAGATALDDGLAQLEDGSGRLVDGLGKLETGAGDLADGAGRLDQGAGELQTGLG
+KLSDGATSLDSGLAQLETGSGDLKTGLDSLSDGATQLHDGLASGTDKIPALSEDAADEAA
+LVMSRPVQVDMDVLNPAGVYGRGVAPLFFSIALWVFGIAAFNVMRPVNGRLLAGRRNPLL
+LALSAWLPVGLLSVVGSLVMLAATVPLGIDPVHPWHLVGLVVFTALAFSLFAHLVMTALG
+TPGSAVLLVTLILQLGSAGGTYPADVLPPFFRWVSPLMPMTHSINAIRYALSGGQPAQFW
+GAVAFLAVFGAACLFLDMAVVRRRQRFRMKDLHPALEK*
+>NZ_CP097650.1_2084
+MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR
+GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPQQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGTASAKDGASQLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGAASAQDGAGRLADGLDQARGGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVVPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA
+EDGAGARIADAQAALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDDGLAQLQDGAGELHTGLGTLDDGAHELASGLSDGVDRVPALTEDERDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLILQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGLDQRF
+WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001724.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f689c7f1f810b587b5cbd622539689e97f425838
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001724.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_2140
+MSSTPTDADHHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV
+LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA
+LRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLSVAPEAV
+VGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA
+VASAPVPRDAVVLTLPPVREN*
+>NZ_CP033200.1_1865
+MSSTPTDADHHGPGPAPDPAHLDDLPPATLVARGLTLRGSRGPVFGSLDLVLPPQTHLAV
+LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA
+LRARTAVAHTTDVVELEPALTAAEVVDERCLTDGVRRRAGRARFALLADAVRLTVAPEAV
+VRELSAPDRALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA
+VASAPVPRDAVVLTLPPVREN*
+>NZ_CP040019.1_532
+MSSTPTDADHHGPGPVSVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV
+LGTQGSGRSALLLALTGRLRGVRGELVLTGGPVDVALDGPERPAARAYRPLIDATRHPYA
+LRARTAIAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLTVAPEAV
+VGELSAPDRALLAAVVACLRPARLVTFDDVDATLTLDELVALHAALDVLKDHGHPFAVSA
+VASAPVPRDAVVLTLPPVREN*
+>NZ_CP083691.1_463
+MTEDQTPAPIETDDVVAERAPEPAPGGSHQVGRALTARGLTLRSIRGTVFGPVDVDLPPG
+VPGAVLGTQGSGRSALLLALVGRLQGVGGELTLGDMDGIRHPHRLRRATTVARITDYVEL
+EPLLTIRECIDEHCLAEGISRRTGRKRFARLEAAVGFHPDHGDQVSSLPVEDRTILTCML
+ACLRPADVIVYDDIDSSLTRPQLEHVYRVLETLGRLGHRFVVSALTSAPVPRGAVVVELP
+TPGHDDLPAALPTRPSLED*
+>NZ_CP097650.1_2085
+MSSTPTDADHHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV
+LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA
+LRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLSVAPEAV
+VGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA
+VASAPVPRDAVVLTLPPVREN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001726.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001726.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce5141ed10b186ea318dd1f353bc5bd8772b5e63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001726.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_2142
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVVGGPLGVLLGSVVARRVDPAKARVLAICLAGV
+GGTVALVRGVAGTLG*
+>NZ_CP033200.1_1867
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVVGGPLGVLPGSVVARRVDPAKARVLAICLAGV
+GGTLALVRGVAGTLG*
+>NZ_CP040019.1_529
+MSVVVLTGADGGARLGHTAPMDMSLVMLVPALVALAALMVGGALQRVSGMGVGMIAGPTL
+SLLLGPVAGVSLANVAAVVSAVLLFALLRRHVDWGRFLRLAPLLIVGSFAGAWAVRSLDV
+HALEVLLGGSVLVAIAASLGLQRRFTASGSAPAALAGTAAGFMNTTAAVAGPALAVYAVA
+SRWEQRSWAATLQPIFLLANLTSLATKSLFGTAVPASVDVHWTVWTAVVVGGPIGVLIGS
+RIAPRVNPSRARLLAICVAGVGASVALLRGIVGLLA*
+>NZ_CP083691.1_465
+MAATAAAAVRTAERARSGGGVTVPVWHAPAVASRRRGARAHTAGVSISLAAVVFLCVAVG
+GVLQRISGMGVGMVAAPTLSLLVGPVAGVTMSNAAASVSALILFWMLRRHVDWPRFLRLA
+PLLVVGALAGAWTVRVMDHAWLEVVLGACVLVAIAAVLGLQDRLTLRGSAAVFGSGAVAG
+FMNTTAGVAGPALAVYAVASKWEQRSWAATLQPIFLTANVTSIVLKASLGATAGAAAVPW
+WAWAAAVAGAPAGIAVGSRLARRVDPGRARRVAVTLAGVGAAVTLVRGLASL*
+>NZ_CP097650.1_2087
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVAGGPLGVLLGSVVARRVDPEKARVLAICLAGV
+GGTVALVRGVAGTLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001729.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001729.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9d0be5b4ef5a1399abb3ca0a46e23af497e2f3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001729.fa
@@ -0,0 +1,27 @@
+>NZ_CP042169.1_2146
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A*
+>NZ_CP033200.1_1871
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A*
+>NZ_CP040019.1_525
+MLPAPTARLRFREMTEADLDAMAALLGDPAVMRFYPAPRTREQAAEWIAGNRRRYAQDGH
+GLWVIETLPEHSDDGEPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACR
+DHARDALGHHELVAIIHPENSVSRRVAEKIGLREAEQDFTGAAEARETMGLASRTVMAMR
+F*
+>NZ_CP083691.1_456
+MTQPIPRHPDPGNTGTDALDDVVREHMLLLRRAVHGLGAYRRPEALDRSAVLLLARLEAQ
+GPMTMAELAAAFGLDVSTLQRQIGAAQRAGFVERFRDPAGGQARLHRATDAGRAALEGEL
+AARRAAVAEVTRSWPAPDVAALARLLRRFNEGSEELREQPWPRERPEAPGAAAVPAGTAR
+LRFREMTEADLDVLVGLLGDPEVMEFYPAPKTRAEVADWIAWNRRSYAEHGHGLWIVETH
+AGAFVGECGLTWQRVNGERRLEVGYHVAPVLQGRGYATEAAAACRDHARDVLGAPELVAI
+VHPENTASRRVAEKIGMEVLEEDRTGVDASYLEAIGAEARTVLGMRLA*
+>NZ_CP097650.1_2091
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001730.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001730.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96151f1bf17fec8c54b6d0f8f737cd358760348c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001730.fa
@@ -0,0 +1,37 @@
+>NZ_CP042169.1_2150
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG*
+>NZ_CP033200.1_1875
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG*
+>NZ_CP040019.1_523
+MTSPRPESDWRPPWQDLPADLPGRLAHALPGIMERIIQTVPDQIPAYAAARDGRYGKNLT
+LGVTTALEQLMSLPGTSRPALSAQSRELMARLGAGEFREGRSMDALLGAYRTSARIVFRD
+LSAECARLGMDMSVVIELGESIWAYIDELSAVSAQAYAEAQSAQAGVRELHRTALAAALV
+RGGAEEKEVERLAALADWRVPARLAVVALPPDAGQAVRARLGRGGLVVERDSEVVAVVGA
+DAPARRRRLLRILAGTAAVVGPAVEWPLAPHSYRVARTLAGQEAARRAAEQRAAARPEGD
+GSAADGPGAEEAVGFEPVGGADPAPGTPILAEEHLARVVLGAEPRVVAELAERVLAPLAE
+LTDAKRAVLEQTLLSWLVHWGQRAPIAAELSVHPQTVGYRVARLRELFGDALEDPDARFD
+LELVLRARAGGMAA*
+>NZ_CP083691.1_453
+MVLSAPPRSPVVTRRLLAALQGTGAVVGPEVDALEVARSLHVARAVLARRDALSGVAPGA
+AVLAEEHLADVVLGAEPEALRRLSERVLAPLDGLSDAKRATLEATLAAWLAHRGARGPMA
+AELNVHPQTVGYRVGRLRELFGGALDDADARFDLELALRSRRGQG*
+>NZ_CP097650.1_2095
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001731.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001731.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85549a1329fc987b9814758c180cc930befdafe3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001731.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_2152
+MTQTPTAPDRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPRTAESRAAATTP
+GLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRVIRWQRRL
+ELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIHSTTWEWD
+FVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWRPRHLLNPVINAGLAPIF
+EWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVLTGSGKAA
+LVGTLLANGLRNIWAHAVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSANISGSKL
+MHFMTGNLSHQVEHHLFPDLPSSRYAEVAPRVREICARYGLPYTTGPLLRQVGSAWKKVF
+RLALP*
+>NZ_CP033200.1_1877
+MTQTPTTPSRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPHTAESRAATSRS
+TAAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRV
+IRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIH
+STTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWQPRHLLNPVIN
+AGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVL
+TGSGKATLAGTLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSA
+NISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPQVREICARYGLPYTTGPLLRQVG
+SAWKKVFRLALP*
+>NZ_CP040019.1_521
+MTQTLPATERTGATAPDDLSLAIPGTTVRGRTARVLPEDRPDTTSWAPQTADAGTDAAAP
+AASETPEAPTADAATRPAANAKPGLLGVVGSPAVRPPGAAHLTDEQVAELGRELDAIRDD
+VLSRRGASDAAYIRRVIRLQRWLEIGGRAALLNARHPAAFVAGTTMLTVAKIVENMEIGH
+NVLHGQWDWMRDPDIHSTTWEWDFVTPSRAWQNTHNDLHHRWTNVIGKDRDVGYNVLRMD
+ESEPWRPRHLLNPVINAGLAPIFEWGIALYDLELDRVHAGEKSRKELMTDLRSVGVKASR
+QFAKDYVATPAVAEFLTGSGKAALVAGLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVD
+GETRGDWYVRQMIGSANISGSKLMHFMTGNLSHQVEHHLFPDLPSNRYAEVAPKVREICA
+RYGLPYTTGPLLKQVGSAWKKVFRLALP*
+>NZ_CP083691.1_452
+MIRSATAGKIIENMEIGHNVLHGQWDWMRDPDIHSTTWEWDFVTPSSAWQHTHNDAHHRW
+TNVTGLDEDLGYNVLRMDEAEPWEPRHLLNPVINAILAPFFEWGIAIYDLELAKVRAGEK
+PVADLRRDLASVAVKAVRQLAKDSLATPIAAELVSRSGSAWRKVFRLALP*
+>NZ_CP097650.1_2097
+MTQTPTTPSRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPHTAESRAATSRS
+TAAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRV
+IRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIH
+STTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWQPRHLLNPVIN
+AGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVL
+TGSGKATLAGTLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSA
+NISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPQVREICARYGLPYTTGPLLRQVG
+SAWKKVFRLALP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001732.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d980b503290608c7705eb9455a3b9c7ebda6abfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001732.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_2160
+MPAQPSPSGHTVHLSTSGVDARITPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA
+HVLDAASPAGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLALDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL
+LVNIGDDAGLRFLGAELGALEEAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLGEA
+GCTERLAAAGPHPAAVLDPAESAALADRIRRA*
+>NZ_CP033200.1_1885
+MPAQPSPSGHTVHLSTSGVDARIAPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA
+HVLDAASPTGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLALDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL
+LVNIGDDAGLHFLGAELGALEEAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLGEA
+GCTERLAAAGPHPAAVLDPAESAALAARIRRA*
+>NZ_CP040019.1_509
+MRAHPSPTGRTVHLSATGEDARILADELGGSVLEIGGAVQSHVDPADPTALRYEYLRRMA
+NVLDGVAPAGAPLRVLHLGAGALTLPRYVQATRPGSEQTAVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLLMDGERFDAVVLDIGTGEDGAAHLTGAEFYGELLGLLTAAGVL
+LVNIGDDDGLRFLGAQLRHMEAACAEAGVPGPWTLASAAMLERLELGNAVLAAGPALRGD
+GAAAGGDAGPEEDGGPLTPAALLARGPHPGAVLDEAASADLARRVAGR*
+>NZ_CP083691.1_451
+MPTQPQDDASSPAPSPTARTVHLAASGVDARILPDPHAGGWMLEVGGAVQSHVDLADPTQ
+VRYEYLRRIANVLDALAPAGEPLRVLHLGGGALTLPRYVAATRPGSVQTVVDLDRELMGL
+VLEELPLPADADVYVVVADARAVVDDLLDPLEGESQAGAWDAVVLDIDTDAGAVAHLTGA
+AFHAELLELLAPGGVLCVNIGDDDGLAYLATQLTALEAACADAAEGAGVPGPWTLGPNSV
+LERRELGNAVLVAGPGLAGMDAAALHAAGPHPAVVLDAHESAALAERITAAP*
+>NZ_CP097650.1_2100
+MPAQPSPSGRTVHLSTSGVDARIAPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA
+HVLDGVAPAGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLAMDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL
+LVNIGDDAGLRFLGAELGALEKAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLREA
+GCTERLAAAGPHPAAVLDPAESAALAARIRRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001734.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001734.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5fb975d3c9f645f19997aa5cabe004cebf0e3488
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001734.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_2164
+MKHEIVLTRGDLTLRPLTPDDGPALRELVDAAMWAGNSAPLPVDGAAMSAHLAELSEREG
+TFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRGG
+LEARLAA*
+>NZ_CP033200.1_1889
+MKHEIVLTRGDLTLRPLSPTDGPALRELVDAAMWAGNSAPLPVDGAAMSAHLAELIEREG
+AFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRAG
+LEARLTA*
+>NZ_CP040019.1_499
+MSHDLHLTHGPIRLRPLTPDDAPRLRAIVDEASWAGMSTPLPETDAAMAEHLRELMGRPG
+LQAFAVERDGEFVGRTALYDPVPTVRVDVGHTVYARPVWGTEVNPACKLLLLGHAFEELG
+VARVGLRCDHRNTRSHRAILRLGATFEGTLRAFRRAADGTVADADHFSVTAPEWPAVRAG
+LETRLGA*
+>NZ_CP083691.1_446
+MPAAQLPADLLLEHGAVRLRPLTLDDAPRLRALVDAGSWAGMSSPLPTSDEAMAAHLAQL
+MAREDLTAFAVERDGEFVGRTAYYEHVPGVRVDVGHTIYAREVWGTEVNPACKLLLLRHA
+FEALGVERVGLRCDHRNTRSHRAILRLGATFEGTLRAFRPAADGTVADVDYFSVLAAEWP
+AVRAGLEARLAGSAPAD*
+>NZ_CP097650.1_2104
+MKHEIVLTRGDLTLRPLSPTDGPALRELVDAVMWAGNSTPLPVDGAAMSAHLAELIEREG
+TFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRAG
+LEARLAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001737.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..033a76960bf4044f76e521437662d783d07b6c08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001737.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_2185
+MTSGPPSPALPAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLL
+HVLTGRITPDVGRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAA
+AALAEAPDDAGAGHRYSTALERAHLYDAWDAGRRVDMDLEGLHACTDREHPLTSLSVGQR
+HRVRLAVTLGSRPDLLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDRALLRAVCTD
+IVDLDPSQDGRPRRYSGGYAGWAKGRRRARAAWEQEYAEQNAERERLELAVEDAREQMQG
+SWRPPKGTGKHQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADMPDGDPRDG
+ADAAAGTAGGPGTAGDDVLLTADAVRVAGRLEQPMGAALVPGGRVLVTGPNGAGKSTLLR
+VLAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVGADEAGVDDLGR
+PLPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALV
+DEMTEALQVTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV*
+>NZ_CP033200.1_1899
+MTSGPPSPALPAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLL
+HVLTGRITPDVGRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAA
+AALAEAPDDAGAGHRYSTALERAHLYDAWDAGRRVDMDLEGLHACTDRERPLTSLSVGQR
+HRVRLAVTLGSRPDLLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDRALLRAVCTD
+IVDLDPSQDGRPRRYSGGYAGWAKGRRRAQAAWEQEYAEQNAERERLELAVEDAREQMQG
+SWRPPKGTGKHQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADMPDGDPRDG
+ADAAAGTAGGPGTAGDDVLLTADAVRVAGRLEQPMGAALVPGGRVLVTGPNGAGKSTLLR
+VLAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVGADEAGVDDLGR
+PLPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALV
+DEMTEALQVTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV*
+>NZ_CP040019.1_699
+MTLTPPHAPALPAGASAHIRAECITLTLGDRTVLDQADVTVSAGSRLAIVGENGRGKTTL
+LHVLAGTLAPDAGTVTRAGTLALVEQDLDADDDRTVGDLIHDAVGESLAVLDRLEAATRA
+LAEGRPGADDDYARALETATALEAWDAERRIDVALEGLSACTDRTRPLNSLSVGQRYRVR
+LAVVLGSAVDLLLLDEPTNHLDAGALEHLTRALREHPGGVAVVTHDRALLKDVAETFLDL
+DPTSDGRPRQYAGGYAGWEKGRSAERAAWEQAHEQQVAEHAALAEAAEAARGRLQDRWRP
+DKGTGKHQRATRAAGVVQAFNRRVRDLEAHEVTVPEPPRALAWPASSTRAARPLLNAEGV
+DVAGRLRGPVSADLTGGDRLLLTGPNGAGKSTLLHVLAGRLDPTAGRVLRHTGARIALLT
+QEAPAWNPRHTARQAFEVHLHRRGLLADDDGGAPPLASLGLLEPRSMDAPVGRLSQGQQR
+RLHLALCLAERPDLLMLDEPSNHLSATLVDELTEALRATRSAVVVATHDRQMLRDLSDWP
+RLELTAEAVAR*
+>NZ_CP097650.1_2119
+MTSGPPSPALPAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLL
+HVLTGRITPDVGRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAA
+AALAEAPDDAGAGHRYSTALERAHLYDAWDAGRRVDMDLEGLHACTDRERPLTSLSVGQR
+HRVRLAVTLGSRPDLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDRALLRAVCTDI
+VDLDPSQDGRPRRYSGGYAGWAKGRRRARAAWEQEYAEQNAERERLELAVEDAREQMQGS
+WRPPKGTGKHQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADRPDGDPRDGA
+DAAAGTAGGPGTAGDDVLLTADAVRVAGRLEQPMGAALVPGGRVLVTGPNGAGKSTLLRV
+LAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVGADEAGVDDLGRP
+LPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALVD
+EMTEALQVTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV*
+>NZ_CP097650.1_2159
+MPTSRSLRSCVWNGTPQGHAAHIRAESIHITLGDRHVLNGVDVTVSVGSRLAIVGDNGRG
+KTTLLHLLAGILQPDSGVVTQAGSLVLVKQDMATEGDRTVGDLIAEATGPSKSALEALDA
+TSAALAEGDDAADAYSAALERATLLDAWDAERRVDIALEGLNACSDRDRVLSTLSVGQRY
+RVRLAVALGSTPDLLLLDEPTNHLDAAGLSFLTERLRDHAGGLALVSHDRALLRDVATTF
+LDLDPTRDGRPRTYAGGYQGWVEGRQRERVSWEQDHAAQVARHAQLTRAAAEARSRLSQG
+GWRPDKGTGKHQRATRAAGVVQAFNRRVEDLERHEIDVPEPPLRLAWPKSSARRGMSIVN
+ASMLTVERRLDTPVSIGVNGGDRLVVTGPNGAGKSTLLAVLGQRLVPTTGYVQVNPSARI
+ALLSQEVPDWDRTSPAHVAYETYLGKLGCRSQAPSLGSLGLLEASATSTPVGRLSQGQQR
+RLHLALCLAQDPDLLLLDEPTNHLSSSLVDDITTELLQTPCAVIVATHDRQMLDDLADWP
+HLDLDPKDMP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001741.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001741.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6107fb3d4dde73e72c951db46b5234810a965a35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001741.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_2199
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMNGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG*
+>NZ_CP033200.1_1911
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG*
+>NZ_CP040019.1_460
+MNGAELADSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPIAVGVTVGSLTAM
+VSAVLIVRLMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVFAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG*
+>NZ_CP083691.1_415
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTAGSLTAM
+VSAVLIVRVMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG*
+>NZ_CP097650.1_2132
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001745.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001745.fa
new file mode 100644
index 0000000000000000000000000000000000000000..789756cc8f9b0e6a13010bdd45b07f8183fae469
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001745.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_2214
+MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV
+IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDRLCERLAGDV
+GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG
+GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET
+PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ
+KPVYALEGSIAVTGSLIQWLRDNLGMIASAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW
+DAAARGVMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE
+LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTTDE
+EEVERTLRLWKKAVERSRDWVDEDVESAQG*
+>NZ_CP033200.1_1919
+MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV
+IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDHLCERLAGDV
+GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG
+GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET
+PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ
+KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW
+DAAARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE
+LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTMDE
+EEVERALRLWKKAVERSRDWVDEDVESAQG*
+>NZ_CP040019.1_445
+MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV
+IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVHNAIVWQDTRTDRLCERLAGDV
+GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGAG
+GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET
+PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEKPVHSDNGLLTTVAYRIGDQ
+KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAASVEDNGGVYFVPAFSGLFAPHW
+DATARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE
+LLMQFQADLLRVPVVRPKVTETTALGAAYAAGLAVGFWSSQDELVANWEEDKRWEPTMDE
+EEAERALRLWKKAVERSRDWVDEDVESAQG*
+>NZ_CP083691.1_478
+MSAPRYVMAIDQGTTSTRAILFDHAGDAVATGQLEHAQHFPRAGWVEHDPLEIWRNTREA
+IGQALSRADATRDDVAAIGVTNQRETAVVWDRTTGRPVHPAIVWQDTRTQHLCERLGGDA
+GPDRWRERTGLPLATYFAGPKVAWILEHVDGAREAAERGDLLFGTTDSWTVWNLTGGVLG
+GQHVTDVTNASRTLLMDLETLEWDAEIAAEMGIPGGMLPRIVSSSAEVGHAAPTSLLGGV
+PIAGILGDQQAALFGQACFEAGQAKNTYGTGNFLLVNTGARPVRSRHGLLTTVAHRIGDE
+PPAYALEGSVAVTGSLVQWLRDNLGLIRDAAEVEELAAGAPDNGGVFVVPAFSGLFAPHW
+DPTARGTIVGLTRYADRRHLARAVLEATAFQSREVLDAVLADVAEAEEGAGVVGGLTELK
+VDGGMVANDLLMQFQADVLGVPVVRPEVTETTALGAAYAAGLAVGFWASTAELAAHWSED
+RRWEPAMDPERAARLLRLWARAVARSRGWIDDDVEALAAETRTAPDATPAGRTP*
+>NZ_CP097650.1_2148
+MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV
+IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDHLCERLAGDV
+GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG
+GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET
+PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ
+KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW
+DATARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE
+LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTMDE
+EEVERTLRLWKKAVERSRDWVDEDVESAQG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001747.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001747.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8443b975426bcce066909b6ec46a422e65cf2a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001747.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_2229
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTCVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRRLPATPILASVAEEAPAPEAPADDA*
+>NZ_CP033200.1_1932
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA*
+>NZ_CP040019.1_436
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+ILPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGKDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA*
+>NZ_CP083691.1_389
+MKLAILSRSLRAYSTQRLKSAALDRGHDVKVLDTLRFGIDLAGDEPDMMFRGKPLSSYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRASQILSRHGIAQPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGKDVRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVEQVELSEEYAETAVRAAHIM
+GLRVAGVDMLEGEDGPLVMEVNSSPGLEGIERATTLDVAGAIVDYIADQAGFPEVDVRQR
+LAVSTGYGVAEIAVLAGSDMAGQSIEDSGLLEKDLQVLTLHRGASVFPNPADSKVLEEGD
+RLLCFGKTENMRALIPARSQRPKRVKKLPKNPIIEAPPAEPAVRPDAESGES*
+>NZ_CP097650.1_2170
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001748.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001748.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52c93974de17a5f84aac5913844a790b98d12240
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001748.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_2230
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVIVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA*
+>NZ_CP033200.1_1933
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVVVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA*
+>NZ_CP040019.1_435
+MSESKHTATAPHGVPPIDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGKAQERVVVVMPLTLAG
+RTFEAEVTLTHRDEMGFRMLVGRTALAAGGFHVDPAASYVGGQPPRGVRRRNRGRA*
+>NZ_CP083691.1_388
+MGHVTESNHTPGRAAARPPHGDAHDAAPRPAQADADARPVREAATGVVVGWREWVGLPEA
+MTPWIKAKIDTGARTSALHAFGIERYTGADGAARVWFEVHPWQASAADARTVDLPVADLR
+AVRSSNGEVQERVVVMMPLRLAGRTVDAEVTLTHRDEMGFRMLVGRTALAKGFLVDPGAS
+YLGGQPPRGVRRRNRGHA*
+>NZ_CP097650.1_2171
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFARDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVVVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001749.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001749.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2572c7437c2af96f38c8d62ca758ffae9fb83218
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001749.fa
@@ -0,0 +1,41 @@
+>NZ_CP042169.1_2231
+MSRRPARAPFAFGGVEVAAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIARCTVGIDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADVGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLHVALGERVSAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA*
+>NZ_CP033200.1_1934
+MSRRPARAPFAFGGVEVPAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPTQLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIGRCTVGIDLHTGADRRSNLPQIRCDLEDSQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADIGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLDVALGERVNAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA*
+>NZ_CP040019.1_434
+MSRRPARAPFAFGGVEVPAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGNEVAGIEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIGRCSVGVDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAAREAGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALGMVDPAEVGL
+TEPGPAAVVDAPGPLPGEVPGDATTDVPEATDATGEDTEAVHADVVDGGQDAPHLVWHSS
+WVRARADGLVHLDVSLGERVAAGDRIGALYNSFGRRVAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA*
+>NZ_CP083691.1_387
+MSAPQKDPDRGGRTGDEAAAEKATGRRRASRAPFELAGVEVRPGRRHEVSLPVSRLVTGA
+EVTLPVHVLHGREDGPTVWVSAAVHGDEVAGIEIVRRVLERLKPSRMRGTLLALPIVNVL
+GVMTGDRYLPDRRDLNRSFPGAARGSLAARIAHLMMSEVVRRCEVGIDLHTGADRRSNLP
+QIRCDLEDPRTRALAESFGAPVLFHARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAI
+SPGVEGVLRVLAALGMVAAEDVGLATPVDAPAPLPGEVPEDRTTEVPEALDATGRDTGGV
+HADVVDGDLAAPHRVWHSRWVRARADGLVHLDVALGEQVTAGDRIGALYDSFGRRRSDVK
+AELTGVVLGRTEAPLVHRGDALVHIGELDGRPAGTFPAPSPGRRTAPSVAEGDPEAEAPP
+AATP*
+>NZ_CP097650.1_2172
+MSPRPARAPFAFGGVEVAAGRRHELSLPISQLVTGADVTLPVHVLHGRDDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIARCTVGIDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADVGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLDVSLGERVSAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001759.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001759.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3306c2c3694c9b8c0d9b43f2e179150d65804e69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001759.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_2245
+MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP
+NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM
+TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI
+GAIVLYLGMFGAYRAGDDLAGWTSAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF
+GWKGIGLRDTGRIAGYTLITMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA
+QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT
+VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGVAVGSVLLALALSIPFRSGSFYLLRVFY
+AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAVASSVSYVYQFVLTHVLTVR
+RFGDYGLASVLRAHVQTGLAALAAAAAGAVVVWLLGGYTGGFAWNSIGTALLTCAVAAVA
+MGPVYLMVLRAMRFPELDDALRPLVARVPALGRLLRVG*
+>NZ_CP033200.1_1950
+MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP
+NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM
+TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI
+GAIVLYLGMFGAYRAGDDLAGWTSAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF
+GWKGIGLRDTGRIAGYTLITMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA
+QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT
+VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGVAVGSVLLALALSIPFRSGSFYLLRVFY
+AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAVASSVSYVYQFVLTHVLTVR
+RFGDYGLASVLRAHVQTGLAALAAAAAGVVVVWLLGGYTGGFAWNSIGTALLTCAVAAVA
+MGPVYLMVLRAMRFPELDDALRPLVARVPALGRLLRVG*
+>NZ_CP040019.1_420
+MASPDPSAHRGAPLPSALGAWHRRPQPPARPEPAPAPGPRPAASGLPTVEEVSAGGVVVR
+EHDGGLEVAIIARYNRGGRLEWCLPKGHPEGVEDHRQAAVREVEEETGIAGDILEPLGAI
+DYWFTVSRHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERRI
+VDLARQVVDRHFPRAPPGAPAPDPPPRTRGSSDHDWVTLEQQPLPAPRAGTPPAPAVADE
+EPTTADPAPATDPEAPAREDRPDETPEGERRAGRSTAIMASGTLISRVLGLVRAMLVTVA
+IGLSTDMADIFEIANSLPNVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGT
+LVMLGGTLVVMAVAAPLMTALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNAN
+GRFGAYMWAPVLNNVVAIAAIGLYLAMFGAYRAGEDVAGWTSTQTLVLAGGHTLGVILQA
+VILFLPLRGLGLGMRPRFGWKGIGLRETGRIAGYTLVTMMVTNVVLLLCQRYVTSATEAR
+DRGELRIPGTEAWSTEMAQAAIPGVAAYNMAMLIAVLPHSVFVLSLATVLFNRLARAMTR
+QDMPAVRRTTAQGLRAFTVPLMFSLAGIVVLAGPLGRVFGSTAETSMVAGIAVGAVLLAL
+ALSIPFRSGSFYLLRVFYAAEDAKVPMVVQVSSSLLMLLLSWAGAMLLPLWSMALWVAIA
+SSVSYVYQFALTHVLTVRRFGDYGFASVLRAHGQTGLAALAAAAAGAVVVWLLGGYTGGF
+AWETIVTALITCAVAAAVMAPVYVVTLKLLRFPELDDALRPVVSRVPALGRLLRVG*
+>NZ_CP083691.1_372
+MSSRTAPRRALPADDAPRPKEVEDVVLPASDPEAPAQAQEEVPEGERRAGRSTAIMAAGT
+MISRVLGFVRAALLTIAIGTTVGTVADIFEVANSLPNVIYLLLVGGVFNVVLVPQLIKHA
+KDADRGADYTSRLMTLAVLVMLAATVLVTAAAAPLMAALTRGWSPEMLQLGTVFALWCLP
+QMFFYGMYALVGQILNANGRFGAYMWAPVLNNVVAIAAIGLYLVMFGRYSGGDLLGRWTP
+EQTLVLAGGHTLGVILQALILFLPLRGLGLGLRPRFGWRGMGLRHTGRIAGYTLFTMAAS
+NIVLLLSHRYINGASAAREDPSVRVPGTEGWDPAMADALIPGLTAYNQAMLISVLPHSVF
+VLSLATVLFNKLARSMAAGDHAAVRETTARGLRTFAAPIMFSLAGVVVLAGPLGRLFGST
+AESAQVTGMAVGAVILLMSLSMPFRSGSFYLLRVFYAAESARIPMVVQVTTSLLTLAVTA
+AGAYLLPLWAITYWAALASVVSHAFQFFFAHVLAVRRFGDYGFTHVLAAYATTGAAGVVA
+GAAGAVVAWLLGAYSGGWAWGSILSALVTCAVVGLVMAPVYVVALRVLRFPELASAAAPL
+ARRVPALGRLLGAR*
+>NZ_CP097650.1_2188
+MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP
+NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM
+TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI
+GAIVLYLGMFGAYRAGDDLAGWTTAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF
+GWKGIGLRDTGRIAGYTLVTMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA
+QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT
+VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGIAVGSVLLALALSIPFRSGSFYLLRVFY
+AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAFASSVSYVYQFVLTHVLTVR
+RFGDYGLASVLRAHVQTGLAALAAAAAGAVVVWLLGGYTGGFAWNSIGTALLTCAAAAVA
+MGPVYLVVLRAMRFPELDDALRPLVARVPALGRLLRVG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001764.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001764.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eec14fa2159b4b8b101741b4561291917e204920
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001764.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_2252
+MSAENVTPAPEAEDAVVETPAGQGSRVAEQDGAAVSEAVRRLEEEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL
+ILDVCGHRERRNVALRTAAQAAVERVRVGEGPVHLEPMGAYERKIVHDVVADAGLTSESE
+GEGARRHVVISADD*
+>NZ_CP033200.1_1957
+MSAENVTPASEAEDAVVETPVGQGSRVAEQDGAAVSEAVRRLEEEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL
+ILDVCGHRERRNVALRTAAQAAVERVRAGEGPVHLEPMGAYERKIVHDVVADAGLTSESE
+GEGARRHVVISADD*
+>NZ_CP040019.1_412
+MSAENVNPAAEAEDAVVETTPAPDAPQAPAAEERTGSDAAVAAGEGAESSAAESASDGVR
+RLEEEGDVAADYVEELLDIADLDGDIDIEVRDGRTYVSVVSEDHDERLNALVGRDGKTLE
+ALQELVRLAVLAATGHRSRLILDICGHRERRDADLRETAQDAVERVRAGEGPVHLSPMGA
+YERKIVHDVVADAGLASASEGEGARRHVVISADA*
+>NZ_CP083691.1_365
+MTAEHEGPLADAAEDSPAVEAPVEATAPDAAVDEQAEAVRRLEEEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVPGEDDEDDRLADLVGPDGKALEALQELVRLAVLTATGHRS
+RLILDIAGHRRRRDAELRTLAGEAVERVRSGAGEVHLDPMGAYERKIVHDVVAEAGLASE
+SEGEGPRRHVVISG*
+>NZ_CP097650.1_2195
+MSAENVTPAPEAEDAVVETPAGQGSRVAEQDDAAVSEAVRRLEQEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL
+ILDVCGHRERRNVALRTAAQAAVERVRAGEGPVHLEPMGAYERKIVHDVVADAGLTSESE
+GEGARRHVVISADD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001765.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001765.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3cc89ed9d1175333f66fe36be3e87ddf905c893
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001765.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_2253
+MFEAILAPFRWLMSWLLGAFHTVLEFAGMPADSGWTWALSILLLVVLIRTLLIPLFVKQI
+KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF
+FFALYQVLIGARGASERGESMDALSADQIRSFEGSTIFGARMSDTFLNSFGDPGSAPVII
+TAIVLIVLMSGSMFYMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVTDSKAEPSSAH
+TQAAGGGAVLNGEVVRQSGQRVQPQRKNRRRK*
+>NZ_CP033200.1_1958
+MFEAILSPFRWLMSWLLGAFHSILEFAGLPADSGWTWALSILLLVVLIRTLLIPLFVKQI
+KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF
+FFALYQVLIGARGAAERGEAMDALSADQIRSFEGSTIFGARMSDTFMNSLGAPGSGPVIV
+TAIVLILLMSGSMFFMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVSNAEATPSSAH
+TQAGRGGAVLNGEVVRQSGQRVQPQRKNRRRK*
+>NZ_CP040019.1_411
+MFEAILAPFRWLMSWLLGAFHTVLEFAGMPADSGWTWALSILLLVVLIRTLLIPLFVKQI
+KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF
+FFALYQVLIGARGASERGESMDALSADQIRSFEGSMIFGARMSDTFLNSFGDPGSAPLII
+TAIVLIVLMSGSMFYMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEQELNERRAAKGLPPVGQKVTDSKAEPSSAH
+TQAAGGGTATLNGEPVRDSGQRVQPQRKNRRRK*
+>NZ_CP083691.1_364
+MFDAILAPFRWIMSWLLGAFHTVLDTIGLPADSGWTWALAILLLVILIRTLLIPLFVKQI
+NAQRAMQTMQPELQKLQAKYKGKKDQLSRQAMALEQQALMREHKANPFAACLPLLIQMPF
+FFALYQVLVGARGAAERGESMDALSAETIRSFESSQIFGARMSDTLMGSIGQPGGAAVVV
+VAIVLILLMTGSMFFMQKMLMTKNMTQTALEGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRHNPTPGSLAEQELNERRAAKGLPPVGKKVASSEAKPGSAH
+TEAAQGAVVNGEVLREGGQRVQPQRKNRRKK*
+>NZ_CP097650.1_2196
+MFEAILSPFRWLMSWLLGAFHSILEFAGLPVDSGWTWALSILLLVVLIRTLLIPLFVKQI
+KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF
+FFALYQVLIGARGAAERGEAMDALSADQIRSFEGSTIFGARMSDTFMNSLGAPGSTPVIV
+TAIVLILLMSGSMFFMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVSNAEATPSSAH
+TQAGRGGAVLNGEVVRQSGQRVQPQRKNRRRK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001772.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001772.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b8975b96caf6455f3f023f8377e5f6ded13a976
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001772.fa
@@ -0,0 +1,30 @@
+>NZ_CP033200.1_1814
+MWIVLALALVVGLLLGLMGGGGSILMVPLLTYVAGLEPKQAIAGSLFVVGVTSLVSVLLH
+SRHGTVRWRTGLIFGAASMVGALLGGVVGGFLPGTLLLIAFAVMMLFTAWAMIRPKKTQP
+AAAPSVEASADVEPRRHPLGKILLEGVVVGFVTGIIGAGGGFLVVPALVLLGGLPMSAAV
+GTSLLVIAMKSFAGLGGYLTSVTLPWDLLLWVTGVAVVGGLIGVPLVKRVPEKALKKGFG
+WFVLAMGLVILVRELIGLLV*
+>NZ_CP040019.1_600
+MAWLAVVLAVAVGLLLGLMGGGGSILMVPLLTYVAGLDPKEAIAGSLFVVGVTSLVSVGL
+HARAGNVRWRTGLVFGLAGMVGAALGGVVGGFLPGTVLLIAFAVMMLVTAWAMIRPKRPT
+AAPAEGGHAPGRALGRIVLDGVVVGFVTGIVGAGGGFLVVPALVLLAGLPMSAAVGTSLL
+VIALKSFAGLGGYLTSVTLDWPFLLAVTGVAVLGALIGAALVNRVPDKALEKGFGWFVLA
+MGVVMLVTELVGLLA*
+>NZ_CP040019.1_2607
+MSGTLILTLVLAVGVGLALGTLGGGGSILTVPLLTYIAGMPPKEAIAASLLIVGVTSLSS
+LVVHARHRRVRWRTGLIFGAAGMVGAFAGGLIGGQLPGAVLMVAFAIMMIATAIAMVTRK
+PRRDTDQPTADAGTERAHSLPMLRTMLEGIVVGLITGIVGAGGGFLVVPALVLLGGLSMP
+VAVGTSLLVIAMKSFAGLAGYLTTVTLDWPLVAAVTAMAVLGALLGARLSGRIPADALQK
+VFGVFVLLTGTLVLVIELPPAWAIAAGGLGLITVVLVLVCRLTALNCPFGLARPTPG*
+>NZ_CP083691.1_524
+MVPLALLVVLAAVVGLLLGLMGGGGSILTVPLLTLTAGMDPQEAIAGSLVMVGASSLVAA
+LVHATRGAVAWRTGLTFGAASMVGALAGGFVGRDLPGPVLMVGFAVIMLISAVKMIRPRR
+KGAGHDDAAPVPLGRVLLQGVGVGLITGVVGAGGGFLIVPALVLLARLPMPVAVGTSLLV
+IAMNSAMGLVSQLGATALDWAVLGPMAAAAAAAGVVGVVLAHRVPAAALKRGFGWFVLAM
+GVLILAQQALELLP*
+>NZ_CP097650.1_2033
+MWIVLALALVVGLLLGLMGGGGSILMVPLLTYVAGLEPKQAIAGSLFVVGVTSLVSVLLH
+SRHGTVRWRTGLIFGAASMVGALLGGVVGGFLPGTLLLIAFAVMMLFTAWAMIRPKKTQP
+AAAPSVEASADVEPRRHPLGKILLEGVVVGFVTGIVGAGGGFLVVPALVLLGGLPMSAAV
+GTSLLVIAMKSFAGLGGYLTSVTLPWDLLLWVTGVAVVGALIGVPLMKRVPEKALKKGFG
+WFVLAMGLVILVRELIGLLV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001780.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001780.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6085b60ed98e0e10476f9f38eb313ac73e19fd47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001780.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_10
+MGKDLFEHEQQQTLSREQAAARLRDLADQLSRQNEVRVEHGGRDVVVTVPDRVGLEVELE
+VEDGGDAELEITLSW*
+>NZ_CP033200.1_1984
+MGKDLFEHEQQQTLSREQAAARLRDLADQLSRQNEVRVEHGGRDVVVTVPDRVGLEVELE
+VEDGGDAELEITLSW*
+>NZ_CP040019.1_370
+MSDEIFEHETTETMTREQAAARLRELADQLSRQNEVRIEHAGRDVVVTVPDQVELEVELE
+IEEGGESELEISLSW*
+>NZ_CP097650.1_10
+MGKDLFEHEQQQTLSREQAAARLRDLADQLSRQNKVRIEHGGRDVVVTVPDRVGLEVELE
+VEDDGDAELEITLSW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001781.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001781.fa
new file mode 100644
index 0000000000000000000000000000000000000000..570bbdf4dce8d6390eea07526f62da6c8741f582
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001781.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_38
+MSEHQQHVGRRDPRISDEAIERGRRAHELDRAHVFHSWSAQRDLNPMTILDAEGSWVWDG
+EGRPMVDFSGQLVFTNVGHRHPKIVAAIREQAETLATVAPQHVNDARSEAARLITEWLPE
+SINHVFFTNAGAEANDHAVRMARLHTGRHKVLSAYLSYHGATRLTANLTGSLRRVGSDSA
+SDGVVHFQPAYTYRSAFGSENDEQEAERALAHLRDVIELEGPSTVAAVVLEAVPGTAGIF
+MPPPGYMAGVKELCREHGILLIIDEVMVGFGRVGEWFGHQLTGVTPDIVTFAKGVNSGYV
+PLGGVAMSDDVYESFATTPYPGGLTYSGHPLACAAAVAAITAMEEECMVANAKRIGEEII
+GPRLAEIAAAHPSVGDVRGAGAFWAVELVKDRQTRERLAPLGQVAPVMGRMMAEAKDRGL
+LLFMAENRFHLCPPLNISDEDLRFGLDVLDQVLALADEEVAAG*
+>NZ_CP033200.1_2007
+MSEHQQHVGRRDPRISDEAIERGRRAHELDRAHVFHSWSAQRNLTPMTILDAEGSWVWDG
+EGRPMVDFSGQLVFTNVGHRHPKIVAAIREQAETLATVAPQHVNDARSEAARLITERLPE
+SINHVFFTNAGAEANEHAVRMARLHTGRHKVLSAYLSYHGATRLTANLTGSLRRVGSDSA
+SDGVVHFQPAYTYRSAFGSESDEQEAERALAHLRDVIELEGPSTVAAVILEAVPGTAGIF
+LPPPGYMAGVKELCREHGILLIIDEVMVGFGRVGEWFGHQLTGVTPDIVTFAKGVNSGYV
+PLGGVAMSDDVYESFATTPYPGGLTYSGHPLACAAAVAAITAMEEEGMVAHAKRIGEEVI
+GPRLAEIAAAHPSVGDVRGAGAFWAVELVKDRQTRERLAPLGQVAPVMGRMMAEAKDRGL
+LLFMAENRFHLCPPLNISDEDLRFGLDVLDQVLALADEEVAAG*
+>NZ_CP033200.1_2120
+MTAPAEAGLLDRDAAHLWHPYGAAGARQLYAVRGARGVHLDLEGPGGERHRAIDAMASWW
+SVVHGHGHPALVEALTRQAAAFPHVMFGGLTHAPAVDLAERLVAHTPAALEHVFLADSGS
+VSVEVALKLALQYQATRGRPSRRRFLTVRGGYHGDTAAPMGVCDPVDGMHAAFTSLVARH
+LFLPRPPAARWVPEGFAAAPTAPDAAPAGHWEADDAALAAWEDEARAFTAAHADEIAGVI
+LEPVLQGAGGMRVYDPRCLTVLRELCDEHGLLLIADEIATGFGRTGRWLACEGAGVAPDV
+LCLGKALTGGTMTGAAMLCTAEVAETVSRRERGMPGALLHGPTFMGNPLMCAVASASLDL
+LTDPRDGWAAQVPRVEAGLRAGLAAAADLPAVTDVRVLGAVGVVELDRTVDVEPVTRAAV
+ARGAWVRPFRRLVYVMPPYVSTDDDVATICAAVTGAVEEVCA*
+>NZ_CP097650.1_33
+MSEHQQHVGRRDPRISDEAIERGRRAHELDRAHVFHSWSAQRDLNPMTILDAEGSWVWDG
+EGRPMVDFSGQLVFTNVGHRHPKIVAAIREQAETLATVAPQHVNDARSEAARLITERLPE
+SINHVFFTNAGAEANEHAVRMARLHTGRHKVLSAYLSYHGATRLTANLTGSLRRVGSDSA
+SDGVVHFQPAYTYRSAFGSESDEQEAERALAHLRDVIELEGPSTVAAVILEAVPGTAGIF
+LPPPGYMAGVKELCREHGILLIIDEVMVGFGRVGEWFGHQLTGVTPDIVTFAKGVNSGYV
+PLGGVAMSDDVYESFATTPYPGGLTYSGHPLACAAAVAAITAMEEEGMVAHAKRIGDQII
+GPRLAEIAAAHPSVGDVRGAGAFWAVELVRDRQTRERLAPLGQVAPVMGRMMAEAKDRGL
+LLFMAENRFHLCPPLNISDEDLRFGLDVLDQVLTLADEEVAAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001784.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001784.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd678cd2221ca57eb7414ce4977676e524399bd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001784.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_49
+MDDPVDARLAAAVSHDPRATLAQLSERVGLSTSAVQARLRRLESTGVITGYRALLDPEAV
+GRPLSAFIEISPLDPRQPDDAPELLESIAAIEACHSVAGDAAYILFVRVGSPRELEALVT
+EIRQTASVATRTTVVLQTFYEHRPMLELPAED*
+>NZ_CP033200.1_2018
+MDDPVDARLAAAVSHDPRATLAQLSERVGLSTSAVQARLRRLESTGVITGYRALLDPEAV
+GRPLSAFIEISPLDPRQPDDAPELLESIAAIEACHSVAGDAAYMLFVRVGSPRELEALVT
+EIRQTASVSTRTTVVLQTFYEHRPMLELPAED*
+>NZ_CP040019.1_338
+MDDPVDARLAAEVSRDPRATLAQLSERVGLSASAVQARLRKLESTGVITGYQAILDPEAV
+GKPLAAFIEITPLDPRQPDDAPELLEPIAAIEACHSVAGDAAYMLFVRVGSPRELEALVS
+EIRHTASVNTRTTVVLQTFYEHRPMLPLPDAGE*
+>NZ_CP097650.1_44
+MDDPVDARLAAAVSHDPRATLAQLSERVGLSTSAVQARLRRLESTGVITGYRALLDPEAV
+GRPLSAFIEISPLDPRQPDDAPELLESIAAIEACHSVAGDAAYMLFVRVGSPRELEALVT
+EIRQTASVSTRTTVVLQTFYEHRPMLELPVED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001789.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001789.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a1fc4bba1abbb9dcd10f98d2357f183afc4a93b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001789.fa
@@ -0,0 +1,29 @@
+>NZ_CP042169.1_116
+MLVLVINSGSSSLKYQLRELADDGTDAPVPVLAQGLVERIGVPGSGVPDHAAALEQVEAE
+LAEATGGRTIDAAGHRVVHGGERFTAPARVTNEVIRAIERLAPLAPLHNPAAAQGLRAMA
+ERWPDMPQVVVFDTSFHQTMPREAWQYALPDEVYTEHGIRRYGFHGTSDDLVTGLAAEHL
+GIPRGEFRAVVLHLGNGASATAIRDGVSVDTSMGYTPLAGLVMGTRSGDLDPSVVTHLMR
+NHGYDAEELDTLMNRRSGLLGLAGEADMRQVLENAASGDGRARNALDVASYRLAKYVGGY
+HVAVGGAQAIVFTAGIGENSAPFRARVLDRLEALGVAYDAEANRARVAGPHTISAPESAI
+PVLVVPTDEEQAIARLTWELAR*
+>NZ_CP040019.1_252
+MLHLGNGASATAIRDGASVDTSMGFTPLAGLVMGTRTGDLDPSVVTHLMRTQGHSAEEMD
+TLMNKESGLLGLAGHADMRQVVEAADAGDRRARTAPDVASYRLAKYVGGYHVAVGGAQAI
+VFTAGIGENSAPFRARVVERLGALGVELDAAANEAGLSAAGDDGVAVISAPGSAIPVLVI
+PTDEEQAIARLTWELTRG*
+>NZ_CP083691.1_187
+MTASPATMTLPTVSARQLPEDALLVLVVNSGSSSLKYQVRELTPDGRDTDQPVVLKGLVE
+RIGVAGSDVPDHAAALERVEAEITAVVGSRRLAAAGHRVVHGGERFQRPELVTNEVIRAI
+ERLAPLAPLHNPAAAQGLRAVAQRWPDLPQVVVFDTSFHQSMPREAWQYAIPDELYTEHG
+IRRYGFHGTSHDLVTGLAAEHLGLERSEFDGVVLHLGNGASATAIRGGRSIDTSMGYTPL
+AGLVMGTRSGDLDPSIVTHLITAHGMSAEDVDAMLNKESGLLGLSGNADMRQVLEAAEAG
+HRASRDALRIASYRLAKYVGGYHVAVGGAKAIVFTAGIGENSAPFRARVLDRLEPLGVRY
+DHARNMVRGDEPRTISTDDSAIPVLVVPTDEEMAIAQLTHHVVEQAEAWTLG*
+>NZ_CP097650.1_124
+MLVLVINSGSSSLKYQLRELADDGTDAPVPVLAQGLVERIGVPGSGVPDHAAALEQVEAE
+LAEATGGRTIDAAGHRVVHGGERFTAPARVTNEVIRAIERLAPLAPLHNHAAAQGLRAMA
+ERWPDMPQVVVFDTSFHQTMPREAWQYALPDEVYTEHGIRRYGFHGTSHDLVTGLAAEHL
+GIPRGEFRAVVLHLGNGASATAIRDGVSVDTSMGYTPLAGLVMGTRSGDLDPSVVTHLMR
+NHGYDAEELDTLMNRRSGLLGLAGEADMRQVLENAASGDGRARNALDVASYRLAKYVGGY
+HVAVGGAQAIVFTAGIGENSAPFRARVLDRLEALGVAYEAEANRARVAGPHTISAPESAI
+PVLVVPTDEEQAIARLTWELAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001790.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001790.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b034f0fbe8df7e78b83a8be6344bbccff976e141
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001790.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_125
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHWAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL*
+>NZ_CP033200.1_2095
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHRAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL*
+>NZ_CP040019.1_244
+MTSTPYEDGIDQRELQEDLLAEPDSATDPGPQDGRDGQPVRGSSDDPQHWAGDGRAEDSL
+RNAESEAMHIQQDAEDRTRADEGDVEIL*
+>NZ_CP097650.1_133
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHRAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001794.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001794.fa
new file mode 100644
index 0000000000000000000000000000000000000000..927746b0763c70c4ce110cf5852d865ff79fd225
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001794.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_170
+MTATQDAPAVDPRPAAALDPEALVDRIEAGHRLTADEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERARRATADDGAPAGGCC
+AGTDDAGPCGSGAAVAAEDVRPDTGAEGAVKPELRRRGAGTAEPANA*
+>NZ_CP033200.1_2119
+MTATQDAAAVDPRPAAALDPEALVDRVEAGHRLTAEEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERARRATADDGAPAGGCC
+AGTDGAGSCGSGAAVASEAGAAEDARPDTGAEGTVKPELRRRGAGTAEPANA*
+>NZ_CP040019.1_216
+MTAAQDAAVVAPALDPEELVDRIEAGHRLTAAEAVAVLDAPDAETFRLVAAASRLRERHF
+GRTVKVNYLVSLKTGLCPEDCTYCSQRLGTEAQILKYTWLKPDEAVRQAGLGIAGGASRV
+CMVASGTGPTDRDVDRVTEMIGRLKDEHPQVEVCACLGKLKDGQAERLKAAGVDAYNHNL
+NTAESHYESICTSHTYADRVDTVERATAAGLSSCSGLIAGMGETHAQLAEAVLALRELDS
+DSIPVNFLMPFDGTPLAGHVQLTPLECLRILAVVRLACPDKELRIAGGREMHLRSLQAVG
+LQVANSIFLGDYLTSEGQDAEADLSMIADAGFTVLGAAAAPADDDGAPDGGCCGGGGCGE
+GGVEDASTRGGTSPSPSPAPRRRGAGTAEPANA*
+>NZ_CP097650.1_162
+MTATQDAAAVDPRPADALDPEALVDRIEAGHRLTADEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERAQQAAADDGAPAGCCG
+GGCVGTHDNSKNGAAATPSKPVLRRRGAGTGAAANA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001797.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001797.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7e85e034f973f7eb33ac242448f32ba1616c506
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001797.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_194
+MDRTAPTPPANALAPDLPEDIAREAIAFRRLLHGHPELDLHLPRTQAAVLERLEALRAEA
+GEDAATGRPALETSVGRALSSVVVVLRGGAPLPEGARRPVVLLRGDMDALPVTEETGLEY
+APAVPGTMHACGHDLHTAGLYGALAWLVRRRGELTADVVAMFQPGEETGGGALHMIQEGL
+LEAAGRPVDAAYAIHVSSGTYPRGVLRSRPGAIQAGCDDLVVTVHGRGGHGSVPHLAQDP
+VPVAAEMVLALQSVVTRQFDAFDTVVATVGHLSAGTAANIIPDSATLALTLRTFSADARA
+RLRAAVERMVHGIAAAHGMSAQVRADCAFPVTANDADAVAFARGVVEDLYGADAYRELPE
+PEPGSEDFSEVLQRVPGAYVLLGAVPEGVDPDEAPVNHSPQAVFDDAVVPRAAQVLAELA
+LRTAPVPAS*
+>NZ_CP033200.1_2145
+MDRTAPTPPANALAPDLPEDIAREAIAFRRLLHGHPELDLHLPRTQAAVLERLEALRAEA
+GEDAATGRPALETSVGRALSSVVVVLRGGAPLPEGARRPVVLLRGDMDALPVTEETGLEY
+APAVPGTMHACGHDLHTAGLYGALAWLVRRRGELTADVVAMFQPGEETGGGALHMIQEGL
+LEAAGRPVDAAYAIHVSSGTYPRGVLLSRPGAIQAGCDDLVVTVHGRGGHGSVPHLAQDP
+VPVAAEMVLALQSVVTRQFDAFDPVVATVGHLSAGTAANIIPDSATLALTLRTFSADARA
+RLLSAVERLVHGIAAAHGMSAQVRTDCAFPVTANDPDAVAFVRGVVEDLYGADAYRELPE
+PEPGSEDFSEVLQRVPGAYVLLGAVPEGMDPDEAPVNHSPQAVFDDAVVPRAAQVLAELA
+LRTAPGPAS*
+>NZ_CP040019.1_196
+MTPETADALAPRVPDGLAQDVIALRRDLHAHPELDLHLPRTQAAVLDRLAPLQERAGQDA
+RTGGPALEVSTGRELSSVVLVLRGAKPLPAGTRRPVVLLRGDMDGLPVTELTGLDWAPPT
+PGTMHACGHDLHTAGLYGALAWLVERRDELAADVIGMFQPGEETDGGAARMIDEGLLEAA
+GPHPDAAYAIHVYSGKYPHGALVSRTGAIQAGCDDLIVTVRGRGGHGSVPHLAQDPVPVA
+AEMVLALQSLVARQFDAFDPVVATVGHLSAGSAANIIPDTATLAITLRTFSADARERLVP
+AVRRMVDGIAAAHGMSAEVRADCAFPVTVNDGEKVDFARGVVEDLYGAEAWQELPEPEPG
+SEDFSEVLVRVPGAYLLLGAVPPGVDPETAEGNHSPRAVFDDAVLPRAVEVLAELALRTP
+PVPEG*
+>NZ_CP097650.1_196
+MDRTAPTPPANALAPDLPEDIAREAIAFRRRLHGHPELDLHLPRTQAAVLERLEALRAEA
+GEDAATGRPALETSVGRALSSVVVVLRGGAPLPEGARRPVVLLRGDMDALPVTEETGLEY
+APSVPGTMHACGHDLHTAGLHGALAWLVRRRGELTADVVAMFQPGEETGGGALHMIQEGL
+LEAAGRPVDAAYAIHVSSGTYPRGVLISRPGAIQAGCDDLVVTVHGRGGHGSVPHLAQDP
+VPVAAEMVLALQSVVTRQFDAFDPVVATVGHLSAGTAANVIPDSATLALTLRTFSADARA
+RLRAAVERMVHGIAAAHGMSAQVRTDCAFPVTANDADAVAFVRRTVEDLYGADAYRELPE
+PEPGSEDFSEVLQRVPGAYVLLGAVPEGVAPDEAPVNHSPQAVFDDAVVPRAAQVLAELA
+LRTAPVSAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001799.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001799.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5ea36be121ba11c9db7239396d28c980b7e8751
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001799.fa
@@ -0,0 +1,48 @@
+>NZ_CP042169.1_212
+MTRTVPARRRTTLAAAVAAVSLAVTAAAPALSAPGNGNGNGNGNGSASQGQARSNDLSAT
+RGNKVNDAAALAPHLVGQTLDWEACDFGSERLNARFNAIPGTACADVTVPRDWKNPEDGH
+TITLRVAKTETSKGNPERQGIALVNPGGPGGSGLPWGPAMAERAPELAEQYDFIGFDPRG
+VGQSTALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVLGEEKT
+SYIGYSYGTWLGSWYQRVFPQHTHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLP
+YVARHDEIFGLGDNPMQIRQRWEDVGGTRTQLGMIVAGSFLLPAMYDTSQYLDAGSVIAA
+YIRIMESEAAATDPAGQRTQIERILAEARASLPAEERDSFDRFAARGLETVGEREQLVAA
+TQAGDAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMYWPAQT
+SMPAQPGGKGAPNTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTEC
+VDAPIRDYFLTGAQPAEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRI
+THDAIERQLIDSRAVTPDVEAFLED*
+>NZ_CP033200.1_2162
+MTRTVPARRRTTLAAAVAAVSLAVAAAAPALSAPGNGNGNGSASQGQARSNDLSATRGNK
+VNDAAALAPHLVGQTLDWDACDFGSERLNARFNAIPGTACADVTVPRDWKNPEDGHTITL
+RVAKTETSKGNPERQGIALVNPGGPGGSGLPWGPAMAERAPELAEQYDFIGFDPRGVGQS
+TALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVLGEEKTSYIG
+YSYGTWLGSWYQRVFPQHAHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLPYVAR
+HDEIFGLGDDPMQIRQRWEDVGGTRTQLGMIVAGSFLLPAMYDTSQYLDAGSVIAAYIRI
+MESEAAATDPAGQRTQIERILAEARASLPAEERDSFDRFAARGLETVGEREQLVAATQAG
+DAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMYWPAQTSMPS
+QPGGKGAPNTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTECVDAP
+IRDYFLTGAQPAEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRITHDA
+IERQLIDSRAVTPDVEAFLED*
+>NZ_CP040019.1_152
+MTRTAPTRRRTTLAAAVAAAAALTISAAAPALSAPGNGNGNGNGQSSASQGQARSNDLST
+TRGNQVNDAAALAPHLLDQELAWEACDFGSPALNTRFGAIPGTACADVTVPRDWKDPQDG
+HTITVRVAKTETSKGNPDRQGIALVNPGGPGGSGLPWGPAMAERAPELAEQYDFIGFDPR
+GVGQSTALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVMGEEK
+TSYIGYSYGTWLGSWYQRVFPQHAHRFLLDSAVDVSRDGLQTTWNLQPRSRDRQFQDMML
+PYVARQDAVYGLGTDPMEIRQRWEDAGGTRTILGQIVAGSYLLPAMYSTSQYPMAASMIA
+AFISIMETETAATDEAGMQAQLERITAEARATVPAADRAAFDRFIEQGSEVVAERDELAA
+AVRTGQPVTFSGTFSAIRCQDGQWNTSEGYWTSWVNDLGRKAPWIAAFMGPSECMYWPAQ
+TSMPSQPGGKDTPSAVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTE
+CVDAPIRDYFLTGEMPAEKSLCEAHPLPGETQTHQVAGTPTHKGDIKISMRTDAVREANR
+ITLDAIERQLLDSRAVTPDVEAFLER*
+>NZ_CP097650.1_213
+MTRTVPARRRTTLAAAVAAVSLAITAAAPALSAPGNGKGNGSASQGQARSNDLSATRGNK
+VNDAAALAPHLVGQTLDWEACDFGSESLNARFNAIPGTACADVTVPRDWKNPEDGHTITL
+RVAKTETSKGNPERQGIALVNPGGPGGSGLPWGPAMAERAPELAEQYDFIGFDPRGVGQS
+TALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVLGEEKTSYIG
+YSYGTWLGSWYQRVFPQHAHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLPYVAR
+HDEIFGLGDDPMQIRQRWEDGGGTRTQLGMIVAGSFLLPAMYDTSQYMSAGAVIAAYIRI
+MESEAAATDPAGQRAQIERILAEARASLPTEERDSFDRFADRGLETVGEREQLIAATQAG
+DAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMYWPAQTSMPS
+QPGGKGAPSTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYGTECVDAP
+IRDYFLTGAQPAEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRITHDA
+IERQLIDSRAVTPDVEAFLED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001800.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001800.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec8665a8e68d116b68d53afe475d4cd51df77375
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001800.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_220
+MTTTHMHTDAEDTIHPTQPAPDAGPLSQAEIDRLFADRHTTQLFSDEPVDLALIERAYAD
+LRWAPTAMNNQPLRLDVVDSPEARARLAPLMIEFNREKTERAPLTLIASYDLDWHRHMGH
+LAPFREGFEEDAEGKPGMREGMGRTNALIQVGYLLVALRAHGLEVGPMAGFDAAAVDAEF
+HADRAWKSLLVINVGHAAADDEKAQQPRQGRLDFDQAAQVL*
+>NZ_CP033200.1_2189
+MTTTHMHTDAEDTIHPTQPAPDAGPLSQAEIDRLFADRHTTQLFSDEPVDLALIERAYAD
+LRWAPTAMNNQPLRLDVVDSPEARARLAPLMIEFNREKTERAPLTLIASYDLDWHRHMGH
+LAPFREGFEEDAEGKPGMREGMGRTNALIQVGYLLVALRAHGLEVGPMAGFDAAAVDAEF
+HADRAWKSLLVINVGHAAADDEKAQQPRQGRLDFDQAAQVL*
+>NZ_CP083691.1_102
+MTTTYMHTDAEDTIHSTQPAPDAGPLSQAEIDRLFADRHTTQLFSDEPVDLALIERAYAD
+LRWAPTAMNNQPLRLDVVDSPEARARLAPLMIEFNREKTERAPLTLIASYDLDWHRHMGH
+LAPFREGFEEDAEGKAGMREGMGRTNALIQVGYLLVALRAHGLEVGPMAGFDAAAVDAAF
+HADRAWKSLLVINVGHAAADDEKAQQPRQGRLDFDQAAQVL*
+>NZ_CP097650.1_221
+MTTTHMHTDAEDTIHPTQPAPDAGPLSQAEIDRLFADRHTTQLFSDEPVDLALIERAYAD
+LRWAPTAMNNQPLRLDVVDSPEARARLAPLMIEFNREKTERAPLTLIASYDLDWHRHMGH
+LAPFREGFAEDAEGKPGMREGMGRTNALIQVGYLLVALRAHGLEVGPMAGFDAAAVDAEF
+HADRAWKSLLVINVGHAAADDEKAQQPRQGRLDFDQAAQVL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001804.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001804.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d670d1050263753f0ff1a4436d452d0de88ee57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001804.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_245
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHKEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY*
+>NZ_CP033200.1_2213
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY*
+>NZ_CP040019.1_108
+MYTRSRNDVEKVEWGGGTSERLLTAKDEMGFAVAHTIVRAGSSSKLQYRHHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY*
+>NZ_CP097650.1_245
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001806.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001806.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d26db732c825dc3c94dc268fbb14537b4ca121d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001806.fa
@@ -0,0 +1,80 @@
+>NZ_CP042169.1_265
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQ
+LDGVRPDFAALIDGRPCGWVELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIA
+LYVSGSPVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPAARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPS
+VVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARRIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGEDALFDDVIGPAQEQGVIFSAQASLYNLYVYFWR
+WAIWKAFQQDPGDQAIISFITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQE
+ENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEKFAALDEVARLDPDDGTWECLP
+GGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADPS
+ADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFFVSPKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAE
+AAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDAYVQRFDEALEGSPVRVPLTVD
+PALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYDP
+ATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVSLGGDQADLLDEILARDLIPANELPEPTPAERKVPKTIKR
+DFSTAQEEMF*
+>NZ_CP033200.1_2236
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQ
+LDGVRPDFAALIDGRPCGWVELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIA
+LYVSGSLVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPAARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPS
+VVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARQIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGEDALFDDVIGPAQEQGVIFSAQASLYNLYVYFWR
+WAIWKAFQQDPGDQAIISFITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQE
+ENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEKFAALDEVARLDPDDGTWECLP
+GGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADPS
+ADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFFVSPKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAE
+AAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDAYVQRFDEALEGSPVRVPLTVD
+PALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYDP
+ATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVSLGGDQADLLDEILAGDLIPANELPEPTPAERKVPKTIKR
+DFSTAQEEMF*
+>NZ_CP040019.1_75
+MDRDAVNALAEEYSRGIGQALSMGVAAEPEAQLTVPFAAFLSRFAQEVELGRLDLLREAQ
+LDGVRPDFAAALDGRPCGWIELKAPGHTVVGERWRGREKSQWALLSQLDALLVSNGELLA
+LYVAGAPVETCALPVDGAAGWDPDRLRRVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLAEGLEHSYDSVVEAKAAWDHTMQHTTSPEEFSGDVAQVVAYSMAIAGLSGQADRNADG
+VVSLEEAKHALETAHRNVLAASLGPILGIPALMQHIAPEVGAITRLVAGMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPEARSRAGVYYTPISVVECQVRVVDALLRERFGQNLGFGAPS
+VVTLDPATGSGTYPLAIIDRAESVAREERGDAGAKQVAMNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMPTGLFGDARVLAEAAESARRVKRDQQ
+ITVAIGNPPYDRVTSGTGGWVEQGSGSGDALFDDVIKPAQDSGVIFSAQASLYNLYVYFW
+RWAIWKAFQQDPKDHAVISFITASSWLTGPAFVGLRRLAQATASEIWVMDLGGEGRGARK
+EENVFDIQSPVAIVTLVRTGKASREAKVFYRRFRGSRAEKFTALDRIQRLDAADGWEQIA
+APGGAPFMPASGGEDWTAMPQLADLFPWQQPGIMYNRAWPVASDQNTLRRRWQELLSDDD
+ADARAGKYVTGNSGRTIHTAVAGLPTLASLPADAEPRPIVRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFLVSPKTARINGGPAVTVSTAVPDKHHYVGSFGGKDVIPLYRDAA
+AAEPNVTVGLLELLADRLGHDVTPEDLAAYVMAVAAHDGYAQTFDEALETSPVRIPFTAD
+ASLWDAAVALGERLLWLQTYGERFTSADRPRGRVPRVPGLGWSEAVTHIPADTASLSYDA
+ASRELRVGDGVVTGVSPEVRAFSVSGMNIVDKWLGARTAKGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVALGDQQAELLAAILAGELITAADLPVPTAAERKVPKTIKR
+GVSPHQEGLL*
+>NZ_CP097650.1_263
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQ
+LDGVRPDFAALIDGRPCGWVELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIA
+LYVSGSLVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPAARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPS
+VVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARQIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGEDALFDDVIGPAQEQGVIFSAQASLYNLYVYFWR
+WAIWKAFQQDPGDQAIISFITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQE
+ENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEKFAALDEVARLDPDDGTWECLP
+GGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADPS
+ADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFFVSPKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAE
+AAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDAYVQRFDEALEGSPVRVPLTVD
+PALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYDP
+ATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVSLGGDQADLLDEILAGDLIPANELPEPTPAERKVPKTIKR
+DFSTAQEEMF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001807.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001807.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4bc3dbd6f6ac5d13e838dd1ce87b9b6ae535cb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001807.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_268
+MTGSAPAQLRPLRATDAPAVLAAFHAGTVGMADPAEVTDDASARAYVDGLVQAEGTDAVA
+VVERGTDTLIGLVAVVRDEAHGTGALTAWLHQGWRGDAIMSRAATTVADAELAEGGLERI
+ELAHRADSPTAGAVARAAGLRHEGTQRGRLRTGGRRLDVHLYGRLAADPLPEERVRPLPW
+ASDARPWADR*
+>NZ_CP033200.1_2239
+MTGSAPAQLRPLRPTDVPAVLAAFHAGTVGMADPAEVTDEASARAYVDGLVQAAETDAVA
+VVERGTDTLIGLVAVARDEAHGTGALTAWLHQGWRGDAIMSRAATTVTDAELAEGGLERI
+ELAHRADSPTAGAVARAAGLRHEGTQRGRLRAGGRRLDVHLYGRLAADPLPEERVRPLPW
+ASDARPWADR*
+>NZ_CP040019.1_71
+MTGTARAQLRPLHSDDADAVFEGFRSDPVGMARQGDVSDEASARFYVDRMLESEATDAVA
+VVDPATDRLIGLVSVVRDEENRSGWFSYWLNSAWRGDAIMARAAATVADAELAEGGLERL
+ELGHRANNPTSGSVARAAGFLHEGTQRGHFLIDGRRQDVHLYGRLPSDPQPAEKVRPLPW
+ASDERPWSGR*
+>NZ_CP097650.1_267
+MTGSAPAQLRPLRPTDVPAVLAAFHAGTVGMADPAEVTDEASARAYVDGLVQAAETDAVA
+VVERGTDTLIGLVAVARDEAHGTGALTAWLHQGWRGDAIMSRAATTVTDAELAEGGLERI
+ELAHRADSPTAGAVARAAGLRHEGTQRGRLRAGGRRLDVHRYGRLAADPLPEERVRPLPW
+AADARPWADR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001808.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001808.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1fea30448d76500afe06433d0bbe65cca1ebce0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001808.fa
@@ -0,0 +1,28 @@
+>NZ_CP042169.1_277
+MPEGDSLVRVAHRLRPVLEGRVLTHADLRVPRHATADLTGWTVAEVLPRAKYLLMRLTPP
+AARPGARPLTLISHLKMEGRWLVSALDARWGAPAWQVRAVLETAEHRVLGAQLGLLTLVP
+TADETTVLGHLGPDLLDPAWDTPDDGAALLAEGMRRLTARPERPVGLALLDQRLVSGIGN
+IYRCETLLLAGIDPHRPIGEVEDVAGLVLLARDLLRANVPPAAPATGARRRTTGVRPNPG
+RPFGVEVLVPAGPPLGTAPGRTPGARGGGAPSYWVYGHDRAPCLRCRGPVRQEDYGSAED
+DARRLWWCPHCQG*
+>NZ_CP033200.1_2255
+MPEGDSLVRVAHRLRLVLEGRVLTHADLRVPRHATADLTGWTVAEVLPRAKYLLMRLTPP
+AARPGARPLTLISHLKMEGRWLVSAVDARWGAPAWQVRAVLETAEHRVLGAQLGLLTLVP
+TADEATVLGHLGPDLLDPAWDTPDDGAALLAEGVRRLTARPERPVGLALLDQRLVSGIGN
+IYRCETLLLAGIDPHRPIGEVEDVAGLVLLARDLLRANVPPAAPAAGARRRTTGVRPNPA
+RPFGVEVLVPAGPSPGTAPGRTPGARGGGAPSYWVYGHDRAPCLRCRGPVRQEDYGSPED
+DARRLWWCPHCQR*
+>NZ_CP083691.1_40
+MPEGDSLVRAAHRLRPVLAGRVLTHADLRVPQLATARLTGWTVSEVEPRGKWLLMRLTPP
+ADRPDAAPHTLVSHLKMEGRWMVTGRDARWPAPAWQVRAVLETAEHRAVGAQLGRLELAP
+TAEEDRLLGHLGPDLLDPAWDDPARGAELLAEGVRRLTARPERPVGLALLDQRTTCGIGN
+IYRCESLLLAGLDPHRPVAAVPDVSGLLTLARDLLRANVPPAAPFIGWPRTTTRVRPDPS
+GPYGLRVVVEDRGFPGGLPGGPVPDDAPHASATSTSGAGLGRRGDLPRGPHYWVYGHRTT
+PCGRCGGPVTFEEYGSPEDDERQLWWCRTCQR*
+>NZ_CP097650.1_283
+MPEGDSLVRVAHRLRPVLEGRVLTHTDLRVPRHATADLTGWTVAEVLPRAKYLLMRLTPP
+TARPGARPLTLISHLKMEGRWLVSAIDARWGAPAWQVRAVLETAEHRVLGAQLGLLTLVP
+TADEAAVLGHLGPDLLDPAWDTPDDGAALLAEGVRRLTARPERPVGLALLDQRLVSGIGN
+IYRCETLLLAGIDPHRPIGEVEDVAGLVLLARDLLRANVPPAAPAAGARRRTTGVRPNPA
+RPFGVEVLVPAGPSPDTAPGRTPGARGGGTPSYWVYGHDRTPCLRCRGPVRQEDYGSPED
+DARRLWWCPHCQR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001815.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001815.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b21c589a693cfa530db3ed23a9237ed05ec4420
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001815.fa
@@ -0,0 +1,28 @@
+>NZ_CP042169.1_367
+MAPWLPTRSRRPFPQVTEAGEVPAVTPTFEGRASHPPAEDVEDQGAAFDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSSSTSASAGSSSPAASSSSAASASPSATLTEMVTET
+AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAA
+VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFP
+DKASITDATNNVLTSQIAMPEEQSSQVYATSAYDGSTANFAKVSLETDNVFSDGYETQLP
+QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPAQP*
+>NZ_CP033200.1_100
+MAPWPPTRSRRPFPQVTEGGGAPAVTPTFEGRAFHRPAEDVEDQGAAFDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSGSTSASAGSSSPEASSSSAASASPSATLTEMVTET
+AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAA
+VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYAGRWPHLHFEVFP
+DKASITDATNNVLTSQIAMPAEQSAQVYATSAYDGSTENFAQVSLETDNVLSDGYETQLP
+QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPARP*
+>NZ_CP083691.1_2389
+MAPWLPTRSRRPFPQVTEGGEAPAVTPTFEGRAFHRPAEDVEDQGAAFDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSSSTSASAGSSSPAASSSAASASPSATLTEMVTETA
+GPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAAV
+YLWHADALGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFPD
+KASITDATNNVLTSQIAMPEEQSSQVYATSAYDGSTANFAKVSLETDNVFSDGYETQLPQ
+ITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPARP*
+>NZ_CP097650.1_373
+MAPWLPTRSRRPFPQVTEAGEVPAVTPTFEGRAFHHPAEDVEDQGAALDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSGSTSASAGSSSPAASSSSAASASPSATLTEMVTET
+AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTAAEGVPLTVTMNVIDMANGDAAMTGAA
+VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFP
+DKASITDATNNVPTSQIAMPEEQSAQVYATSAYDGSTENFADVSLETDNVFSDGNETQLP
+QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPAQP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001816.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001816.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9ac766850ab02d49aea64843b308f808f30df34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001816.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_370
+MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARPIASYGAPAPGTLGG
+VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA
+DGHVAAAIENGKVGRMLDRLTALVPEIR*
+>NZ_CP033200.1_103
+MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARPIASYGAPAPGTLGG
+VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA
+DGHVAAAIENGKVGRMLDRLTALVPEIR*
+>NZ_CP040019.1_2518
+MAAVRALRTLLAEGYATPEAPVAVTGAGWPDYDARVLPGLAAAQELAGVDVDYLRHVDRV
+SDAGIDAASLADLGTLFTYVLRGERFSEGHIGAALANGKVGRMLDRLAELVPQVR*
+>NZ_CP097650.1_376
+MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARQIASYGAPAPGTLGG
+VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA
+DGHVAAAIENGKVGRMLDRLTALVPEIR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001822.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001822.fa
new file mode 100644
index 0000000000000000000000000000000000000000..138948cd79e4b206447ac10222f6519e109e5f14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001822.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_547
+MDSRVNSGGVVGKVDNLTCLAGLVTTEDPARVRALRGTVLAVALLNGAYLVVEIILALGI
+GSVALVADSVDFFEDFAVNLLIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKIG
+DPDPPAAGVLLGAAVGSLLVNLVCVALLARVRTDGGSLTRAAWLAARNDLVAGAVLIALS
+GITVLTASGWADIIVGVLLVLLNGSAAKEIWEAATEEHLAAQALAGEVDDD*
+>NZ_CP033200.1_280
+MNRAAVADRRRTRTLRGTVLAVALLNGAYLVVEIILAVGIGSVALVADSVDFFEDFAVNL
+LIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKIGDPEPPAAGVLLGAAVGSLLV
+NIVCVVLLARVRVDGGSLTRAAWLAARNDLVAGVVLIALSGITVLTASGWADIIVGVLLV
+LLNGSAAKEIWEAATEEHLAAQALAGEVDDD*
+>NZ_CP083691.1_2209
+MDAMTETSHPRPDPARVRALRGTVLAVSLLNLAYMLVEIGVALGIGSVSLVADSVDFFED
+FAVNMLIVIALGWPLARRARVGKVMAGIIVLPAIAALAMAAVKVGDPEPPATGPLFWTGV
+GSLLVNLVCVGLLARFRADGGSLTRAAWLAARNDLIAGIVLIALAGATALTASGWADIIV
+GVLLVVLNGGAAKEVWQAATEERLAAQALAGEFDDD*
+>NZ_CP097650.1_549
+MNEVPEADRRRTRALRGTVLAVALLNGAYLVVEIILALGIGSVALVADSVDFFEDFAVNL
+LIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKVGDPDPPAAGVLLGVAVGSILV
+NLVCVALLARVRTDGGSLTRAAWLAARNDLVAGVLLIALSGITVLTASGWADIIVGVLLV
+LLNGSAAKEIWEAATEEHLAAQALAGEVDDD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001824.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001824.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70d5c2c3bc6fe8d1b511d0aee8f9a30b1a5ad776
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001824.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_555
+MAAAVALVPIGYLFLRTAQGGFGPWLDAVVSPRVGALAATSLALTAVVTALCLVIGVGAA
+WLVTRTDTPGRGLLAVLLALPLAVPSYVAAFTWVSVSDLLPGVEAGRFEGFWAAVTVMTL
+YTYPYVYLPVAAALSRIDPGQEDVARSLGRGPAATLFTVTLAQVRPAIAGGALLVALYVL
+SDFGAVAILRLDTFTRAIFTALEVGFNRQLALTLATVLVLLTVLVLWGESRTRRADDGVR
+SGRTVRRVSVHRLGRSRWVGTGLLAVVTGAALGVPAVSLVRWMGEGTSLSAVRDRWLDAV
+SGSVVLAGAGAALTLALALPIGILAARHPGRVSRIAERAAFLAHGLPGVVVGLSLVFLGV
+SLVPALYQTTWMVAFAYATLFLPLAVTSVAGAVAQSSPALEEAARSLGSSGAEVLRRVTL
+PLALPGVGAGVALVALTAMKELPATLLLRPTGMDTLATRLWNATSVGRYAEAAPYALTLV
+LLAAVPTWVVVHRTGIVAAVRGRSSAPSTPNEVSE*
+>NZ_CP033200.1_296
+MAAAVALVPIGYLFLRTAQGGFGPWLDAVVSPRVGALAATSLALTAVVTALCLVIGVGAA
+WLVTRTDTPGRGLLAVLLALPLAVPSYVAAFTWVSVSDLLPGVEAGRFEGFWAAVTVMTL
+YTYPYVYLPVAAALSRIDPGQEDVARSLGRGPAATLFTVTLAQVRPAIAGGALLVALYVL
+SDFGAVAILRLDTFTRAIFTALEVGFNRQLALTLATVLVLLTVLVLWGESRTRRADDGVR
+SGRTVRRVSVHRLGRSRWVGTGLLAVVTGAALGVPAVSLVRWMGEGTSLSAVRDRWLDAV
+SGSVVLAGAGAALTLALALPIGILAARHPGRVSRIAERAAFLAHGLPGVVVGLSLVFLGV
+SLVPALYQTTWMVAFAYATLFLPLAVTSVAGAVAQSSPALEEAARSLGSSGAEVLRRVTL
+PLALPGVGAGVALVALTAMKELPATLLLRPTGMDTLATRLWNATSVGRYAEAAPYALTLV
+LLAAVPTWVVVHRTGIVAAVRGRSSAPSTPNEVSE*
+>NZ_CP040019.1_2310
+MAAAVAVVPIGYLFLRTAQGGFGPWLDAVVSPRVGALAATSLALTAVVTALCLVIGVGAA
+WLVTRTDTPGRGLLAVLLALPLAVPSYVAAFTWVSVSDLLPGVEAGRFEGFWAAVTVMTL
+YTYPYVYLPVAAALSRIDPGQEDVARSLGRGPAATLFTVTLAQVRPAIAGGALLVALYVL
+SDFGAVAILRLDTFTRAIFTALEVGFNRQLALTLATVLVLLTVLVLWGESRTRRADDGVR
+SGRTVRRVSVHRLGRSRWVGTGLLAVVTGAALGVPAVSLVRWMGEGTSLSAVRDRWLDAV
+SGSVVLAGAGAALTLALALPIGILAARHPGRVTRIAERAAFLAHGLPGVVVGLSLVFLGV
+SLVPALYQTTWMVAFAYATLFLPLAVTSVAGAVAQSSPALEEAARSLGSSGAEVLRRVTL
+PLALPGVGAGVALVALTAMKELPATLLLRPTGMDTLATRLWNATSVGRYAEAAPYALTLV
+LLAAVPTWVVVHRTGIVAAVRGRSSAPSTPNEVSE*
+>NZ_CP097650.1_556
+MAAAVALVPIGYLFLRTAQGGFGPWLDAVVSPRVGALAATSLALTAVVTALCLVIGVGAA
+WLVTRTDTPGRGLLAVLLALPLAVPSYVAAFTWVSVSDLLPGVEAGRFEGFWAAVTVMTL
+YTYPYVYLPVAAALSRIDPGQEDVARSLGRGPAATLFTVTLAQVRPAIAGGALLVALYVL
+SDFGAVAILRLDTFTRAIFTALEVGFNRQLALTLATVLVLLTVLVLWGESRTRRADDGVR
+SGRTVRRVSVHRLGRSRWVGTGLLAVVTGAALGVPAVSLVRWMGEGTSLSAVRDRWLDAV
+SGSVVLAGAGAALTLALALPIGILAARHPGRVSRIAERAAFLAHGLPGVVVGLSLVFLGV
+SLVPALYQTTWMVAFAYATLFLPLAVTSVPGAVAQSSPALEEAARSLGSSGAEVLRRVTL
+PLALPGVGAGVALVALTAMKELPATLLLRPTGMDTLATRLWNATSVGRYAEAAPYALTLV
+LLAAVPTWVVVHRTGIVAAVRGRSSAPSTPNEVSE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001826.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001826.fa
new file mode 100644
index 0000000000000000000000000000000000000000..916f73bcd91dc6d56ac5e26c27c3b59874038d4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001826.fa
@@ -0,0 +1,23 @@
+>NZ_CP042169.1_559
+MVPLMVVTLFTVVASQIRGAGERLPALAAVVPLFAAFAAVMVALGVVAARWTHLDVPAGR
+ALVFSGATRNSLVMLPLALALPASLDPAPLVVVTQTLVELGVMVSLVRLVPRLLPLHGQS
+AGAGARRTVT*
+>NZ_CP033200.1_301
+MPSSPPRRALVAALLVGVLLVLLAPCVDYVIAFTALAGGAAERLLAAAPLLMLVQLVVLP
+VLLRVVAGEAAVAAVDVGPFVRALVLLILAPLALAALLQWGTARGRGGVRRTAAGVVRGC
+TAAMVPLMVVTLFTVVASQIRGVGERLPALAAVVPLFAAFAAVMVALGVVAARWARLDVP
+AGRALVFSGVTRNSLVVLPLALALPASLDPAPLVVVTQTLVELGAMVSLVRLVPRLLPLH
+GQSAGAGAGRTVT*
+>NZ_CP040019.1_2306
+MESAQSRRAAAVAWMERHQAALYAAGIAAGAVVGWVVPGAGRLAVLVEPVLGLLLLATFL
+AVPFAALGAALRDVRFLAALLVLNFAVVPAVVFGLSRFVAHDDALLVGVLLVLLAPCVDY
+VIAFTGLAGGAAERLLAAAPLLMLLQLLLLPVLLRVCAGPAAVAAVDVGPFVRALVLLIL
+LPLALGALVQGVARRGAPGPRRAARAVEAATGAAMVPLMAATLFLVVASQVRAVGERLPA
+LAGAVPVFVGFVAVMVPLGLAVAALARVDARSGRALVFSGATRNSLVVLPLALALPPSLD
+PAPLVVVTQTLVELVAMAVLVRLVPRLLPERAAPAEEAALAVRPEPDVTGS*
+>NZ_CP097650.1_560
+MPGADAWAVLVEPVLALLLLATFLAVPFAALGAGLRDGRFLGALLVLNFVVVPAVVFGLS
+RFVAHDDALLVGVLLVLLAPCVDYVIAFTALAGGAAVAAVDVGPFVRALVMLILVPLALA
+ALLQWGAVRGRGGVRDTAAGVVRGFTVAMVPLMVVTLFTVVASQIRGVGERLPALAAVVP
+LFVAFAVVMVALGVVAARWARLDVPAGRALVSSGATRNSLVVLPLALALPASLDPAPLVV
+VTQTLVELGAMVSLVRLVPRLLPLHGQSAGAGAGRTVT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001828.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001828.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d191b018914a5aa66bd2317fba6c26e1a76e9ab6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001828.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_603
+MASKDWARKISDVPEGTRRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA
+SLTVGVSWPVGARWFRHAGGMTPLSLAEPTGRYLSFAEREEIAILHAQGQGVRQIARTLG
+RDPGTISRELRRNCATRSGKQEYRATVAQWKAQEAARRPKPAKLATNQRLHDYVQARLNG
+VVLGPDGVAVPGPVGPGFKGRKMKPRRADRRWSTAWSPEQISHRLRLEFPDDVSMRISHE
+AIYQSLFIQGRGALKRELVACLRTGRALREPRARTRNKPQGHVTEDVVFSKRPPEAADRA
+VPGHWEGDLIIGTERSAIGTLAERKSRATILVHLPRLEGWGERPPVKNGPSLGGYGAEAM
+TAALIKAMATVPEQLRQSLTWDRGKELAGHVQFTMATGTKVFFADPHSPWQRPTNENTNG
+VLRQYFPKGTDLSRWSAEDLAAVAYTLNNRPRKVLDWKTPAEVFAEQLRSLSTHGVATTG
+*
+>NZ_CP040019.1_718
+MASKDWARKISDAPEGARRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA
+SLSVGVSWPVGARWFRHAGGMTPLPLAEPTGRYLSFAEREEIAILHAQGHGVRQIGRALG
+RDPGTISRELRRNCATRSGGKEYRATVAQWKAQQAARRPKPAKLATNQRLHDYVQARLNG
+VVLGPDGVAVQGPVGPGFKGRKMKPRRADRRWSTAWSPEQISHRLRLEFPDDVSMRISHE
+AIYQSLFVEGRGALKRELVGCLRTGRALREPRARTRNKPQGHVTEDVVFSKRPPEAADRA
+VPGHWEGDLIIGLQRSAIGTLAERKSRATILVHLPRLQGWGEQPPVKNGPSLGGYGAAAM
+SAALTKAMTGLPQQLRQTLTWDRGGELAGHAQFTMATGTRVFFADPHSPWQRPTNENMNG
+LLRQYFPKGTDLSRWSADDLAAVAYTLNNRPRKVLGWKTPAEVFAEQLSSLETSGVATTT
+*
+>NZ_CP040019.1_730
+MRISHEAIYQSLFVEGRGALKRELVGCLRTGRALREPRARTRNKPQGHVTEDVVFSKRPP
+EAADRAVPGHWEGDLIIGLQRSAIGTLAERKSRATILVHLPRLQGWGEQPPVKNGPSLGG
+YGAAAMSAALTKAMTGLPQQLRQTLTWDRGGELAGHAQFTMATGTRVFFADPHSPWQRPT
+NENMNGLLRQYFPKGTDLSRWSADDLAAVAYTLNNRPRKVLGWKTPAEVFAEQLSSLETS
+GVATTT*
+>NZ_CP040019.1_733
+MASKDWARKISDAPEGARRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA
+SLSVGVSWPVGARWFRHAGGMTPLPLAEPTGRYLSFAEREEIAILHAQGHGVRQIGRALG
+RDPGTISRELRRNCATRSGGKEYRATVAQWKAQQAARRPKPAKLATNQRLHDYVQARLNG
+VVLGPDGVAVQGPVGPGFKGRKMKPRRAEVKSLEVV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001836.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001836.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37756e39dc39980e9ea34f205a6d99b42bbaf278
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001836.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_640
+MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRD
+RIDALLDEGSPFLEVGALAAHGLYDGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYY
+PMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFPDREHFGRIFRNQALLSSQRI
+PQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH
+AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTRVVPVDVN
+TPYDVREVIDRLVDGGSVHEFKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAH
+FIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMVTAVATARVPKLTVVIGGSFG
+AGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF
+QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM*
+>NZ_CP033200.1_386
+MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRD
+RIDALLDEGSPFLEVGALAAHGLYGGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYY
+PMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFPDREHFGRIFRNQALLSSQRI
+PQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH
+AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTSVVPVDVN
+TPYDVREVIDRLVDGGSVHEFKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAH
+FIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMVTAVATARVPKLTVVIGGSFG
+AGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF
+QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM*
+>NZ_CP040019.1_2256
+MTASTTAPDSESAPTAAERNAAGHARLEQEVAELVARTALGGPERSRERHTARGKLLVRD
+RIDALLDEGSPFLEVGALAAHGLYDGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYY
+PLTVKKHLRAQEIALENHLPCLYLVDSGGAFLPRQDEVFPDREHFGRIFRNQALLSSRRI
+PQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH
+AERSGVADHLADDDLHAMQILRDIVATLPPPPAPAWEVAPAQEPAKDPAELTSVVPVDVN
+TPYDVREVIDRIVDGGSVHEFKPLYGTTLVTAFARIDGHPVGILANNGILFGDSARKGAH
+FIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMVTAVATARVPKLTVVIGGSFG
+AGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMDAAEVEAF
+QAPVRQQYEDQGSPLYSTARLWDDGIITPGQTRRVLSLALDVISRPPLPDTRFGLFRM*
+>NZ_CP097650.1_609
+MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRD
+RIDALLDEGSPFLEVGALAAHGLYGGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYY
+PMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFPDREHFGRIFRNQALLSSQRI
+PQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH
+AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTSVVPVDVN
+TPYDVREVIDRLVDGGSVHEFKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAH
+FIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMVTAVATARVPKLTVVIGGSFG
+AGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF
+QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001837.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001837.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e9034bdfe2f4ba984e73f324027061a815f7bed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001837.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_642
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAKHEFPYEIVAQMGEMGLFGLP
+FPEEYGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTEEQKQRWLPDL
+VAGTHLAGFGLTEPGAGSDAGGTQTTAALEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGHDGRPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFTDARVPEENL
+LGARGRGFAHFLEILDEGRIAIAALATGAAQGCVDESVAYATQRTSFGQKIGQFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEIGEGTTEVQLMLIARELGL*
+>NZ_CP033200.1_388
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAQHEFPYEIVAQMGEMGLFGLP
+FPEEYGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTEEQKQRWLPDL
+VAGTHLAGFGLTEPGAGSDAGGTQTTAALEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGHDGRPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFSDVRVPEENL
+LGARGRGFAHFLEILDEGRIAIAALATGAAQGCVDESVAYAKQRTSFGQKIGQFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEVGEGTTEVQLMLIARELGL*
+>NZ_CP040019.1_2253
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAKHEFPYEIVAQMGEMGLFGLP
+FPEEFGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTQEQKEAWLPDL
+VAGRHLAGFGLTEPGAGSDAGGTQTTAVLEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGADGKPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFSDVRVPEENL
+LGTRGRGFANFLEILDEGRIAIAALATGAAQGCVDESIAYAKQRTSFGQRIGEFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEVGEGTTEVQLMLIARELGL*
+>NZ_CP097650.1_611
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAQHEFPYEIVAQMGEMGLFGLP
+FPEEYGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTEEQKQRWLPDL
+VAGTHLAGFGLTEPGAGSDAGGTQTTAALEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGHDGRPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFSDVRVPEENL
+LGARGRGFAHFLEILDEGRIAIAALATGAAQGCVDESVAYAKQRTSFGQKIGQFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEVGEGTTEVQLMLIARELGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001844.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001844.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9a96dc2877ec1a6047feac4977b6ac896296b49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001844.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_819
+MNHEANLTAWWSSGLLLLGAAGFTTVGLVRRALGADRRRSLLAWLTPAALLAAMSLDEST
+QIHEQAGQLWEVLPFAGENPLPAFQWLILGAPAAIVVLGLLALCTVALPRRTRALTVAGG
+AVFFFGAIVLEAVPLVFGIGRSTLAYHVATHAEELTEMIGASVLVVAPWAHLHLRPAPGH
+LQVTADGVPDAGADDVVLGAGPGPAARLDDCD*
+>NZ_CP033200.1_550
+MSLDESTQLHEQAGRLWEALPFAGENPLPAFQWLILGAPAAIVVLGLLALCTVALPRRTR
+ALTVAGGAVFFVGAIVLEAVPLVFGIGRSTLAYHVATHAEELTEMIGASVLVVAPWAHLH
+LRPAPGHLQVTADGVPDADADDVVLGAGPRPAARLDDCD*
+>NZ_CP040019.1_2049
+MVSMKRSTEQSDVPAPLADPGSGAGSVTASGAVRPAEADPAAGQPVQGRWARRVALTLIG
+VSVALAAWSFAIPFLFGLGVRELPWWRQFFDLNHETNLTAWWSSGLLLLGAIGFAVVGLV
+RRSLRADRPLALLAWLTPSALLAAMSLDEFTQIHERLGEVWDALPFTPENPLHAFQGLIL
+GVPIALAVIALLALTAMMLPRRTRALTVTGIVVFFVGAIGLEAVPLVFNIARASWAYHAV
+THLEELTEMIGSSLLIVAPWVHLHLRRAPGSLLVTTDGLPAAAEHDDAAPAGR*
+>NZ_CP097650.1_777
+MSRPPEPRPAPAPTARAAAARPATPPGVQGRWARRAAGGLIGVSVLLAAWSFALPFVFGL
+GPRQVPWWREVFDVNHEANLTAWWSSGLLLLGAAGFTTVGLVRRALGADRRRSLLAWLTP
+AALLAAMSLDESTQLHEQAGRLWEALPFAGENPLPAFQWLILGAPAAIVVLGLLALCTVA
+LPRRTRALTVAGGAVFFVGAIVLEAVPLVFGIGRSTLAYHVATHAEELTEMIGASVLVVA
+PWAHLHLRPAPGHLQVTADGVPDADADDVVLGAGPRPAARLDDCD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001854.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001854.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4cb76a681672dc79c4e609a78353fa6e79b652b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001854.fa
@@ -0,0 +1,28 @@
+>NZ_CP042169.1_1035
+MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLML
+AAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVIG
+EMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVGG
+YDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEAV
+QNAAACSGHLRILVQPDHTPESVPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLHEA
+LASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA*
+>NZ_CP033200.1_764
+MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLML
+AAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVIG
+EMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVGG
+YDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEAV
+QNAAACSGHLRILVQPDHTPESVPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLHEA
+LASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA*
+>NZ_CP040019.1_2277
+MTQSPVFVILATIALIALSALFVIMEFSLLAARRHRLEAEAGTSRAARAALRSVDELTIM
+LAGAQLGITLATFALGAITKPAVDAWLGPVLTGWGLPAAVAGTASFFLSLLLVTFLHLVV
+GEMAPKSWAIAHPEFAAKAVAGPARAYVWAVRPLLAFANAVANRLVAASGVTPTDRAAVG
+GHDADSIRQLVEHSASSGALDEQAHGQISGALDLQDATVGDLVSPPRDLVTVPADATAED
+VQAASVASGHLRILVRPADGPDDGVPGVVHVRDTMVLGPREPVAPLVQEALTLPVDTALH
+EASSAMRAAGRQLAVVTSEGRTVGVVTLTDLFRRVLPVSG*
+>NZ_CP097650.1_983
+MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLML
+AAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVIG
+EMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVGG
+YDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEAV
+QNAAACSGHLRILVQPDHTPESVPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLHEA
+LASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001855.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001855.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8006272d31cee0c07d5c19add36a9dda0257bd2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001855.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_1036
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER*
+>NZ_CP033200.1_765
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER*
+>NZ_CP040019.1_2278
+MDPILLLILGTVVILVIILANGFFVAQEFAYMSVDRVRLAAAAENGDEAARRALAVTRRT
+SFMLSGAQLGITVTGLLVGYVAEPMVGEALTQLLGGTAIPASVVIAVSTVGVLLVATVVQ
+MIVGELYPKNLAIANPDPLARALARPTQVYLALFGWLIWVFDKSAEALLRLLRIEPVHDV
+DSTATAQDLDRIVEDSRDSGTLPAELSVLLDRILDFPERDAEHAMVPRSQTDEVGPETTV
+AEVRALMAAAHTRYPVISADHQPLGVVHLQDVLALGHAPAPDLLVTDVMRPATVVPTVMP
+LPDVTRALDDADDQLACVIDEHGGFVGVLTLEDLAEELVGDLRDEHDDEAHEEIVPVVVG
+ESWALRGDVHLDELERAIGHPLPEGEAETVSGLLIESLGRLPEEGERVAVDLPEDTRDYG
+GDVLYDRRLEVDVRRVERHVPADVEVHLVETPREDETEEDPR*
+>NZ_CP097650.1_984
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001861.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001861.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f0e235df816348960232175dbade24a6e0ff9b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001861.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_1169
+MSGSGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAVAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHIVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHDPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPACRPPGAAHPAPETFDLLSALAAGGWATADASGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP*
+>NZ_CP033200.1_898
+MSGSGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAMAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHTVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHNPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPECRPPGAAHPAPETFDLLSALAAGDWATADTSGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP*
+>NZ_CP083691.1_1545
+MSGARHGGYSANSFRTEAIVLRTHRLGEADRIVEAITPEHGVLRCVAKGVRKSSSRFGSV
+VEPFMHSTLQVARGRGELHTITQAQLLHPYATAVAADYEAFAVAAALAEGVERIPALDAD
+GRRAQYLLFHGALAALARRAHDPRMILHSFLLRTLTQAGWAPTFDRCARCGAPGPHTAVN
+VALGGAVCAEHRPPGSASPAPETFALLTALTAGDWAVVDTAGPLARREAAGIVSAYLQFH
+AERRLVALSVLDQEIAPPAPRAERSA*
+>NZ_CP097650.1_1125
+MSASGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAVAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHTVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHDPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPECRPPGAAHPAPETFDLLSALAAGDWATADASGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001866.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001866.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a276da92569c3673bc6402abd62147b1da5b7a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001866.fa
@@ -0,0 +1,17 @@
+>NZ_CP042169.1_1339
+MSVTSEIARARSLIRVVPDHPSPGVAFQDITPLLADARALRECVEALVAPFEGRFDLVAG
+LEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGTASIEVSEDLRAGSRVL
+LLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELRALGGRAVVPDTHVLFAA*
+>NZ_CP033200.1_1069
+MSVTSEIARARSLIRVVPDHPSPGVAFQDITPLLADARALRACVEALVAPFEGRFDLVAG
+LEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGNASIEVSEDLRAGSRVL
+LLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELTALGGRAVVPDTHVLFAS*
+>NZ_CP083691.1_1853
+MSGVALSAAGRQAADVPGLERAATLFRSVPDFPTDGVVFQDITPVLADPAALRAVVEAMI
+APFEGAYDAVAGLDARGFLLAGFAAALTGTGVIPLRKAGKLPVSVAHVDYALEYGAASLE
+APPELAVPGVRVLILDDVLATGGTLAAARDLAERCGAEVAGSAVVLEVEGLGGRERCPDA
+LTLFSA*
+>NZ_CP097650.1_1293
+MSVTSEIARARSLIRVVPDHPSPGVAFQDITPLLADARALRECVEALVAPFEGRFDLVAG
+LEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGTASIEVSEDLRAGSRVL
+LLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELRALGGRAVVPDTHVLFAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001867.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbde84342b5ed107c8db1735b352404a2b978d38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001867.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_1361
+MTEHTRDDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLNEGV
+DLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVREE
+LHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGVD
+AGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVKG
+GRR*
+>NZ_CP033200.1_1101
+MTEHTRDDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLHEGV
+DLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVREE
+LHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGVD
+AGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVKG
+GRR*
+>NZ_CP083691.1_1375
+MTEHTQHDDAARPALVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHVLDSG
+VDLADPDAIAGAARAMDLRQSTDPDVESVVVGGTDVTDAIREDRVTDVVSTVAVVIPVRE
+ELQRRQRAAIAGAGRIVAEGRDITTVVAPDAHARVLLTASAEARMARRSGQLQRAGAGER
+DAATLERQVSGRDARDSAVSTFDRPAEGVALVDSTELDFEQTVAAVLAAVQDQAGVDAVP
+GR*
+>NZ_CP097650.1_1310
+MTEHTRDDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLHEGV
+DLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVREE
+LHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGVD
+AGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVKG
+GRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001873.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001873.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a5a93141a33f8c506d010d4ef86412e4eadfead
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001873.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_1406
+MARVKRAVNAHKKRRTMLERASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVKTAREALPAD
+VNAPAVSR*
+>NZ_CP033200.1_1148
+MARVKRAVNAHKKRRTMLERASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVQTAREALPAD
+VNAPAASR*
+>NZ_CP083691.1_1326
+MARVKRAVNAHKKRRTALNRASGYRGQRSRLYRKAKEQLLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGIEVDRRMLAEIAVSDAATFTALVETARTALPAD
+VNAPAASR*
+>NZ_CP097650.1_1355
+MARVKRAVNAHKKRRTMLERASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVKTAREALPAD
+VNAPAASR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001875.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001875.fa
new file mode 100644
index 0000000000000000000000000000000000000000..848a501e127593f07043a21d37f814f39c56eb04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001875.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1429
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVARELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVRSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD*
+>NZ_CP033200.1_1171
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVARELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVRSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD*
+>NZ_CP083691.1_1302
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVALELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVSSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD*
+>NZ_CP097650.1_1378
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVARELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVRSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001877.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001877.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbbe688fa55fb1a287752f5e315cf559c07b8c43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001877.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_1458
+MLATTLEQISVAGARGRPRIRPDRLIADKGYPSKANRAWLRRHGIAATIPERADQITHRR
+RRPGRPIDFGEDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARNYHAGLSLAATLHWL
+TTLL*
+>NZ_CP083691.1_624
+MTTKIHLVCDGKGRTLAFVLTGGQVADTSMFPDTIDEIRVVGVKGRPRTRPERVIADKGY
+PSKKNRAWLRQRGIATTIPERDDQIAHRRKKPGRPIDFGRDQKRRYKGRNAVERCFNKLK
+QWRGIAARSDKTPRNFHAGLSLAATLQWV*
+>NZ_CP083691.1_1712
+MNYKKSGDEPADHAIGRSRGGLTTKSHLVCDGKGRVLAFVVTGGQVADTSMLATTLELIS
+VAGARGRPRARPDRLIADKGYPSKANRSWLRRHGIAATIPERADQIAHRRRRPGRPIDFG
+EDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARSYHAGLCLAATLHWLTTTL*
+>NZ_CP083691.1_2187
+MNYKKSGDEPADHAIGRSRGGLTTKSHLVCDGKGRVLAFVVTGGQVADTSMLATTLELIS
+VAGARGRPRARPDRLIADKGYPSKANRSWLRRHGIAATIPERADQIAHRRRRPGRPIDFG
+EDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARSYHAGLCLAATLHWLTTTL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001884.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd53d5dd5d1403845a0bda447e3c2d034e3293c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001884.fa
@@ -0,0 +1,49 @@
+>NZ_CP042169.1_1606
+MDTPTPPHPTGSHTTRTPARPRLRRFVREFSYPHGIHPALVPGVSVEDRRVRYGVDRVIL
+AVVGLLVVGFVVWGVLQPDAVLAVSSAALDWVMVHAGWLFVLLAIGMVVFLLVLAFSRYG
+EIPLGLDGEKPEYSTASWSAMLFAAGIGIGIIFFGPYEPLTYYLAPRPGAYEAGSEEAVT
+GALAQAALHWGVNAWAIYAIVGLSVGYVSYRRGRVPLMSSIIAPLFGDSPRSDSVGARLI
+DGLAIIATLFGTAASLGIGALQIGRGVEIVSGWSAPGNTVALGIIVVLTIGTIVSAVSGV
+ARGIRWLSNINMLLALGLALFFFVVGPTAFLLNIVPGVLMDYVSSAPDALGASMAEGEDM
+QEFLSNWTIFYWAWWVSWAPFVGVFMAKISKGRTIRQYVLGALFIPAAVIVGAFTIIGGT
+TIWLQRTRGSVAPDGTAASLPAPAEIFWVVLDQLPGGGLVAPVVIIMLAVFFITTADSAS
+IVNSQLSQRGDPAPRRMITVFWALCMAGIAVVMLLTGGDTALTGLQNLITITALPFTVVL
+VLMAVALQRELANDPFAIRDRYQRAAVEKATVRGLVEYGDDFAFTVERTPPGSWYAAGEG
+FDSTAAEITDWYRRTDEDGNPVDYDYVLGEYLDEGDGDDADGPAGAGPSGR*
+>NZ_CP033200.1_1322
+MDTPTPPRPTGSHTTRTPARPRLRRFVREFSYPHGIHPALVPGVSVEDRRVRYGVDRVIL
+AVVGLLVVGFVVWGVLQPDAVLAVSSAALDWVMVHAGWLFVLLAIGMVVFLLVLAFSRYG
+EIPLGLDGEKPEYSTASWSAMLFAAGIGIGIIFFGPYEPLTYYLAPRPGAYEAGSEEAVT
+GALAQAALHWGVNAWAIYAVVGLSVGYVSYRRGRVPLMSSIIAPLFGDSQRSDSVGARLI
+DGLAIIATLFGTAASLGIGALQIGRGVEIVSGWSAPGNTVALGIIVVLTIGTIFSAVSGV
+ARGIRWLSNINMLLALGLALFFFVVGPTAFLLNIVPGVLMDYVSSAPDALGASMAEGEDM
+QEFLSSWTIFYWAWWVSWAPFVGVFMAKISKGRTIRQYVLGALFIPAAVIVGAFTIIGGT
+TIWLQRTQGSVAPDGTAASLPAPAEIFWVVLDQLPGGGLVAPVVIVMLAVFFITTADSAS
+IVNSQLSQRGAPAPRRTITVFWALCMAGIAVVMLLTGGDTALTGLQNLITITALPFTVVL
+VLMAVALQRELANDPFAIRDRYQRAAVEKATVRGLVEYGDDFAFTVERTPPGSWYAAGEG
+FDSTAAEITDWYRRTDEDGNPVDYDYVLGEYLDEGDGDGADGPAGAGPSGR*
+>NZ_CP097650.1_1503
+MNWPVFAGTAGIVVGFALWAMLLPAQADSVISATVSWIAESFGWYYVLTAGVVVVFVVVV
+ALSRLGRVRLGPDHAVPQFSMFTWSAMLFAAGIGVDLMFFATSGPATNLLTPPDLEPMSD
+EAARMAPLWTIFHYGIPGWAMYALMGMAFGLFAYRYHMPLSIRSAIAPIFGRRVHGGIGH
+AAEIGATVGTIFGISVSLGIGVVFLNAGLALILDVPVTTGVQIALMALAVGITIISTVSG
+VDKGIRRLSELNVYLAVVILLWVLVTGRTTDLLNALVQNIGDFFASFPSMMMRTFAYTDG
+TAAYPAEQWMSDWTLFFWAWWIAWSPFVSLFLARISRGRTLREFVLGVLLIPFAFIMLWV
+SIMGNAAIGLFRDGDDALLQEAVTAPEAGFFSLLQQFPGATFLIGLAVFTGLFFYVTSAD
+SGSLIMAKMTSKGSVEDSDGAPWLRITWAVITGLLTLSMLFIDGVYTLQKATVIVGLPLS
+VLVYLVMISLWRVLHSESLAMDSRTASLPHVLSGRVRDANSRATWRQRLARRMNFATAKQ
+AAAYVDREVSPALSEVAAELREHGADVDVTRGTHPESGVPWVDLTVRFPGQTDFKYQVYP
+VAYPVPSFAGSLSAAQDTYVQLEVFSAKGSRGRDVMGYSREQLCANILDDYEAHLAFMTM
+TGDDSLLAARIDAEAPEVWTDADHSPATDALPTVALQTTDPETEGARP*
+>NZ_CP097650.1_1536
+MDTPTPPRPTGSHTTRTPARPRLRRFVREFSYPHGIHPALVPGVSVEDRRVRYGVDRVIL
+AVVGLLVVGFVVWGVLQPDAVLAVSSAALDWVMLHAGWLFALLAIGMVVFLLALAFSRYG
+EIPLGLDGEKPEYSTASWSAMLFAAGIGIGIIFFGPYEPLTYYLAPRPGAYEAASEEAVT
+GALAQAALHWGVNAWAIYAVVGLSVGYVSYRRGRVPLMSSIIAPLFGDSQRSDSVGARLI
+DGLAIIATLFGTAASLGIGALQIGRGVEIVSGWSAPGNTVALGIIVVLTIGTIFSAVSGV
+ARGIRWLSNINMLLALGLALFFFVVGPTAFLLNIVPGVLMDYVSSAPDALGASMAQGEDM
+QEFLSSWTIFYWAWWVSWAPFVGVFMAKISKGRTIRQYVLGALFIPAAVIVGAFTIIGGT
+TIWLQRTQGSVAPDGTAASLPAPAEIFWVVLDQLPGGGLVAPVVIVMLAVFFITTADSAS
+IVNSQLSQRGAPAPRRTITVFWALCMAGIAVVMLLTGGDTALTGLQNLITITALPFTVVL
+VLMAVALQRELANDPFAIRDRYQRAAVEKATVRGLVEYGDDFAFTVERTPPGSWYAAGEG
+FDSTAAEITDWYRRTDEDGNPVDYDYVLGEYLDEGDEDGADGPAGAGPSGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001886.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001886.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98f2a16d97c3f27eb6da0713b64d61db38a30f0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001886.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_1630
+MRPTRRQFAQGMAAGLAGLVLPPAVASSAVAAPQGPNPRSGRGRDERAIQAALDAVVQWP
+AVGAVCSVVGPARRFDTASGTRGLHANAPARANSVARIASVTKGMVATVALQEVERGTLS
+LDSTIGGVLPGLWPDVEDRVTLSMLLNHTSGMPDAIWVIMRGQSLFELDFDELADVVSRS
+YGQRELVELAKQADWWFEPGTDYGYSNTGYVVVEMMVEAVTGRRMPELIRDRVFRPAGMH
+RTRLEHGTLVRGAEMQDAAVRPHEAKALETIDQSIFASAAAVNTTAADVTRFYQALMRGE
+LVSQQTVDLMVTPVGPATQAGYGYGLFLVADPAPEHAGEVLVGHDGAGFGSVSLALCSRD
+GERAFAFTYIGRPYWQEGWDEVFAKELALMRTAFVVNAADAPASRDRLVRGGAAASRRAV
+ADMAARGARLV*
+>NZ_CP040019.1_1177
+MSTSRRRLTQGLAAGAACLALPAGLSAPAAAAPSARSSRTPDSAALQAALEALVQWPVAG
+AVCAAASPAGLVELAAGRRSTASPAPARPQSVARVASVTKAMTATVAFQEIERGTLRLDS
+TIGEVLPGLWPGRESVTLGQLLNHTSGMPDAVWVLMDHVSLWDLPLEHVRDVVARSYPPR
+ELVELAKQDGWWFEPGTDWGYSNTGYVVAQLMVEAAAGRPLSSLIRDRVFRPAGMHRTRL
+EEGALVRGAEMEDAAVRPGQTMRLQTIDQSVFAGAAAVNATAGDVVRFYQALMRGRLVGQ
+ASVDAMVTPVGAARAAAYGYGIFQVPDPVRAGEVLYGHDGGGFGSASLAVSSRDGSRAMA
+FAFVGRPYWAAGANEVWPRQTAVLRAAMSLSGTAGRPGGSAGRAAAGAAHAAVGGTRLG*
+>NZ_CP083691.1_1194
+MTRDTPSADRPPLSADALRPIAAALDRWLATQTEVRRVPGVQAAVRLGDELILSTAHGVA
+DESTGERLTTRHLFRVASHSKTFTAVAVLRQVELGTLRLDDTVGALLPGYADTPLAGVTL
+RELLSHTAGAVRDGADADHWILDRPFPDAAALQALVRDHGTAYAPQEHFKYSNIGYGMLG
+AVLEHVTGRPYAEHVRASVLDPLGLTDTHADLTDDVAARAATGHTRAGGRARARVTVEQT
+TTGALAAATGFVSRAEELSAFYASLALGARGVLSDRSLRLMHRAEATFRRGGGTGTYGLG
+LLGQEVGGRRLLGHSGGFPGQITRTLFDPATGLAVSVLTTAVDGPAEALAVGVVQLIDLL
+TAPAADWQALPGGVTAADLDRLAGRYVSLWGATDVLRGGTAERPRLVLLDPAAPAPADAA
+EELRALDATTLRVEDADGFGACGEPIPFDLDAAGRVTRMRVTGVSAWPEEAYRARRGDAW
+RHADGVDGAEAEPDAHEEAAPVLVQAAAFADLDPATAYRLWALRQAVFVVEQDCPYQDMD
+GRDMEPATVHLWVCDEEDAPIGTVRLLDDGDHARIGRVVVDRAHRGRGVAAALMEAALEQ
+VGERACVLDAQAHLEHWYGRFGFAADGPEFLEDGIPHVPMRRPEAGRRTP*
+>NZ_CP083691.1_2069
+MDFIVRPCTPEDEPSWLRCRVLAFLDTQNHDDVHAAHPVPDPDVADPADSLQWVAVVRDG
+PDAGTVAGILDASVGAADGDDAGLATIDTLAVHPDHRRRGLAGRLFEAVLERLPERVGHV
+DVWTREDEAANAWYRAHGFARDHVYLQVHLESWVDGDDVAALIRTPPALSAPVKGLFHAS
+LEDEAWIRERFHRVVRVSRYVRPVGMTG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001891.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001891.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f07252dd965fc8ac08da2b55d4acd6b31dde7d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001891.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_1752
+MFNPTAPVNEQLALYSDLFMLIAALVYAAAFILFTIDMATASATIRRLEADLAAQRGQVR
+TAPARETVGAAVGGSTAVGASASDAARPTGAAERGVDADGALVDEDMDYTGGGRRPVANV
+AVAVLAVGWALHAFAVVARGLAASRVPWGNLYEFMTTGALVITTVYLLFLLRKDLRFVGT
+FVTGIVVAMMCAATMGFPTPVGHLQPPLQTPWLVIHVSIAVLASSLFALTAAMSVLQLVQ
+DRAEKRAAAGERSWAFLRLVPAAQGLENWSYRLNAVGFVMWTFTLIAGAIWAEAAWGRYW
+NWDTKEVWTFVIWVVYAAYLHARATRGWTGARAAWLSIVGFACIVFNYTIVNTYFPGLHS
+YAGLPG*
+>NZ_CP033200.1_1460
+MFNPTAPVNEQLALYSDLFMLIAALVYAAAFILFTIDMATASATIRRLEADLAAQRGQVR
+TAPARETVGVAVGGSTAVGASDSDTARPAAAEPGVDADDDLVDEDMDYTGGGRRPVANVA
+VAVLAVGWALHAFAVVARGLAAYRVPWGNLYEFMTTGALVITTVYLLFLLRKDLRFVGTF
+VTGIVVAMMCAATMGFPTPVGHLQPPLQTPWLVIHVSIAVLASSLFALTAAMSMLQLLQD
+RAEKRAAAGEPTWSFLCLVPSSDSLENWSFRINAVGFVMWTFTLIAGAIWAEAAWGRYWN
+WDTKEVWTFVIWVVYAAYLHARATRGWTGARAAWLSIVGFLCIVFNYTIVNTYFPGLHSY
+AGLPS*
+>NZ_CP083691.1_985
+MFNPTAPVNEQLAYYSDLFMFIAALVYAGAFILFAVDMATASATIRRLEAELDAQAGVDR
+DVASRVRERQLAGVGAGSGVGTPAGGAHALGTDASASSAGRSDAELVDDDMDYTGAGRRP
+VANVAVAVLAVGWALHAFAVVARGVAASRVPWGNLYEFMTTGALVIVTVYLAFLIRKDLR
+FVGTFVSGLVVAMMCAATMGFPTPVGHLQPPLQSGWLVIHVSIAVLSSSLFALSAAMSAL
+QLLQGSAEKRAAAGRRGWSFLRLVPSARALENWSYRINAVGFVMWTFTLIAGAIWAEAAW
+GRYWNWDTKEVWTFVIWVVYAAYLHARATRGWTGTRAAWLSITGFLCIVFNYTIVNTFFP
+GLHSYAGLPA*
+>NZ_CP097650.1_1673
+MFNPTAPVNEQLALYSDLFMLIAALVYAAAFILFTIDMATASATIRRLEADLAAQRGQVR
+TAPARETVGVAVGGSTAVGASDSDTARPAAAEPGVDADDDLVDEDMDYTGGGRRPVANVA
+VAVLAVGWALHAFAVVARGLAASRVPWGNLYEFMTTGALVITTVYLLFLLRKDLRFVGTF
+VTGIVVAMMCAATMGFPTPVGHLQPPLQTPWLVIHVSIAVLASSLFALTAAMSVLQLLQD
+RAEKRAAAGERSWAFLRLVPAAQGLENWSYRLNAVGFVMWTFTLIAGAIWAEAAWGRYWN
+WDTKEVWTFVIWVVYAAYLHARATRGWTGARAAWLSIVGFLCIVFNYTIVNTYFPGLHSY
+AGLPG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001893.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001893.fa
new file mode 100644
index 0000000000000000000000000000000000000000..13ca6ba6dab8b5534a057d460f97eda2507a1805
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001893.fa
@@ -0,0 +1,28 @@
+>NZ_CP042169.1_1793
+MSGERVGFTGAEALWLPGWRHVYSGKVRDLYEPADAEPGRSATLLVVASDRISAYDHVLE
+PPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVAGRAMVVKRLDMFP
+VECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSAKAEVGEHDENITF
+EQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVDPATGQVVLGDEVL
+TPDSSRFWDAEDYEPGRPQASFDKQFVRDWLTGPDSGWDKTSGEAPPELPADVVAKTRDR
+YVEAYERLTGRPFDA*
+>NZ_CP033200.1_1500
+MSGERVGFTGAEALWLPGWRHVYSGKVRDLYEPADAEPGRSATLLVVASDRISAYDHVLE
+PPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVAGRAMVVKRLDMFP
+VECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSAKAEVGEHDENITF
+EQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVDPATGQVVLGDEVL
+TPDSSRFWDAEDYEPGRPQASFDKQFVRDWLTGPDSGWDKTSGEAPPALPADVVAKTRDR
+YVEAYERLTGRPFDA*
+>NZ_CP040019.1_1004
+MSHETPASDTTPHSGAAPRGFAGAEALELPGWRHVYSGKVRDLYEPADAAPGESETLLVV
+ASDRISAYDHVLSPPIPDKGAVLTQLTLWWFERLSEGYNGAAGAPVEHHVVSTDVPEAVA
+GRAMVVKRLRMFPVECIARGYLTGSGLAEYRESGTVTGLPLPTGLVDGSRLDPAIFTPSA
+KAEVGEHDENITFEQMSERVGAEAAERLRYLTLDLYSRAEAIARDAGIILADTKVEFGVD
+PATGQVVLGDEVLTPDSSRFWDAEDYEPGRAQASFDKQFVRDWLTSDASGWDRASGAEPP
+ELPADVVEKTRARYVEAYERLTGRPFEA*
+>NZ_CP097650.1_1713
+MSGERVGFTGAEALELPGWRHVYSGKVRDLYEPADAEPGRSATLLVVASDRISAYDHVLE
+PPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVAGRAMVVKRLDMFP
+VECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSAKAEVGEHDENITF
+EQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVDPATGQVVLGDEVL
+TPDSSRFWDAEDYEPGRAQASFDKQFVRDWLTGPDSGWDKAGGEAPPALPADVVAKTRDR
+YVEAYERLTGRPFDG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001905.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001905.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7340bbdaa61c9cbe99c541f77becfc44e985dc13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001905.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_1863
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGQVRYVKPHGALYN
+TIVRHEAHAQAVVDGVRAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVSIKAFA*
+>NZ_CP033200.1_1570
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGQVRYVKPHGALYN
+TIVRHEAHAQAVVDGVKAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVAIKAFA*
+>NZ_CP083691.1_860
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAATCRAAVAAG
+VTIGAHVGYRDLAGFGRRFLDCSPTELADDVLYQIGALEALAGAAGATVRYVKPHGALYN
+TIVHHEEHAQAVVDGVAAFGADLPLLLLPGSVALEKAEKAGLRGVAEAFADRGYTPQGTL
+VSRREPGAVLHDEDEVAARMVRLATEGVVTAVDGSDVRVAAESICVHGDTPGAVSMAAAV
+RRALEDAGVTIASFA*
+>NZ_CP097650.1_1783
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGRVRYVKPHGALYN
+TIVRHEAHAQAVVDGVRAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVSIKAFA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001910.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001910.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e2c6c3eb2cd60852220336c4edab9dd52b8b27f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001910.fa
@@ -0,0 +1,8 @@
+>NZ_CP042169.1_1921
+MTVGLTLYVLMWPVLVLAVLVSIARGFFADWAAARREGRSII*
+>NZ_CP033200.1_1626
+MTVGLTLYVLMWPVLVLAVLVAIARGFVADWAAARRQGRSII*
+>NZ_CP040019.1_865
+MTLGLTLYVLMWPVLVLAVLASIAAAFFKDWREARREGRSII*
+>NZ_CP097650.1_1847
+MTVGLTLYVLMWPVLVLAVLVAIARGFVADWAAARREGRSII*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001916.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001916.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4addc39bb9b78ef52df9ea3f99ed3b42560752fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001916.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1981
+MVGITLRHMEYLVAVIDEGSMTAAAARLHVTQATVSMALAECERRLGVPLLVRQPAKGVA
+ATLAGHRMAVQARRILGLVHEMEASVPAMPGELAGDLEVGCVPSLSPQAVPVLAEHFSRR
+HPRVTLHYREGAATDLQREVLQGRLEMAVMFSRQQAPGLRSIEVARAQLKVMLPEGHRLA
+AAHEVAFADVAQEPAILIDLPPSTERSLEFMRAAGVEPTLRWSSNNLATVASLVGAGLGW
+SLRYTLPGEQPAARGLVEIPVADPTPPNAVCAVVPDGDRVDQRVRHALEVLRRVLSEEEG
+RPDVDCA*
+>NZ_CP040019.1_134
+MEPLNLSSPGLSPAVWRVTTVSRVEIRHLRSFVAVAEERHFGRAAERLHIAQPPLSQQIK
+QLEAALGVTLLERTTRRVDLTDAGRLLLDRSRQLLTDLASLEHDVREVGRGAAGILRVGF
+VGSATYRLMPAIVRAARDAMPGVRLQITGEKITPALEDALLENRLDVAVLRPPVRAAELT
+LTPVEAGRLLLAVPAGHRLAAEDGPVALADLVDEEFVSYPRDSALTAIVQEAARRVGFRP
+RLVQRAGETSTVMAFVAAGLGVAVVPDDVRRPGAVSGVAFRPLSDMPDVELAVAAKADAR
+SPLVPAFVELACRTAAALAEAGEDPTPDPDRPAQET*
+>NZ_CP040019.1_791
+MDVHQAKAFLAVAEELHFGRAAGRLQIAQPALSRTVKQLERSLGTDLFVRSTRRVELTAA
+GLALLEPARTLVQASQTAREAVQSALAGETGTVRLGFAGASTHGVVGQLARSVRRRRPGL
+TLEIHSSQFSHLGLERVLEGSLDVAIGRWDFIPHELASRVIAHEEAIVALPADHPHAQET
+GPIDVGLLRDEPWVTLPSGLGSALANRLTTLATSAGFAPRVVQQAPDSFTQMVLVAAGLG
+CAVTLDSVRDNSATPGVVYRPVAGDNPPLEVRMLWRSLDASPALRAVLDLAPAAEPAGVA
+PARTDAAD*
+>NZ_CP083691.1_96
+MEIRHLRSFVAVAEERHFGRAAERLHIAQPPLSQQIKQLEAELGVRLLDRTTRRVDLTEA
+GRLMLERTRSLLADLASLEHDDDIASAVKPELLLDVQQGADGNSTVYDFVLDPVSEKTHP
+TAIRD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001918.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001918.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0aad6be4f1e0a75d1493f9882fc7b15eb4d257f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001918.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_1990
+MTTKDSRTRSLIDVDVLEYHRLLTPEQQEKLGEIRAALAEIVTPHVAEAWSRDEFPHEIA
+RRVGELGYNHISGMTEDPLFRGHLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+TWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTPGYEATKIEHKTAVKIVQNADITFTDVRIPAENKLEKANT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERTQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEAAGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADVGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL*
+>NZ_CP033200.1_1708
+MTTTDSRTRSLIDVDVLEYHRLLTPEQQEELTEIRAALAEIVTPHVAEAWSRDEFPHEIA
+RRVGELGYNHISGMTEDPLFRGHLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+TWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTLGYEATKIEHKTAVKIVQNADITFTDVRIPAENKLEKANT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERTQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEATGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADVGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL*
+>NZ_CP083691.1_717
+MTTTDSRTRSLIDVDVLEYHRLLTPEQQEKLTEIRAALAEIVTPHVAEAWSRDEFPHEIA
+RRVGELGYNHVSGMTEDPLFRGHLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+TWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTPGYEATKIEHKTAVKIVQNADITFTDVRIPAENKLEKADT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERTQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEAAGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADTGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL*
+>NZ_CP097650.1_1925
+MTTTDSRTRSLIDVDVLEYHRLLTPEQQEKLTEIRAALAEIVTPHVAEAWSRDEFPHEIA
+CRVGELGYDHISGMTEDPLFRGYLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+KWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTSGYEATKIEHKTAVKIVQNADITFTDVRVPAENKLEKANT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERAQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEAAGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADVGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001919.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001919.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c9a30f3fd44dd523d4100cbd5faafa378ab9ac2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001919.fa
@@ -0,0 +1,56 @@
+>NZ_CP042169.1_1992
+MSEHMITWDQDADGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSA
+KKTFFAGGDLDSLAQAGPEDVESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEI
+ALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMVGVERALMEWLLQGTARDARA
+AMEKGIIDEVVTDPADLVPAAKRWILEHRDDADAAAKPWDVKGFRIPGGTPAQASFASRL
+PAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQA
+FHSDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAA
+ERGRERVGALLEGRVAKGRMSREDADAVLARVQPTEDYQDLAHVDAVIEAVFEDVELKDS
+VFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHFFSPVDRMKLVEIIRGEQT
+SQRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARH
+AGFPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQ
+GAGFYEYPEEGPKHLWPGLAEHFATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPS
+ANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADRYGERFRPGDTLRQRAERG
+EGPGR*
+>NZ_CP033200.1_1710
+MSEHMITWDQDTDGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSA
+KKTFFAGGDLDSLAQAGPEDVESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEI
+ALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMVGVERALMDWLLQGTARDARA
+AMEKGILDEVVTDPADLVPAAKRWILEHRDDADAAAKPWDVKGFRIPGGTPAQASFASRL
+PAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQA
+FHSDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAA
+ERGRERVGALLEGRVAKGRMSREDADAVLARVQPTEDYQDLAHVDAVIEAVFEDVELKDS
+VFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHFFSPVDRMKLVEIIRGEQT
+SPRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARH
+AGFPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQ
+GAGFYEYPEQGPKHLWPGLAEHFATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPS
+ANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADRYGERFRPGGTLRQLAERG
+EGPGR*
+>NZ_CP083691.1_715
+MTENTITWDQDAEGVVTLTMDDPTAKVNTMNGHWQESMRAAVERLEQERESITGVILTSA
+KKTFFAGGDLDQLGPSGPEDAEDVFAMTEHVKSLLRRLEKLGRPVVAAINGAALGGGLEI
+ALACHRRVAVDDPRIKVGLPEVTLGLLPGGGGITRLVRMLGLEKALMDWLLQGTQYRPAQ
+AKEKGVIDELVSSPEELLPAARRWILEQGAAAAKAREGGPEETDEALGAPSYAVKPWDRK
+GFRLPGGTPQQPQLASRLPAFAATLVKTLHGADLPAPRAILSAAVEGAQVDFDTASRIET
+RYFTSLVTGRVSTAMVQAFHTEMGAIRAGAGLGERVSERHTIATAAVLGAGMMGAGIAHA
+LATSGIDVVLKDVSKENAERGKAHCADLVGKAVARGRMDQSAADEVLGRIRTTDDYADIA
+GVDAVIEAVFEDFDLKSEVFAEVEKVVGRQTLLCSNTSTLPITQLQGPRERAADFVGLHF
+FSPVDRMKLVEIIRGEQTSQETVERAYDLVQQIRKVPILVNDGRGFYTSRVFGTLVLEAA
+AMVEEGVDPQRVERTARQAGFPGAPLAMLDEVSLTLTQHVRREAEKAAEAAGTERAEQPG
+ERVVDRMVEEFDRPGRARGAGFYEYPAEGPKHLWPGLREHFAAEVDVSDEDLKDRFLYRM
+ALETAACFEAGVLTDTASADIGGILGIGYPPHTGGPATFATNRPGGLADFVSRADALADA
+YGERFRPSDWLRERAAAGQGLA*
+>NZ_CP097650.1_1927
+MSEHMITWDQDADGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSA
+KKTFFAGGDLDSLAQAGPEDVESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEI
+ALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMVGVERALMEWLLQGTARDARA
+AMEKGIIDEVVTDPADLVPAAKRWILEHRADADAAVKPWDVKGFRIPGGTPAQASFASRL
+PAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQA
+FHSDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAA
+ERGRERVGALLEGRVAKGRMSREDADAVLARVQPTEDYQDLAHVDAVIEAVFEDLELKDS
+VFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHFFSPVDRMRLVEIIRGEQT
+SPRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARH
+AGFPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQ
+GAGFYEYPEQGPKHLWPGLAEHFATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPS
+ANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADRYGERFRPGDTLRQRAERG
+EGPGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001920.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001920.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c55cd60fa58025bb2b09fea39fc29fa1effda929
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001920.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_1993
+MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV
+SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAMNQAAARIRSGWESLLVAGGV
+ESMSRVPMGSDGGAWAMDPATSLATDFVPQGVSADLIATREGFSRAELDRFAAQSHRRAA
+AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSSVETLATLKPSFEALGREAGFDAVAL
+EKYSSLAGIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM
+LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV*
+>NZ_CP033200.1_1711
+MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV
+SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAVNQAAARIRSGWESLLVAGGV
+ESMSRVPMGSDGGAWAMDPATSLATDFIPQGVSADLIATREGFSRAELDSFAAQSHRRAA
+AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSTVETLAKLKPSFEALGREAGFDAVAL
+EKYSSLAEIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM
+LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV*
+>NZ_CP083691.1_714
+MTRDAYLFDAVRTPRGLGKPTGSLHEVKPVGLLGGLFDALRERHPEWDPAGVDDVVLGVV
+TPVGDQGGDIARVAALKAGMPESVAGVQLNRFCGSGLEAVNQVAARIRSGWEDMLIAGGV
+EAMSRVPMGSDGSAWAMDPATALDLHFVPQGISADLIATRQGFSREDLDRFAVQSHHRAA
+QAWSEGRFEGSVIPVTDMNGLTVLDRDETIRPDASLETLAGLRPSFAAMGEQAGFDAVAL
+NRYTDVDEIHHVHHAGNSSGIVDGAALTLIGGEEAGRRAGLTPRARIVSAAVVGSEPTIM
+LTGPTPACRKALDVAGMTASDIDLVEINEAFAAVPLQLMRDLGWNEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLQTGIATLCIGAGMGVATIVERV*
+>NZ_CP097650.1_1928
+MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV
+SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAVNQAAARIRSGWESLLVAGGV
+ESMSRVPMGSDGGAWAMDPATSLATDFIPQGVSADLIATREGFSRAELDRFAAQSHRRAA
+AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSTVETLATLKPSFEALGREAGFDAVAL
+EKYSSLAGIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM
+LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001926.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001926.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d28e6bd74cb4b0cdc97abdf07a97bf149082415
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001926.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_2044
+MTPARPTVSVVVPVLDDAEHLRVCLALLAAQSRPALEVVVVDNGCVDDSAVLARAAGARV
+VHEPRRGVPAAAAAGLDAAVGELLVRCDADTRMPADWLERIVARFDADSGLDALTGPGTF
+HDQPGLRGRVRAALYTGAYRWGAGAAVAATPVWGSNCALRAEAWQAVRTRVHRERGDVHD
+DLDLSFQLALAGRRIRFDPDLRVEVAGRIFHSLRQRVRQGRMAVTTLQVNWARLSPGRRW
+LRRAARSRPRPHWGRGPDGQSRD*
+>NZ_CP033200.1_1763
+MTPARPTVSVVVPVLDDAEHLRVCLALLAAQSRPALEVVVVDNGCVDDSAVLARAAGARV
+VHEPRRGVPAAAAAGLDAAVGELLVRCDADTRMPADWLERIVARFDADSGLDALTGPGTF
+HDQPGLRGRVRAALYTGAYRWGAGAAVAATPVWGSNCALRAEAWQAVRTRVHRERGDVHD
+DLDLSFQLALAGRRIRFDPDLRVEVAGRIFHSLRQRVRQGRMAVTTLQVNWARLSPGRRW
+LRRAARSRPRPHWGRGPDGQSRD*
+>NZ_CP040019.1_663
+MSGGRPAGALTVSVVIPVLDDAAHLRECLRHLARQTRPADEVIVVDNGSADESSAVARKA
+GARVVAEPLRGISAAAAAGYDAAVGDVILRCDADTRPPPDWVARAAGRFEAEPDLAALTG
+PGTFYDQPRLLARLRSRAYGAAYRFGAGAAVAGTALWGSNLGLRAEAWRAVRGRVHRRRP
+DVHDDLDLSFHLGLADVGSVVHDRRLHVGAAGRIFTSLPARVRQLRMAVTTLRLNWALLS
+PGMRWVRRARRSR*
+>NZ_CP097650.1_1985
+MTPARPTVSVVVPVLDDAEHLRVCLALLAAQSRPALEVVVVDNGCVDDSAMLARAAGARV
+VHEPRRGVPAAAAAGLDAAVGELLVRCDADTRMPADWLERIVARFDADPGLDALTGPGTF
+HDQPGLRGRVRAALYTGAYRWGAGAAVAATPVWGSNCALRAEAWQAVRTRVHRERGDVHD
+DLDLSFQLALAGRRIRFDPDLRVEVAGRIFHSLRQRVRQGRMAVTTLQVNWARLSPGRRW
+LRRAARSRPRPHWGRGPDGQSRD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001927.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001927.fa
new file mode 100644
index 0000000000000000000000000000000000000000..906cd4ee433f1029ab68368b5ef3091a3348d326
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001927.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_2045
+MPVGAAGGRDAAPTRAIADMLPLIPADLLRALGLILVPVAAVHAGWPSAAAMLLVFGSQW
+LTRWLAPGGVLDWAAQAVLLLAGWLSVIGLYPRVPSLDLLVHAAASAVVACLTALVVGAW
+LRRRGTEAGQAVALLGPGLAGLGIAAAAVALGVVWELAEWWGHTAVTPEIGVGYTDTIGD
+LAADLVGAGIGAALAVRRGRTR*
+>NZ_CP033200.1_1764
+MPVGAAGGRDAAPTRAIADMLPLIPADLLRALGLILVPVAAVHAGWPSAAAMLLVFGSQW
+LTRWLAPGGVLDWAAQAVLLLAGWLSVIGLYPRVPSLDLLVHAAASAVVACLTALVVGAW
+LRRRGTEAGQAVALLGPGLAGLGIAAAAVALGVVWELAEWWGHTAVTPEIGVGYTDTIGD
+LAADLVGAGIGAALAVRRGRTR*
+>NZ_CP040019.1_662
+MLPLIPADLLRALGLVLIPAAWAVAGWPSAAVMLLVFGAQWLTRWLVPGSALDWGAQAVL
+LAAGWFSVTGLYHRVEALDLVMHAAASAAVVGLVAVAARARLRRRGEDPGALVRRLGPVL
+SAAALTGAGVGLGVLWELAEWWGHTVVTAEIGVGYDDTIGDLAADLLGAGAGAALAVRGQ
+LRAAGSAR*
+>NZ_CP097650.1_1986
+MPVGAAGGRDAAPTRAIADMLPLIPADLLRALGLILVPVAAVHAGWPSAAAMLLVFGSQW
+LTRWLAPGGALDWAAQAVLLLAGWLSVIGLYPRVPWLDLLVHAAASAVVACLTALVVGAW
+LRRRGTEAGQAVALLGPGLAGLGIAAAAVALGVVWELAEWWGHTAVTPEIGVGYTDTIGD
+LAADLVGAGIGAALAVRRERTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001929.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001929.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a94d8a61e6fbe6a379cf7a05ee9ca0d0c56550fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001929.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_2060
+MRPDRHSAPTSAAALAREAAILAGAGAAILLQVAHRPVGAGVAGHSRFTEDPMRRLRHTL
+AYIYAVTLPEAAPARDAVVDRVRAAHGSVRGVDAGGRPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGQGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRTRKPRGAVDVEATRREVRPVWENGADV*
+>NZ_CP033200.1_1780
+MRPDRHSAPTSAAALAREAVILAGAGAAILLQVAHRPVGAGVAVHSRFTEDPMRRLRHTL
+AYIYAVTLPEAAPLRDAVVDRVRAAHRPVRGLDAGGHPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGQGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRMPELGDAVAVRATRRDVRSVWENGGDV*
+>NZ_CP040019.1_648
+MPREAHGPVSAAGLAREAAILAGAGAAILLQVAHRPVAAGVAAHSRFTEDPMRRLRHTLG
+YIYAVTLPEAAGARDAVVARVRAAHAPVRGADHEGRPYNAADADAQLWVAATLYWAGEQV
+RRRLWGALDPADADRLYRGFAPLATSLEVPAAAWPADRAAFAAYWDARIAGLEVTDDARA
+VAADLFSGRGVPAPLRAALPLARFVTAGLLPARARAGLGWDWSRRDSIREARLWVLTRTL
+YRPLPAAVRGVVVRGILRGLRRMSEAGGPAS*
+>NZ_CP097650.1_1999
+MRPDRRSAPTSAAALAREAVILAGAGAAILLQVAHRPVGAGVAVHSRFTEDPMRRLRHTL
+AYIYAVTLPEAASLRDAVVDRVRAAHRPVRGVDAGGHPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGHGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRTRKPRGAVDVEATRREVRPVWENGADV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001932.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001932.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b230c76bbab3474ea3bb84030b5e394efaf79d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001932.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_2099
+MSTAAPAPARPTTATSRPPADSPLDSRLPAILRAEPVSRHMRIVLYVIVGLMVLGEILTL
+VLGPMVAAGLSADPELAAIFEEDGGLTGERREPLLRWVLFLASVLVTLLFGWQPTLAAVF
+VLLGSAFGLAGLVEADHAHLTPQAFSGGVILGAAMVTRYSHRVFVWFALGALILLTVAGE
+ALTDGTWADEDSLKGVMVVTLIVALCVAVPAFMIRRSRHRARDREAALRRAEEAAACAAE
+AERQRIAAELHDVVAHGLTVISMQAAMLPTQRDPEKRAASEKAIEQAARQSLVDLRRMLT
+ALRGSSRNAQTAEGDAVVDLPARLDEFEARLHAAGFAVERSLTELEELPRSLELTVLRVV
+QESVTNILKHAPRRGTVRLTSELEGADRLVLCIASPMDEGEPRRDRVVVAMASGFGLAGM
+RERVAVFGGTLMAGPLGGCWVVRAELPLR*
+>NZ_CP033200.1_1824
+MSIAAPAPARTTTATSPPPAESPLGSRLPAILRTEPVSRHTRIVLYVIVGLMVLGEILTL
+MLGPTVAAGLSADPELAGILEEDGGLTGEGREPLLRWVLFLASVLVTLLFGWQPTLAAVF
+VLLGCTFGLVGLVEADHAHLTPQAFSGGVVLGAAMVTRYSHRVFVWFALGALILLTVAGE
+VLTDGTWADEDSLKGVMVITLIVALCVAVPAFMIRRSRHRARDREAALRRAEEAAACAAE
+AERQRIAAELHDVVAHGLTVISMQAAMLPTQRDPDKRAAAEKAIEEAARQSLVDLRRMLT
+ALRGSSRNAQTAEGDAVVDLPARLDEFEAQLHAAGFAVERSLTELDELPRSLELTVLRVV
+QESVTNILKHAPRRGTVRLTSQLEGADRLVLCIASPMDEGEPRRDRVVVAMASGFGLAGM
+RERVAVFGGTLTAGPLGGCWVVRAELPLR*
+>NZ_CP040019.1_586
+MATVSIGRPDSPVWGPFGARRLSLRIRLIVWISLAVVFGIDVVLAFSGTGVTAAEALPQL
+AGEYLLIGLIAQHAPLGVIAYAIAFTAGARWWDYEALSIVFAGAALMLGLSAQRGLLLLA
+GGLFAAWFVIAGPVLGSFSTAAAVAFAVSAALGVAAGLGLRWLARRFDSALRLAEERQTQ
+LEQAQRDERHRLALELHDVVGHGLTVIALQAGMLPTVTSPVQRTEVEQAIADTARQSLTD
+LRTMLGVLRGSAPGLGPAEDAEPPRPVRELVAEYRDRLTAAGFDVHVRLEAEAEVPDSLR
+HTLRRIVQEASTNVLRHAEPGGRVDVEIRHDGCETSVLVRSPLPARRRQEPAPHSGYGLA
+GMDERVRILGGRITHGPVDGSWVLDVTLPSQERAAQA*
+>NZ_CP097650.1_2043
+MSIAAPAPARTTTATSPPPAESPLGSRLPAILRTEPVSRHTRIVLYVIVGLMVLGEILTL
+VLGPTVAAGLSADPELAALLEEDGGLTGEGREPLLRWVLFLAGVLVTLLFGWQPTLAAVF
+VLLGSAFGLVGLVEADHAHLTPQAFSGGVVLGAAMVTRYSHRVFVWFALGALILLTVAGE
+VLTDGSWADEDSLKGVMVITLIVALCVAVPAFMIRRSRHRARDREAALRRAEEAAACAAE
+AERQRIAAELHDVVAHGLTVISMQAAMLPTQKDPEKRAAAEKAIEQAARQSLVDLRRMLT
+ALRGSSRNAQTAEGDAVVDLPARLDEFEARLHAAGFAVERSLTELDELPRSLELTVLRVV
+QESVTNILKHAPRRGTVRLTSQLEGADRLVLCIASPMDEGEPRRDRVVVAMASGFGLAGM
+RERVAVFGGTLTAGPLDGCWVVRAELPLR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001935.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001935.fa
new file mode 100644
index 0000000000000000000000000000000000000000..655822eb79aa0703185af4cd6c483a47f7b2e879
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001935.fa
@@ -0,0 +1,44 @@
+>NZ_CP042169.1_2116
+MSSGLPETAAVPSGHGSTRRRRPTSLARRIGAGVLLILMATILAYSFYAAGITKALLTES
+ASRDASEAWIRASEQLTAPSPGGGGDGGPGQGDLRVPGTLGQPEGTVVALVPLSGLEEHQ
+QDALIGHRVGDAGESVPLTAREAHDLLHALRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVTRQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALDRFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSATGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP*
+>NZ_CP033200.1_1842
+MSSGLPETAAVPSGHGSTRRRRPTSLARRIGAGVLLILMATILAYSFYAAGITKALLTES
+ASRDASEAWIRASEQLTAPSPGGGGDGGPGQGDLRVPGTLGQPEGTVVALVPLSGLEEHQ
+QDALIGHRVGDAGESVPLTAREAHDLLHALRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVTRQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALERFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSAAGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP*
+>NZ_CP040019.1_564
+MSSAPPDPADASSGRGGPRPRRQSSLARRTGAGVVVILLITLTAFALFAGNTTRALTAES
+ASRNTTAAWTRAAEQLASLEAGTAFDAEPTAGDPQVPGTLGQPEGTVVALVSPADLEDHQ
+AGTLRGHRVGKAGESVPLDARQSHDIIHAIRGEPIGAPVDAAVSGEGYRFKALPMTSPGP
+WVGADQLLVVGVPTGALTAVSRRGLLMVVLGLSLTVVVTALAVFLWLRRGLAPLGEVAAM
+AERVAGMDLAHTGIDRRQTRMPKRLLQGPDEVVVVAEAMDRFTGAVEDALEERRRQEQQL
+RSFIADASHELRTPLASVRGYAEMIAMTEDLSETGRRSLDRVLHQAGRMSALVDDMLLLE
+RLESVSRGRAVGLAPSGEVPAADPVDLPEVLLEAVVDARAAWPDHQWVLDLPETLGEEGQ
+GCVTGDPAQLARLVGNLLSNGAKHTPAGTTVTTSLRIGRPLPHQVVVSVHDDGGGIPAEH
+RERLFERFARGASAGGPGREPSTGLGLAIVRSIARSHGGEASVASEAGWTRFDVVLPCAR
+WTARAQAEAAGRGGPEAPEGTGAPRE*
+>NZ_CP097650.1_2062
+MSSGLPETAAVPSGHGSTRRTQPTSLARRIGAGVLLILVATILAYSFFAAGITKALLAES
+ASRDASEAWIRASEQLTAPSPGGGGDARPGEGYLRAPGTLGQPEGTVVALVPLSGLEAHQ
+QDALTGHRVGDTGESVPLTAQEAHDLLHAVRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVARQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALERFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSAAGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001939.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001939.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0bc970c0af99221cfcfc2459446f284aa85a41a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001939.fa
@@ -0,0 +1,17 @@
+>NZ_CP042169.1_2137
+MSPADPTADVAAGPAGPAAVAEAFAAAWNAADADALADLFAEDADFVNVVGVWWTRRRQI
+RVNHALGFRWMFPASRLVLGQVRVRELGDVAVVHAPWTMTGQTAPDGDEAGERTGVLLLV
+VRRTEAGAWEAVAGQNTDSVPEAQTHLADDDGLAAVHYHPSAWIDPDDDPDGPEAC*
+>NZ_CP033200.1_1862
+MSPADPTADVAARPTGPAAVAEAFAAAWNAADADALAELFAEDADFVNVVGVWWRRRRQI
+RVNHALGFRWMFPHSRLELGRVRVRELGDVAVVHAPWTMTGQTAPDGDEAGERTGVLLLV
+VRRTETGAWEAVAGQNTDSVPGAQTHLADDEGLAAVHYHPSAWFDPDEDPDGPEAC*
+>NZ_CP040019.1_537
+MSPADPSPRLLARPPASPAAVAEAFEAAWNAADADALADLFAEDADFVTVLGVWWTRRRQ
+IRLDHARAFRWMFPESRLEMDEVRVRDLGDVAVVHAPWTMTGPGVGGEVGEATGTVGVRE
+AGGDGSGGGDGERTGVLLLVVRRDEAGAWEVVAAQNTDRSPEPRPRPADEDDLLAEVHPH
+PSAWLHPDDDGPASRLSARPRLGWAVHEPVPPLPLPNSPSPPLPLPQGELSCRWPV*
+>NZ_CP097650.1_2082
+MPPADPTADVAARPAGPAAVAEAFAAAWNAADADALAELFAEDADFVNVVGVWWTRRRQI
+RVNHALGFRWMFPASRLVLGQVRVRELGDVAVVHAPWTMTGQTAPDGDEAGERTGVLLLV
+VRRTEAGAWEAVAGQNTDSVPEAQTHLADDDGLAAVHYHPSAWIDPDDDPDGPEAC*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001945.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001945.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55d1aa8654f770ee16fbe30e8e350343bf4df050
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001945.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_2162
+MQIAEQERIASPTFVLAWVVSFLQFLAFYALVTTMAVYAVRQFAASDAGAGLASSAFVIG
+ATLSRVVTGHVVDRFGKRRVLVVALVAVALSCTLYLVASSLPALVAVRMLHGASYAFAST
+AVMALAQAAIPDGRRAEATGHLALGTTLATAIGPALGLFLAGSIGYVWLFRATLGITVVS
+LVLGLLVREAPAAAGVDGERAAGEVPLEHPAPAVGFRLRSVLHPAVLPISGFMLLVGLSY
+AGILTYLNAYSVERGLTAGAGLFFLAYAAAMLVMRLTLGTLQDRRGDDAVVYPALLCFTA
+ALLVLAFATRDWQVVLAGALSGLGYGTLMPAAQAIAVNAVPSHQLGAGISTLMLFADVGL
+GLGPVLLGGLVASAGYGAMYAALAGVLVVAAGYYFVMHGRRHGRRETVARA*
+>NZ_CP033200.1_1887
+MQIAEQERIASPTFVLAWVVSFLQFLAFYALVTTMAVYAVRQFAASDAGAGLASSAFVIG
+ATLSRVVTGHVVDRFGKRRVLVAALVAVALSCTLYLVASSLPALVAVRMLHGASYAFAST
+AVMALAQAAIPDGRRAEATGHLALGTTLATAIGPALGLFLAGSIGYVWLFRATLGITVVS
+LVLGLLVREAPAAADVDGERAAGEVPLEHPAPAVGFRLRSVLHPAVLPISGFMLLVGLSY
+AGILTYLNAYSVERGLTAGAGLFFLAYAAAMLVMRLTLGTLQDRRGDDAVVYPALLCFTA
+ALLVLAFATRDWQVVLAGALSGLGYGTLMPAAQAIAVNAVPSHQLGAGISTLMLFADVGL
+GLGPVLLGGLVASAGYGAMYAALAGVLVVAAGYYFVMHGRRHGRRETVARA*
+>NZ_CP083691.1_457
+MHHPVTAPAEAAPRIVTPVFAVAWLVNFAQYLTFYLLATTMALYAVKQFGAGDAAAGFAS
+SAFVVGATVARIFAGHVVDSLGRRRMLLVSLSVVTLACAAYLPASSLGLLVAVRLVHGAM
+YAVASTAVMTLAQSVIPASRRAEGTGYFALGTTLATALGPAAGLMLVSAAGYPGMFWATT
+AVAAVGLAFGLALRVPDEPASARPHLVRGFRLGGILHPAVVPIGVFMLLVGVAYAGVITY
+LNGYAEQRGLGAGAGLFFLAYALVTLVMRFVLGRVQDRRGDNAVVGLGLVCFAASLVLLA
+VARQDAVVVLAGALCGLGYGTLMPAAQAIAVRLVPPHQMGTGISTLYLGVDVGIGLAPLP
+LGALLAAGGYLWMYLVLAGFVVLAGVYYVLVHGRTPAARAVAR*
+>NZ_CP097650.1_2102
+MQIAEQERIASPTFVLAWVVSFLQFLAFYALVTTMAVYAVRQFAASDAGAGLASSAFVIG
+ATVSRVVTGHVVDRFGKRRVLVVALVAVALSCTLYLVASSLPALVAVRMLHGASYAFAST
+AVMALAQAAIPDGRRAEATGHLALGTTLATAIGPALGLFLAGSIGYAWLFRATLGITVVS
+LVLGLLVREAPAAADVDGERAAGEAPLEHPAPAVGFRLRSVLHPAVLPISGFMLLVGLSY
+AGILTYLNAYSVERGLTAGAGLFFLAYAAAMLVMRLTLGTLQDRRGDDAVVYPALLCFTA
+ALLVLAFATRDGHVVLAGALSGLGYGTLMPAAQAIAVNAVPSHQLGAGISTLMLFADVGL
+GLGPVLLGGLVASAGYGTMYAALAGVLVIAAGYYFVMHGRRHGRRETVARA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001947.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001947.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6bdbfaf72f5c061500fe686f5c7c691087cee6c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001947.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_2166
+MTHRNPEDNALRGAPEPRTLAEACDLVTTPDLDVSADGMFGQYGGAHLPPQLAGPMAEVA
+RAYAEARQDPEFYAEYRRLLRDAVGRPSPLTPLDRLSDELGGARIVLKREDLNHTGAHKI
+NHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGAIDVAKQHPNVVR
+MRLLGTKVVSVEREGRSLKEAVDSAFEVYAADPEKYLFAIGSVVGPHPFPTMIRDFQSVV
+GREARAQFQERFGALPSAVVAAVGGGSNAMGAFTAFLDDADVALVGVEPGGRSATKGEHA
+MTMTQGRDGVLHGMATLVLADDDGTPDPVHSIASGLDYPGVGPQHAHFARLGRVRYVAED
+DAAVLDAFQRLTRLEGVIPALESAHAVAHAIRLAPQMGRDERILVNLSGRGDKDVDYVAE
+KLGLTGEADEVVR*
+>NZ_CP033200.1_1894
+MTHRNPEDNALRGAPEPRTLAEACDLVTTPDLDVSADGMFGQYGGAHLPPQLAGPMAEVA
+RAYAEARQDPEFYAEYRRLLRDAVGRPSPLTPLDRLSDELGGARIVLKREDLNHTGAHKI
+NHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGAIDVAKQHPNVVR
+MRLLGTKVVSVEREGRSLKEAVDSAFEVYAANPEKYLFAIGSVVGPHPFPTMIRDFQSVV
+GREARAQFQERFGALPSAVVAAVGGGSNAIGAFTAFLDDADVALVGVEPGGRSAAKGEHA
+MTMTQGRDGVLHGMATLVLADDDGTPDPVHSIASGLDYPGVGPQHAHFASVGRVRYVAED
+DAAVLDAFQRLTRLEGVIPALESAHAVAHAIRLAPQMGRDARILVNLSGRGDKDVDYVAE
+KLGLTGEADEVVR*
+>NZ_CP083691.1_445
+MTHRNPEDNALRAADAARPEPRTLAEATDLVHTPDLTAGADGMFGTYGGAVLPPELAGPM
+AEVAEAYEEARHDPEFYAEYRRLLRDVVGRPSPLTPLDRLSDELGGARIVLKREDLNHTG
+AHKINHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGSIDVAKQHP
+NVVRMRLLGATVVSVDREGRSLKEAVDSAFDVYASDPAHYLFAIGSVVGPHPFPTIVRDF
+QAVVGREARAQFLERYGALPSAVVAAVGGGSNAMGAFTAFLDDADVRLIGVEPGGRSATK
+GEHAMSMAQGVDGVLHGMATKVLQDEQGVPDPVHSIASGLDYPGVGPQHARLAQLGRVEY
+VAEDDAAVLEAFQRLTKLEGIIPALESAHAVARAIRMAPGLGTDQRILVNLSGRGDKDVD
+YVAETLGLTGDADEVVR*
+>NZ_CP097650.1_2106
+MTHRNPEDNALRGAAEPRTLAEACDLVTTPDLDVSADGMFGQYGGAHLPPQLAGPMAEVA
+RAYAEARQDPEFYAEYRRLLRDAVGRPSPLTPLDRLSDELGGARIVLKREDLNHTGAHKI
+NHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGAIDVAKQHPNVVR
+MRLLGTKVVSVEREGRSLKEAVDSAFEVYAADPEKYLFAIGSVVGPHPFPTMIRDFQSVV
+GREARAQFQERFGALPSAVVAAVGGGSNAMGAFTAFLDDADVALVGVEPGGRSATKGEHA
+MTMTQGRDGVLHGMATLVLADDDGTPDPVHSIASGLDYPGVGPQHAHFARVGRVRYVAED
+DAAVLDAFQRLTRLEGVIPALESAHAVAHAIRLAPQMGRDERILVNLSGRGDKDVDYVAE
+KLGLTGEADEVVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001951.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef012011909bebb106fea93a9d373e8efcd681f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001951.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_2216
+MGVNGLPGTGKTTTLRDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRAREL
+RPEVAGFEMVVASANNAAGESISEEIPQVESRIVV*
+>NZ_CP033200.1_1920
+MPAPSLGEEDKRAIPALQPSLSSSNVTAHEHTGHPQAARIDVVARADVVEAGGPGLMGVN
+GLPGTGKTTTLGDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRVRELRPEV
+VGFEMVVASANNAAVENLSEEIPQRSAIKDSRNVDADYFAELAAALGGSRGEEDALGEDS
+LTSEQPGTSGLATAPMATAPTPPRSARRRPTRG*
+>NZ_CP040019.1_444
+MPAPSLGEEDKRAIPALQPSLSSSNVTAHEHTGHLQAACIDVVARSEVVEVGGPGLMGVN
+GLPGTGKTTMLRDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRARELRPEV
+VGFEMVVASANNAAVENLSEEIPQRSAIKDGRHVDADYFACLATAAVGGSGGGRGRPG*
+>NZ_CP083691.1_394
+MGDTRGRTQQDIVRFWQLQELFDPQPLPKLTPRTSPPFGKRVITWRAEDGDVALPWNRLA
+PPPPTTKGAAREWRHTLYLRIYALEDAYQTLHSAFPADADAYDERPGGRSAAAGALVDAD
+GRLIGGTGVLSSALWGIGRLCRGEGFDDSLVDGFEAAGEAFVDAADRAAGVPDDDAFGEQ
+PVLTAGMLVALIRLAQHSAGVEGMPALAGHEVRIASQVVSASSGDETPDIDFLNSFYLSD
+LHRVGEAIARGDVGPALDAYLTPDGDVDTQRRVDVVARPDIVDAGVEPARVPAGRWPAKT
+SYALARSQQFAVNRALNELGAEPGLMGVNGPPGTGKTTMLRDILAANVVERARKLAGFAD
+PSGAFTGRTLAWTGEGRRHRTVHELRPELTGFEMVVASANNAAVENISEEIPHRDAIKDS
+GRADADYFADLATAALGLGVENADEDGAPGACDGPAAEQPAAASSGAWGLVAARLGNKVN
+RARFRDAVLFGGASGGRGARGRGLDTLLKDWAASPSAPAQWTAAREAFHRALHEVDRGLT
+ERRDAAQRTVRTAAAREAVRAAERRLAELSRQRTAKWAGAEAIRRELSAAQAEAGRIRDA
+LDLHRDAKPGFWETITSFGVAGQQWRETYQPLLEAWSTADAGRAALAADTEAAERRLSEL
+EAQIVHLDGECARRRGDLADLEAAVRADEERFGGRHPSAVVDAQTRETTTPWLDEEMEKA
+RTELFLAALELHRAFIAAAARDLRPSFQAAMEVMAGAAPRDLEAEKRRAAWQVFFLLVPL
+VSTTFASFDRMFTGMGRESLGWLFVDEAGQASPQYAAGAIWRANRAVVVGDPLQLEPVVT
+IPVTVSRSLAKAHGVSSTWIAPEASVQRLADRVSRYGTTLPQGEDDVWVSSPLRVHRRCD
+DPMFALSNDLAYGGLMVSGVQRKGPEEDPFERTGDGEIFASSWMDTPARTPGTHLQPNQI
+ERVRRGIEACRRWGIPCTEIIAISPFREVADALRVLSDEFPGLTAGTIHTAQGREADVVF
+FVLGGAPDKPGARNWASSRVNLANVAVSRAKRRLYVIGDREAWSRHNYFRQIAEALPRAA
+EPDAGRER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001952.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecb4d2aadbef6bcfc079bd66679ddca0181c50ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001952.fa
@@ -0,0 +1,22 @@
+>NZ_CP042169.1_2217
+MPHSDPVPEPFVLTLGSVLDAAGLDPHEVLAIRHTYKESGLPSRAAATPERVLAYTREQH
+HLGKFPKEPARHWLIFMGEGGRRSRLTAVYENRGEAVAERTERYRYYDVAPVPLLASLEE
+RLVVEWSADPVNWAKRGPLAARFPVLEIADPTTEAFPGFDHVLLSYGGLQSMVTETRYAG
+WRTALQAVRGIYLIADETAGQCYVGKADGERGVLGRWEAYARDGHGGNVALRDALELDPA
+QPERYTFSLLRVFGSNTPQAQIDAAEKHYKEALMTRRFGLNRN*
+>NZ_CP033200.1_1921
+MESTQPVPEPFVLTLGAVLAAAGLDPHDVLAIRHTYKESGLPSRAAATPERVLAYTREQH
+HVGKFPKEPARHWLIFMGEGGRRSRLTAVYENRGEAVAERTERHRYYDVAPVPLLASLEE
+RLVVEWSADPVNWAKRGPLAARFPVLEIADPTTEAFPGFDHVLLSYGDLQSLVTETRYAG
+WRTALQAVRGIYLIADETAGQCYVGKADGERGVLGRWAAYARDGHGGNVALRDALELDPA
+QPERYTFSLLRVFGSSTPQAQIDAAEKHYKEALMTRRFGLNRN*
+>NZ_CP040019.1_443
+MESTQPFVLSLGAVLAAAGLDPHDVLAIRHTYKESGLPSRAAATPERVLAYTREQHHVGK
+FPKEPARHWLIFMGEGGRRSRLTAVYENRGEAVAERTERYRYYDVAPVPLLASLEERLVV
+EWSADPVNWAKRGPLAARFPVLEIADPSTEAFPGFDHVLLSYGDLQSMVTETRYAGWRTA
+LEAVRGIYLIADETAGQCYVGKADGERGVLGRWEAYARDGHGGNVALRDALELDPAQPER
+YTFSLLRVFGSNTPQVQIDAAEKHYKEALMTRRFGLNRN*
+>NZ_CP083691.1_392
+MPLLASLEERLVVEWSADPVNWVKRGHLAARFPVLEIADSTTEAFPGFDHVLLSYGDLQS
+MVTETRYAGWRTALQAVHGIYLIADDAASQCYVGKADGERGVLGRWEAYARDGHGGNVAI
+RDALELDPAQPERYTFSLLRVFGSNTPQAQIDAAEKHYKDALMTRRFGLNRN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001953.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001953.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b632a794b2b79362f8184dad9272103da98a1be2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001953.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_2227
+MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPVRGDDTRGWAP
+PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD
+DVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPDAPMKAGVALVDVLT
+AKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGAGVVPRRMGNDHPSI
+APYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALED
+ALSAQTAAHWRDVLQAERLPAGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRHP
+VQWDPPVAHPRHAPPALGADTAAVNTWLDAR*
+>NZ_CP033200.1_1930
+MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPERGDDTRGWAP
+PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD
+EVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPDAPMKAGVALVDVLT
+AKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGAGVVPRRMGNDHPSI
+APYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALED
+ALSAETAAHWRDVLQAERLPVGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRHP
+VQWDPPVAHPHHAPPALGADTAAVNTWLDTR*
+>NZ_CP040019.1_792
+MEHTDEPRGGGPLEGIVIADFTRVLAGPYATMLLADMGATVIKVESPGGDDTRTWRPPEH
+EGVSTYYLSVNRNKRAVALDLSDREDLDTAYALLDRADVFLENFKPGGLAKFGLDPDSVA
+ERWPHLVHASITGFGTASGTALPGYDLLAQAVSGMMTVTGEPDGAPQRSGVAIFDVITGL
+HAAIGVLGALQERTRSGRGQHLELNLLSSALSGLVNQTSAAIAGGVTPHRMGNEHPSLYP
+YGPFRAADRELIIAVGNDRQFARLVEQLGRPELAEDPRFLTMKDRNAHRGELGPLLEEAL
+AAQSAGEWFEQLRDAGIPCSPILTLPEGVEFAAGLGLDPVVEVGEQRIPTVRHPIRFSRT
+PARHELAPPALDADRDWVRAWIDQTPPSTAADAD*
+>NZ_CP097650.1_2168
+MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPVRGDDTRGWAP
+PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD
+DVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPDAPMKAGVALVDVLT
+AKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGADVVPRRMGNDHPSI
+APYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALED
+ALSAQTAAHWRDVLQAERLPVGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRHP
+VQWDPPVAHPHHAPPALGADTAAVNTWLDAH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001958.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001958.fa
new file mode 100644
index 0000000000000000000000000000000000000000..084ffaf9acf1ba8625f2bd7e280e17b3ba54bafa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001958.fa
@@ -0,0 +1,33 @@
+>NZ_CP033200.1_225
+MTWVVTGGAGYIGAHVVRALQGAGMDVAVVDDLSTGFADFVPADVPLLRADVGDVGQVAT
+YLTRVGAAGVVHVAGYKFAGESVREPLHTYRVNVRGTLGVLEAMERAGVPAIVFSSSAAV
+YGTPDVERVTEATATAPESPYGESKLIGEWLLADQGRATGLRHTSLRYFNVVGSADPALS
+DTSPHNLFPLVFRALDRGERPRLFGADHPTPDGTCVRDYVHVADVARAHVAAARALAESR
+ALAPVYNLGSGAGTSVRQIMEAVGRVTGRDVDPVVEPRRPGDPARIVADGSLAARDLGWE
+NRHTVEDMVRSAWEARRPPETR*
+>NZ_CP040019.1_1202
+MPHDESMCMMNVSAPEPTRPQLPPLARHALLIIWDSVSWILALLAFLVVRYDFGLSPTQW
+DWVLAFTLIAVVGQVAAGLVTQFYLGRHRVGSFSDAGWTAVIVCAIALAIGLALSVAAPA
+FPRGVALTMPPLALVIMLAGRFLVRNVAAGRPRADASAAVPAIVYGAGNAGHQVSQLMRQ
+AEEPPYRIVGFVDDDKGKSRLRIHGLGVRGRGTDLAEVAAELGAEAVIYAISNADAEHVE
+WVSRVCTEEGLDLVVVPPLREMVGGKVTLGSLRHLSVTDLLGRRPISTDISAISDYVSGK
+VVLVTGAGGSIGSELAVQLHHLGPAKLLLLDRDESALHGVQLDIYGNGLLDTDDIILCDI
+RDEQALQAVFEHHRPQVVFHAAALKHLPMLERFPLEGWRTNVLGTRNVLQAAHSVGVQRF
+VNISTDKAAAPTSVLGATKRLAERLTAWHATTYDLPYLSVRFGNVLGSRGSVLISFRNQI
+EKGGPVTVTHPDVTRYFMTIPEACELVLQAGAIGNPGEVLVLDMGQPVKILDVAKRMIAE
+SGQNIDIHFTGLRPGEKMHEVLFSNAEANATSQHPMISEVQVPDLDPVVVAELPSDRESI
+LAMIDDEPPVERADDTQTPGLDQAGARP*
+>NZ_CP040019.1_2391
+MTWVVTGGAGYIGAHVVRAFRERGLPVAVVDDLSTGHREFVPDGVPFFHADVTDTAALTA
+VLRENEAEGVVHVAGYKYAGESVRVPLTAYRANVQGTASVLDAMAAAQVQSVVFSSSAAV
+YGTPAVERVTEDTPPAPESPYGESKLIGEWLLRDQERAVGIRHTSLRYFNVVGSGWADIT
+DLSPHNLFPLVFSALERGERPHIFGDDYPTPDGTCIRDYVHVQDVAEAHVAAARALTSGV
+GLHSVYNLGSGQGTSVHEIMAAVRDVTGVTDPPEVLDRRPGDPARIVADGTLAAQDLGWR
+MRHSVEDMVRSAWDAHRRLGISASGDE*
+>NZ_CP097650.1_813
+MRLLVTGGAGYIGSHFVSVARQQGRADIVVVDDFSTGLRQRVPADVPVYTIDLASDAAVA
+TLTTLLKEESIDVVVHFAAKKVVADSVVQPEDYFRSNVGATVNVLAAMRAAGAASMIFSS
+SAAVYGEPDSSIVFEDTPTVPINPYGQSKLVSELALANASRAWGLRAVALRYFNVAGAED
+AILADTTTTNLMPAIRDVITRGQRLSVFGDDYPTVDGTCVRDYVHVVDLAEAHLAALPAV
+QGSTDPATRIYNVGTGSGSSVLEVVDAFRRRPGVDLDYDIQPRRPGDPGALTANVSLIEK
+ELGWVARYTRDDIVTSVIDFPPRLVT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001959.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001959.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2f759559f0903dc4b140f7a47bcddd51f726495
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001959.fa
@@ -0,0 +1,20 @@
+>NZ_CP033200.1_242
+MQKNTSTLSRRKVTAGIAWSVPAVAAVAAAPFAAASPTGCAAVTTGTAEKFPGGGHPDGI
+KQAYGFTITITNTSPTPVYVDPGTVTVEFKGHPTRSGEALLYTASPCEGGTRLAAMDPEL
+LLQPGESETYYYVVNQTGNSAQESGCVKGKLQLALPKGAPEGADLCNDGVVDFSNCFDTT
+PPTAGC*
+>NZ_CP040019.1_2372
+MQQNTSSLSRRKVTTGIAWSVPAVVAVAAAPFAAASPSCITSSAGRVVKYPGNSSGYDLK
+QAYGFTVTVTNPTRGKLRVTAKSVSLILDKKVLRGSLLIYTADPCAGGVPVDPNSDLLVL
+EPGESQTLFLVANNTGNSANTSGCIYAKLGVKLVDGSVPVANLCDEHDVVEACFDETSPT
+ATC*
+>NZ_CP083691.1_2250
+MQTTPKTVNRRTVSAGIAWSVPAVAAVAAAPFAAASPTGCVNVTSGTAEKFPGGGHPDGI
+KQAYGFTITITNTSPTPVYVNPGTVTVVFGGHTTRNGEARLYTASPCRGGKRLAAMDPEL
+LLQPGQSKTYYYVVNNTGNSAQESGCVKGKLQLALPKGAPEGADLCNGGIVEFKNCFETT
+PPTAGC*
+>NZ_CP097650.1_512
+MQKNTSTLSRRKVTAGIAWSVPAVAAVAAAPFAAASPTGCAAVTTGTAEKFPGGGHPDGI
+KQAYGFTITITNTSPTPVYVDPGTVTVVFGGHTTRNGEARLYTANPCRGGKRLAAMDPAL
+LLQSGQSKTYYYVVNNTGNSANESGCVEGKLQLALPKGAPEGADLCNDGVVEFSNCFETT
+PPTARC*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001961.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001961.fa
new file mode 100644
index 0000000000000000000000000000000000000000..535315c31a640611190de9634ecea62dc639adff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001961.fa
@@ -0,0 +1,26 @@
+>NZ_CP033200.1_310
+MIMGFIDQMRAKGHAVESICRVLRQEGCQIAARTYRAWRRRSASARDTSDAVLLNVLHDL
+VGTPEGLYGRRKMTAWLRREGHQVGAGRVDRLMRVAGMNGVRRGRPVRTTVPAKDGCRAG
+DLLNRDFTAAAPNTKWVADFTYVRTWAGFVYVAFVLDCYSQRILAWHAATAKTTPLVLTP
+LRIALWDRDRHGHPVQPGELIAHSDAGSQYTSLRFAEHLAAEGIAASIGTVADAYDNALM
+ECVIGLYKTECITTTIFHNGPYKTIADVEYATAGWVEWYNNRRLHSSLAMTTPAEYETAY
+YAALNRELAPT*
+>NZ_CP040019.1_2229
+MIMGFIDQMRAKGHAVESICRVLRQEGCQIAARTYRAWRRRSASARDTSDAVLLNVLHDL
+VGTPEGLYGRRKMTAWLRREGHQVGAGRVDRLMRVAGMNGVRRGRPVRTTVPAKDGCRAG
+DLLNRDFTAAAPNTKWVADFTYVRTWAGFVYVAFVLDCYSQRILAWHAATAKTTPLVLTP
+LRIALWDRDRHGHPVQPGELIAHSDAGSQYTSLRFAEHLAAEGIAASIGTVADAYDNALM
+ECVIGLYKTECITTTIFHNGPYKTIADVEYATAGWVEWYNNRRLHSSLAMTTPAEYETAY
+YAALNRELAPT*
+>NZ_CP083691.1_1789
+MIMGFIDQMRAKGHAVESICRVLRQEGCQIAARTYRAWRRRSASARDTSDAVLLNVLHDL
+VGTPEGLYGRRKMTAWLRREGHQVGAGRVDRLMRVAGMNGVRRGRPVRTTVPAKDGCRAG
+DLLNRDFTAAAPNTKWVADFTYVRTWAGFVYVAFVLDCYSQRILAWHAATAKTTPLVLTP
+LRIALWDRDRHGHPVQPGELIAHSDAGSQYTSLCFAEHLAAEGIAASIGTVADAYDNALM
+ECVIGLYRTECITTTIFHNGPYKTIADVEYATAGWVEWYNNRRLHSSLAMTTPAEYETAY
+YAALNRELAPT*
+>NZ_CP097650.1_569
+MRVAGMNGVRRGRPVRTTVPAKDGCRAGDLLNRDFTAAAPNTKWVADFTYVRTWAGFVYV
+AFVLDCYSQRILAWHAATAKTTPLVLTPLRTALWDRDRHGHPVQPGELIAHSDAGSQYTS
+LRFAEHLAAEGIAASIGTVADAYDNALMECVIGLYKTECITTTIFHNGPYKTIADVEYAT
+AGWVEWYNNRRLHSSLAMTTPAEYETAYYAALNRELAPT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001968.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001968.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6034923977500ad51aaf49ce330cb097ac819dbe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001968.fa
@@ -0,0 +1,28 @@
+>NZ_CP033200.1_1654
+MTGRGLRTLGLLVTRAVLLVALCGLALSLVGSLSVHHRQYFGAAECGPAVWDVGIGGGGE
+VWSVAEAATTGRNLTLMASGADPGVRHLAGPAAPCLAGIDVPTLESLRAARGFLLREGSI
+LADRAARSGELAGRPVALASAADWRGLPSDGVIQPTPAFDNAAAYVGFLVGDPADLDGFL
+QNLRTAGLEVDAAPAPSAMTASLGTPVLGVTSSLTGLTLMSVTAFWVLTLRAGDRPSLRV
+LRLLGVSPLRAAVSRARVSLVPFLGAAGISAALWQGMVLTGAVTEPSPLVASGVILVVLL
+GDAVLVSATHVVALWMRAPR*
+>NZ_CP040019.1_837
+MGSRTLGLLVTRAVLLAAVCGLALSLVGSMSVHQRQYFGAAECGDAVWDVGIGGSGEVWS
+ATEAALTGRNLTLMANGADPRVRHLTGPTAPCLAGVDEQMLNSLRMERGFLVREGSVLAD
+RAAGEGELAGRPVALASSARWRGLPSDGVIQPTPAFDNAAAYVGFLVGDPADLDGFLQNL
+RTAGLEVDAAPAPTAMTASLGTPVLGVTSSLTGLTLMSVTAFWVLTLRAGERPSLRVLRL
+LGVSPLRAAVSRARVSLVPFLGAAGISAALWQGMVLTGAVTEPSPLVASGVILVVLLGDA
+VLVAATHVVSLWMRAPR*
+>NZ_CP083691.1_773
+MGTGLLGRLLTRAVLLTALCGLALGIAGSMSVHRQQYFGAEGCGEAVWDVNVVGADRVWS
+ALEAALTGRDLTAMVTGADPGLFHVAGPAASCLTGVDEQTLGSTREAGGFLVRGGGMLAA
+RAGQDGELATRPAVVVPPDRWRGLPSVSLIQPTPVFDDSSSYVGFLVGDAGEIEDLVRRL
+RESGLEVEAAPAATAAEAALRAPTLSATTGLTALTCLSVTAFWALTLHAGQRPAVRVLRL
+LGVSPLRAAASRWAASAVPFAAAAALAAALWLGMILSGTLTTPAPGTAALIVAGAILADA
+ALVALTHVGALWMKRVPR*
+>NZ_CP097650.1_712
+MTRMLVSRFLLLLITLGTAALLASYVGVEKEDRWRMDGTVYEISAFPAGEAWPMIRTSLT
+GPDSGSAATSTSPHVTALAGRPALDVLPDGVAPTAVVPSTSPFAARAAAGELSWPDVDRV
+VVRDLSSAPDRATEADLLVPFLSTDSSSLAGVIGGSPAQVDELVQSLRRAGVVVDVVPLP
+PPWEAAMRRSVHVPLLAVIAGFALLGAQVVWRTTLRSRLLPAVTSHRLVGASPLRAARLG
+VRPAMLAWATAAASAGGVWLVAWPRWDAEIGLTGDTALLWSAVLVVDAILILGTTLSTLW
+VRRAHA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001971.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001971.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce0e393ee051825d2ec286f2247ccb252431a5a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001971.fa
@@ -0,0 +1,36 @@
+>NZ_CP033200.1_1658
+MSLTDAYVFDAVRTPFGKVGGALSGVRPDDMAAHVVRTLVDRAPGLEGLRAASAQAVADA
+AAGRPIEAGTDAAAPQRIDEVVFGNANGAGEENRNVARMATLLAGLPLSIPGTTVNRLCG
+SSLDAAIIASRQINTGEADVVLVGGVESMSRAPWVLPKTTRPFPMHDLAAANTTLGWRLI
+NDAMPPEWTVSLGEATELLRERFGISRERQDEFAARSHRLTARAWDEGRYDSLVAAVPGT
+DLERDETVRPDSTPETLAGLRTVFRRENGTVTAGNASPMNDGASAALLGSSTGADVLGLE
+PLARIAGRATAANEPDFFGYAPVEAVNRALSRAGIGWKDVAAVELNEAFAAQSLACTDAW
+GVDPEIVNAWGGAIAIGHPLGASGTRVLGTLARRLEASGERWGVAALCIGVGQGIAVVLE
+NVAAR*
+>NZ_CP040019.1_833
+MTLADAYVFDAVRTPFGKIGGKLAGTRPDDLAAHVIRTIVDRAPGLEGLRRESAQDVADE
+LKGRPIEAGTDRARPDRIDEVVFGNANGAGEENRNVGRMASLLAGLPVSIPGTTVNRLCG
+SSLDAAIIASRQINTGEADVMLVGGVESMSRAPWVLPKTSRPFPLHNLEAVNTTLGWRLI
+NDAMPKDWTISLGESTERLRERFGITRERQDEFAARSHQLTAKAWEEGRYDSLVAAVPGT
+DLERDETVRPDSTPETLAGLRTVFRKEDGTVTAGNASPMNDGASAALLGSEKGAEILGLQ
+PIARIAGRATAANEPDFFGYAPVEAVNLALKRAGIGWKDVAAVELNEAFAAQSLACLDAW
+GVDPEIVNAWGGAIAVGHPLGASGTRVLGTLARRLQDTGDRWGVAALCIGVGQGIAVVLE
+NVDAR*
+>NZ_CP083691.1_769
+MCVDRTSLARPRGRAYGEAMSLTDAYVFDAVRTPFGKIGGKLAGVRPDDMAAHVVRALVD
+RAPGLEGLRAESAQAVADAAAGHPIEAGTDAAAPQKIDDVVFGNANGAGEENRNVGRMAT
+LLAGLPLSIPGTTVNRLCGSSLDAAIIASRQINTGEADVVLVGGVESMSRAPWVLPKTSR
+PFPMHNLEAANTTLGWRLINDAMPSQWTVSLGEATEQLRERFDVSRERQDEFAARSHQLT
+AKAWDEGRYDDLVTVVPGTDLERDETVRPDSTPETLAGLRTVFRKENGTVTAGNASPMND
+GASAAFLGSEKGAEVLGLPPIARIAGRATAANEPNFFGYAPVEAANVALRRAGITWKDVA
+AVELNEAFAAQSLVCVDAWGVDPEIVNAWGGAIAIGHPLGASGTRVLGTLARRLQATGER
+WGVAALCIGVGQGIAVVLENVDAR*
+>NZ_CP097650.1_1875
+MSLTDAYVFDAVRTPFGKVGGALSGVRPDDMAAHVVRTLVDRAPGLEGLRAASAQAVADA
+AAGRPIEAGTDAAAPQRIDEVVFGNANGAGEENRNVARMATLLAGLPLSIPGTTVNRLCG
+SSLDAAIIASRQINTGEADVVLVGGVESMSRAPWVLPKTTRPFPMHDLAAANTTLGWRLI
+NDAMPPEWTVSLGEATELLRERFGISRERQDEFAARSHRLTARAWDEGRYDSLVAAVPGT
+DLERDETVRPDSTPETLAGLRTVFRRENGTVTAGNASPMNDGASAALLGSSTGADVLGLE
+PLARIAGRATAANEPDFFGYAPVEAVNRALSRAGIGWKDVAAVELNEAFAAQSLACTDAW
+GVDPEIVNAWGGAIAIGHPLGASGTRVLGTLARRLEASGERWGVAALCIGVGQGIAVVLE
+NVAAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001972.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001972.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3114830d8591544ee313cba4bf7a18853fda55a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001972.fa
@@ -0,0 +1,24 @@
+>NZ_CP033200.1_1659
+MTDDVDAPGARPASGGDVVRALASGLAVLRAFTPDTPTLSVSEAATAAGVTRATARRMLL
+TLTELGYAVQDGRRFALTPRVLELGHGYWSGRSVSEILRPILTQASQRLHQSCSAGVLHG
+AHLMYIARVHTERILRVNLDVGTRLPAFTTSMGRVLLADLPEDEACALLAGAPRTPATEH
+TLTDVDALMAELARVREQGHAVVTAELDAHLSSVAVPVRDAEGRVAVAINTALSLGPDHR
+DPGARRAALRTGARVPAPRTPEVAAAVVQALPVLRAAADDAEAALAALQR*
+>NZ_CP040019.1_832
+MLRSFTPGRPSLTVSDAAAAAGTTRATARRVLHTLVHEGYAVQEGRDFRLTPRVLELGHG
+YWTGTSLAEILSPVLTRASQELEQSCSAAVLDGPFLLYIARVHTERIIRVNLDVGTRMPA
+FLTSMGRVLLADLPPATVRRVLEAAPRTPRTPRTVTDVEALLEEIAQVRRQDHAVVTAEL
+DDHLSSVAVPVRGPDGAVVAAINTALPHRTPGAAEPSADEQTRAAVAQALPVLRAAARDA
+EDALVALRR*
+>NZ_CP083691.1_768
+MSLPSTEITSPAPGDGYVRALATGLAVLRAFTPDVPRLTLTEAADAAGVSRATARRSLLT
+LVELGYAVQDGRAFELTPKVLELGHGYWSGRSTSEVLRPVLTRASQRLHQSCSAGVLHGA
+HLMYIARVHTERILRVNLDVGTLLPAFSTSMGRVLLAGLDDAEVRRVLEGAPRTPATAQT
+LTDVDALLEEVRRVRERGHALVHGELDPNLSSVAVPVRDRDGRVVLAVNTALSTRRGRLG
+EALSPAAAEAAAAEALPVLREAADDAEAALELLGR*
+>NZ_CP097650.1_1876
+MTDDVDAPGARPASGGDVVRALASGLAVLRAFTPDTPTLSVSEAATAAGVTRATARRMLL
+TLTELGYAVQDGRRFALTPRVLELGHGYWSGRSVSEILRPILTQASQRLHQSCSAGVLHG
+AHLMYIARVHTERILRVSLDVGTRLPAFTTSMGRVLLADLPEDEACALLAGAPRTPATEH
+TLTDVDALMAELARVREQGHAVVTAELDAHLSSVAVPVRDAEGRVAVAINTALSLGPDHR
+DPGARRAALRTGARVPAPRTPEVAAAVVQALPVLRAAADDAEAALAALQR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001976.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001976.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d67c8da43f88b4f6b76de2ec79cfb1ead9f314e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001976.fa
@@ -0,0 +1,20 @@
+>NZ_CP033200.1_1742
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRALEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP*
+>NZ_CP040019.1_686
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRTLEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VGSFDIEVQSPDEFFMNQLDLDPARVMTALAAQASATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP*
+>NZ_CP083691.1_596
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRTLETMHPDMRASGAA
+RHRAEVMDAAFDDARVEGWEQLVLGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVSDVLERLVPCGAPLFA
+EAARAQLWRVDAERP*
+>NZ_CP097650.1_1965
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRALEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001992.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001992.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ec4ca2d4c36b346719b12fb3fd27a54bac4b014
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001992.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_25
+MSSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG
+GWDSFQRELQQTMRVNGLVNNVQVVNIPGAGGTIALGQLTTLEDANNLMVGGTGQIAAHA
+ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQSMDDLVTAWRADPAHVAWTGGGSFDQL
+VMADIARTADVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV
+VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFAPPGISAEERTELEALIAEAVDTPEWKEA
+VQRNYWNPVPLSGTELEEFIAAEKERIGTLTEEIK*
+>NZ_CP033200.1_1999
+MSSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG
+GWDSFQRELQQAMRVNGLVNNVQVVNIPGAGGNIALGQLTTLEDANNLMVGGTGQIAAHA
+ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQTMDDLVTAWRVDPAHVAWTGGGSFDQL
+VMADIARTAGVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV
+VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFAPPGISAEERTELEALIAEAVDTPEWKEA
+VQRNYWNPVPLSGTELEEFIAAEKERIGTLTEEVK*
+>NZ_CP097650.1_25
+MPSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG
+GWDSFQRELQQTMRVNGLVNNVQVVNIPGAGGNIALGQLTTLEDANNLMVGGTGQIAAHA
+ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQSMDDLVTAWRADPAHVAWTGGGSFDQL
+VMADIARTADVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV
+VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFVPPGVSAEERTELEALIAEAVDTPEWKEA
+VQRNYWNPVPLSGAELEEFIAAEKERIGTLTEEIK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001995.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001995.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d8ed45afbca40d482e1d5af1cec9c98a5885420
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001995.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_35
+MTVDARRLVDKLWSYVHVLRDDGVGVLDYTEQLTYLLFLKMAHERATRPLKPEQVLPEQY
+SWQRLMDARGQDLEAVYTGMLQGLSREPGVVGTIFRKAQNRIQDPAKLRRIIVDLIGAQQ
+WSQSGTDLNGDAYEAILARSASDGSSGAGQYFTPRALIEAIVDAVDPTVEDTVVDPAAGT
+GGFLLVAHDHASREASSMTPTQREKLRDDFVHGYELVDATARLAAMNLLLHGMGRYDGDS
+LIDVRDSLTSAPSRRWSVVLSNPPFGRKSSMTVVGDDGREVREDREIVRQDFVATTSNKQ
+LNFVQHIMTILDVNGRAAVVLPDNVLFEGGAGEVIRRKLLTDFHLHTLLRLPTGIFYAQG
+VKANVIFFDKKPARPGEVWTDAMAVYDLRTNKHFTLKQSPLRRADLDEFVSGYRRPEAQV
+GERWKTFTYDELIARDKANLDITWLRDETLEDMDNLPSPDVLAREIVEDLTAALAEFEAV
+AVSLEEQLSSADGTQEDR*
+>NZ_CP040019.1_202
+MPYAVRVITGDLKTKVDRVWNTFWTGGISNPLEVIEQMTYLLFLRRLDELHTAQEKRAAF
+MNGPIEDPKFTPEQDHLRWSRFRDLDPDTMFLTVSDAVFPFLREYGRQVGGEDSTYSAHM
+KDARFTIPNAGLLATVVDLVDQLPMADRDTNGDLYEYLLSKLASSGVNGQFRTPRHIIDL
+MVRMTAPTPADEICDPACGTAGFLVAASEFIREEHPQVLVDAQQREHFHRSMFHGYDFDS
+TMLRIGSMNMLLHGVESPDIRYRDSLSEGASADAEKYTLILANPPFTGSLDYDSTAADLQ
+RVVKTKKTELLFMALFLRLLKPGGRAAVIVPDGVLFGFTKAHREIRRLLVEEHLLEAVVK
+LPSGVFKPYAGVSTAILFFTKTGTGGTEDVWFYDVRADGFSLDDKRNRVEANDLPDVLER
+WRNRGAEADRARTEQSFLVPRQEIVDNGYDLSLNRYKEIEFEETEHRDPLEIIAELEQLD
+DEIRAGLAELKEMLR*
+>NZ_CP097650.1_181
+MHPIAYADPVITGELKTKVDRVWNTFWTGGISNPLEVIEQMTYLLFLRRLDELHTAAQRR
+AEFTGRPIEDAKFAPHQDHLRWSRFKELDPDTMFLTVSDSVFPFLREYGRQVGGEDSTYS
+SHMKDARFTIPNAGLLATVVDLVDQLPMADRDTNGDLYEYLLSKLQSSGVNGQFRTPRHI
+IDLMVRMTAPTPADEICDPACGTAGFLVAASEFVREEHPEALVDATQRRHFHRSMFHGYD
+FDSTMLRIGSMNMLLHGVESPDIRYRDSLSEGASADAEKYTLILANPPFTGSLDYDSTAA
+DLQRVVKTKKTELLFMALFLRLLKPGGRAAVVVPDGVLFGSTKAHREIRRLLVEEHLLEA
+VVKLPSGVFKPYAGVSTAVLFFTKTGTGGTEDVWFYDVQADGFSLDDKRNPVEANDLPDV
+LERWRNREGEAGRARTEQSFLVPKQEIADNAYDLSLNRYKEIEFEEAEHRDPLEIIAKLE
+KLDDEIRAGLAELKEMLK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001996.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001996.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0882d7a26d798335e906e13c616583dd9ecca190
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001996.fa
@@ -0,0 +1,39 @@
+>NZ_CP042169.1_117
+MPQGIFVSTTSTGAGKSLVSLGLADSLYRRSGTVGYFRPVVPGDDVETDPMVLLMREQYG
+LSPEQARGGLTAAEARTLMAEGRGDEVQQRCVEQYDAMRAAGGVVVVEGTDLISPDPAAD
+LDLNAQLARNLGTPVVAVVSGADLTPEQAADVVDLARRTLDDAGVELLAVMVNRADPRDL
+DAVGAAVRPGRHAWPVYVLPELTELAHPSVAEVADALGLEQMAGQETLDRDVAEVKAVSM
+EGGNFLEVLREGALVIVSGDRSDAILATVASSLTPDFPTPSGMILTNGILPNRQLQRLYL
+GAAFPVFVTHDDTFTTAAKVSRVRSELSSAQPRKTAAALGTWHQRVDGDELLARFDLPRT
+DVVTPLRFLHELISRARADRRRIVLPEGEDARVLRAAEILQRRDVCDLVVLGPAAAVREL
+ASREGVDLSGIELVDPADSPDLERYAQEYARLRAHKGVDAERAREVMQEGAYFGTMMVHL
+GDVDGMVSGAAHTTANTIRPALEFVKTKPGVSIVSSVFFMLLPDRALVYGDCAVNPDPDA
+QQLADIAVASAATAAQFGVDPRVAMLSYSTGASGSGQSVDKVRAATELVRERAPELKVEG
+PLQYDAAVNASVAASKMPGSEVAGQATVFVFPDLNTGNNTYKAVQQSSGAVAVGPVLQGL
+NKPVNDLSRGTTVEDIVNTVAITAIQAQAQG*
+>NZ_CP083691.1_186
+MPQGILVTTTTAGAGKSLVSLGLADSLYRRSGTVGYFRPVVPGDDVEADPMVLLMREQFG
+LTAEQARGGITAAEARSLMAEGRGDELQERCVEVYDRMARECGVVVVEGTDLTGADAAAD
+LELNAGLALNLSTPVVAVVSGAGLGAQEAADAVDLTRHALAEAGADLLAVMVNRADAGRL
+DEIAEAIRPGRRSWPVYVLPELPELAHPSVAEVAAALDLEQVAGRPTQDRDVTEVKAVSM
+EGGNFLEVLREGALVIVSGDRSDAILATLASSLTPDFPTPSGMILTNGILPNAQLQRLYQ
+DAAFPVLATDDDTFGTAADVSRVRSELSSAQPRKTAAALGTWHQRVDGDELLQRIDLPRT
+DVVTPLRFLHDLIERARADRRTVVLPEGEDARVLRAAEILQRRDVCDLVVLGGEAEVREL
+ASREGVDLTGITLVDPATSEDRERYAAEYRRLRSHKGVDLERAREVMLEGAYYGTMMVHL
+GDADGMVSGAAHTTANTIRPALEFVKTKPGVSIVSSVFFMLLPDRALVYGDCAVNPDPDA
+RQLADIAAASAETAAQFGVDPRVAMLSYSTGASGSGDAVDKVRAATELVRAAHPELKVEG
+PLQYDAAVNASVAASKMPGSEVAGQATVFVFPDLNTGNNTYKAVQQSSGAVAVGPVLQGL
+NRPVNDLSRGTTVEDIVNTVAITVIQAQTGSPQPTPKDAP*
+>NZ_CP097650.1_125
+MPQGIFVSTTSTGAGKSLVSLGLADSLYRRSGTVGYFRPVVPGDDVETDPMVLLMREQYG
+LSPEQARGGLTAAEARTLMAEGRGDEVQQRCVEQYDAMRAAGGVVVVEGTDLISPDPAAD
+LDLNAQLARNLGTPVVAVVSGADLTPEQAADVVDLARRTLDDAGVELLAVMVNRADPRDL
+DAVGAAVRPGRHAWPVYVLPELTELAHPSVAEVADALGLEQMAGQETLDRDVAEVKAVSM
+EGGNFLEVLREGALVIVSGDRSDAILATVASSLTPDFPTPSGMILTNGILPNRQLQRLYL
+GAAFPVFVTHDDTFTTAAKVSRVRSELSSAQPRKTAAALGTWHQRVDGDELLARFDLPRT
+DVVTPLRFLHELISRARADRRRIVLPEGEDARVLRAAEILQRRDVCDLVVLGPAAAVREL
+ASREGVDLTGIELVDPADSPDLERYAQEYARLRVHKGVDAERAREVMQEGAYFGTMMVHL
+GDVDGMVSGAAHTTANTIRPALEFVKTKPGVSIVSSVFFMLLPDRALVYGDCAVNPDPDA
+QQLADIAVASAATAAQFGVDPRVAMLSYSTGASGSGQSVDKVRAATELVRERAPELKVEG
+PLQYDAAVNASVAASKMPGSEVAGQATVFVFPDLNTGNNTYKAVQQSSGAVAVGPVLQGL
+NKPVNDLSRGTTVEDIVNTVAITAIQAQAQG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001998.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001998.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67d20dcdb7d8ca2e0e41384844434faf9c17488c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001998.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_160
+MYIHKQKLQHVSSPEKPDAVYARKLQEVIGGQYGEITVAMQYSFQAWNAHIPGKYRDLLF
+STAAEEFGHVEMLATMVAQLLEKAPVGITTDAIQDDPAVAAVIGGTDLQQAIVAGAGARP
+VDSMGNPWTGAYVTASGNLLADMTANLNAEMQGRTQVARLYHMTDDPGIRELLSFLLARD
+TMHQNQWAAAVKELQEDGLEEMPVPSNFPQKKEATEHSYTHYEFSDGQATAEGSWAAGPT
+PDGKGEFSYSSEPPAGVPMPPPTHPDSRFYGTTEVPNRVEKLAGTVQDKLHRE*
+>NZ_CP042169.1_2022
+MYIHKQKLQHVSSPEKPDAVYARKLQEVIGGQYGEITVAMQYSFQAWNAHIPGKYRDLLF
+STAAEEFGHVEMLATMVAQLLEKAPVGITTDAIQDDPAVAAVIGGTDLQQAIVAGAGARP
+VDSMGNPWTGAYVTASGNLLADMTANLNAEMQGRTQVARLYHMTDDPGIRELLSFLLARD
+TMHQNQWAAAVKELQEDGLEEMPVPSNFPQKKEATEHSYTHYEFSDGQATAEGSWAAGPT
+PDGKGEFSYSSEPPAGVPMPPPTHPDSRFYGTTEVPNRVEKLAGTVQDKLHRE*
+>NZ_CP033200.1_1737
+MYIHKQKLQHVSSPEKPDAVYARKLQEVIGGQYGEITVAMQYSFQAWNAHIPGKYRDLLF
+STAAEEFGHVEMLATMVAQLLEKAPVGITTDAIQDDPAVAAVIGGTDLQQAIVAGAGARP
+VDSMGNPWTGAYVTASGNLLADMTANLNAEMQGRTQVARLYHMTDDPGIRELLSFLLARD
+TMHQNQWAAAVKELQEDGLEEMPVPSNFPQKKEATEHSYTHYEFSDGQATAEGSWAAGPT
+PDGKGEFSYSSEPPAGVPLPPPTHPDSRFYGTTEVPNRLEKLAGTVQDKLHRE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002004.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5c7934aa309759b2e83162fa442a7e14bdd5c8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002004.fa
@@ -0,0 +1,9 @@
+>NZ_CP042169.1_355
+MKTIRTIAFILFLCATAFGVMLTLHYLPIPEILPSEITSWVPARDTADATWLIVGMVVAV
+VATAVGFSASHKAVERETQVTS*
+>NZ_CP040019.1_2539
+MKTIRTIAFILFLCATAFGVMLTLHYLPIPEILPSEVTSWVPARDTADATWLIVGMVVAV
+VATAVGFSASHKAVERETQVTS*
+>NZ_CP097650.1_362
+MKTIRTIAFILFLCATAFGVMLTLHYLPIPEILPSEITSWVPARDTADATWLIVGMVVAV
+VATAVGFSASHKAVERETQVTS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002006.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bf3d134c18d9fd40bdc0a90cab7dd0382fd1228
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002006.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_395
+MGTMPTSSALPRTTPDDVPERLLVLPAAQDVAGTPYAHARRLAEQAVADVGGTVVAEGDA
+SATALLMVRPIPVEALAAALAAHPHVSWVQFPFAGIEPFIPLVRSRPDIVWTSAKGTYAP
+PVAEHALLLTLALLRDLPARVRATTWGPSSGRTLNGLNAVVVGGGGIAQEYVRLLKTWDV
+HVTAVRRRAGDVPGADRTVTTDSLDEVLPGAQVVMIAAAATDETRGLFDADRLALLNEDA
+VLVNIARGTLVDTDAVVRALAAGRLHGYGTDVTDPEPLPEGHPLWTEERALITPHTADTP
+QMCVPLLHARVERNLRARAAGTELEGLVDAEGGY*
+>NZ_CP033200.1_124
+MGTMPTSSALPRTRPDDVPERLLVLPAAQDVAGTPYAHARRLAEQAVADVGGAAVAEGDT
+SATALLMVRPIPVDALAAALTAHPHVSWVQLPFAGIEPFVPLVRSRPDIVWTSAKGTYAP
+PVAEHALLLTLALLRDLPARVRATTWGPSSGRTLNGLNAVVVGGGGIAQEYIRLLKTWDV
+HVTAVRRRAGDVPGADRTVTTDRLDEVLPGAQVVMIAAAATEETRGMFDADRLALLDEDA
+VLVNVARGALVDTDAVVQTLAAGRLHGYGTDVTDPEPLPDGHPLWTEERALITPHTADTP
+EMCVPLLHARVERNLRARAAGTELEGLVDAEGGY*
+>NZ_CP097650.1_398
+MGTMPTTSTLPRTRPDDVPERLLILPAAQDVADTPYAHARRLAEQAVADVGGTAVAEGDT
+SATALLMVRPIPVDALAAALAAHPHVSWVQLPFAGIEPFVPLVRSRPDIVWTSAKGTYAP
+PVAEHALLLTLALLRDLPARVRATTWGPSSGRTLNGLTAVVVGGGGIAQEYIRLLKTWDV
+HVTAVRRRAGDVPGADRTVTTDRLDEVLPGAQVVMIAAAATEETRGMFDADRLALLDEDA
+VLVNVARGALVDTDAVVQTLAAGRLHGYGTDVTDPEPLPDGHPLWTEERALITPHTADTP
+EMCVPLLHARVERNLRARAAGTELEGLVDAEGGY*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002007.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4fc156c33fc92c676f8a4302e4e00ac8726f4b56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002007.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_432
+MTAITVVGGTGYAGAAIVAEAARRGHTVTAISRTAPGTQAESVRYVTGDLTRSVPDIAGA
+EVVVAALSPRGDNAGKLRDAYRSLAQAAATNGARFVGIGGFSSLRPAQGAPRFVEGDDLP
+PEFAAEAREMNDILTDLATGSVDVDWLFVSPAAEFGSHAPGEALGRYRVSGEVALFDQDG
+KSAISGADFARAVLDEIETPTRHRAQIHFAY*
+>NZ_CP040019.1_2456
+MTAITVVGGTGYAGAAIVTEAARRGHTVTAISRTAPGTQAEGVDYVTGDLTQSVPDIAGA
+EVVVAALSPRGDNAGRLRDAYRSLAQAAATNGARFVAIGGFSSLRPAEGAPRFVEGDGLP
+PEFAAEAREMNDILADLATGSVDVDWLFVSPAAEFGSHVPGEALGRYRVSGEVALFDQDG
+KSAISGADFARAVLDEIETPTHHRAQIHFAY*
+>NZ_CP083691.1_2435
+MKIAVIGATGMVGSRVVAEARARGHEVAAGSRSGSRQDGWFDVDVADTAAVARVIEDNDI
+TVLAVPPVRTGDGDVTAIRRSHQALIAAAPQGRFIVVGGAGALQLPDGSLLKDSAEFPAE
+YKAESDVFGDILEDYRASQGLAWTMLAPAPMIAPGERTGAYKTETDIPAGETVSAEDFAV
+ALVDEAESGAHRGTRFTVAN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002010.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa86c67b867b856b616e5483581ba2914c019229
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002010.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_477
+MGVPVDRARRLLGAVIVAQMLPEGVVVKGGNGVRLRHGATGTRATRDLDLLARDPQQALK
+DLTGFVDRGWGAAPGSKRELKADPAATRVAFFGTVHEDDPAEPLGVPDPYVLSRAKVTLH
+FLSARTSWVSVPIEIGRDEFEGSTLAQPVEVVAPQVAEAVTALGCGTPRSVAVMAVEQQL
+AQKIHAVTDPHQTRGHDLVDIQLLWHGAEAEGGVDIPLLADLVSRTFMFRSPGRTAAGHT
+PHEWPPPVAHVRTLEQGYLDALEETRVGAEGQARLLQPRVSDAADWLESLITRIARAAGA
+EGSGAQG*
+>NZ_CP033200.1_207
+MGVPVDRARRLLGAVIVAQMLPEGVVVKGGNGVRLRHGATGTRATRDLDLLARDPQQALK
+DLTGFVDRGWGAAPGSKRELKADPAATRVAFFGTVHEDDPAEPLGVPDPYVLSRAKVTLH
+FLSARTSWVSVPIEIGRDEFEGSTLAQPVEVVAPQVAEAVTALGCGTPRSVAVMAVEQQL
+AQKIHAVTDPHQTRGHDLVDIQLLWHGAEAEGGVDIPLLADLVSRTFMFRSPGRTAAGHT
+PHEWPPPVAHVRTLEQGYLDALEETRVGAEGQARLLQPRVSDAADWLESLITRIARAAGA
+EGSGAQG*
+>NZ_CP097650.1_476
+MGVPVDRARRLLGAVIVAQMLPEGVVVKGGNGVRLRHGATGTRATRDLDLLARDPQQALK
+DLTGFVDRGWGAAPGSKRELKADPAATRVAFFGTVHEDDPAEPLGVPDPYVLSRAKVTLH
+FLSARTSWVSVPIEIGRDEFEGSTLAQPVEVVAPQVAEAVTALGCGTPRSVAVMAVEQQL
+AQKIHAVTDPHQTRGHDLVDIQLLWHGAEAEGGVDIPLLADLVSRTFMFRSPGRTAAGHT
+PHEWPPPVAHVRTLEQGYLDALEETRVGAEGQARLLQPRVSDAADWLESLITRIARAAGA
+EGSGAQG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002011.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002011.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d23c8cfbd19a6a4e7fb305515af1d43043efd116
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002011.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_493
+MASFDILYIRPAGSGWGPVHELVQLTRRLFDARLIEVDDTGDVNRLQRASALLPRGPRVR
+DRHLLVMGPQPAAIAHVAHPRLWLPGYRSVAVWIIDSFWTDRTPRLLRDRPHVDRLFITD
+PQLVSEWSGQTGLPVGVLPWGSDTTRFTSAQEGTDRPVDVLRVGRQPRAWSDDARTSRDA
+AAHGLHFAGRPPFSDDPARNQMLVREAMGRARVVLAFSNLVSPAPYTHPTRDYLTGRWTD
+ALAAGCLVAGTAPASAASLLWPGATVEISPTSRDDAWPVLAQLASEWTPQAAADRQSEAR
+RRLDWRYRLRDLCMAMDWAVPDRLTAELATL*
+>NZ_CP033200.1_227
+MSVDVLYVRPGGSGWGPVDVLARLAARLLEGRLVEVEDRGAASWAQRASVLLPRGRRARG
+RRLLVLAGNPAALALAARRDLWWPGHESTAAWIVDSFWTDRIAGIARHRPHFDRLFVTDP
+DLVDEWSALTGRPVDALPWGSDTLAVAADDGPRPVDLLRLGRQPEAWDDDARTAREAQDH
+GLVFRGRPPSSPDPLQNQEAVRAALAQARLVLAFSNLVSPAPYTHPTRDYLTGRWTDALA
+AGCRVAGVAPRSAATLLWPEATLEVSPNSRAEAWPVLAEAAAAWTPERAAEQRRRARREL
+DWRLRLQRLCTAMGWPLPPTLDAELAALG*
+>NZ_CP040019.1_2390
+MTLDILYVRPRGSGWGPVAELVALAARLFDARVAVVDDHGEVSLFRKTAASLPRGRRRPG
+HHLLVVAPHAGMAAYAARPRLWFPGYDSTAVWVIDSFWTDRTPRLLRGTAHVDRVFITDP
+QLVEEWEQITGTPVSVLPWGADTALYPSAAHHRDIDLLRLGRQPKAWADDDATAADARRR
+GLRFAGRPPMNDDPGQNQHNVREALMGAKLVLAFSNLVSPAPYTHPTRDYLTGRWMDALA
+AGCLVAGTAPAAATSTLWDGATLEISPTSREDAWPVLTAAAEGWSPERAAEQQERARRTL
+DWRWRLRQMSSVMGWPEPPRLTQELERLISSPQQG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002015.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35219c81bc1350ddfa5433139b92422ec682a13d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002015.fa
@@ -0,0 +1,9 @@
+>NZ_CP042169.1_563
+MTKSNEESGSDFNSMVAAEVRAWLARSGKRQADLAAALGVSQSGISHRLRARVAFTLEEL
+ATIAEVFDITLAELLGPVILQARRSPHTDMVGAGASGSLPRLDSNQQPFD*
+>NZ_CP042169.1_564
+MSNHTRCVRSNLAAEISRRDLTQARAAALAGLTPDGLSKRMSGQVEFRLGELLELARVLG
+VPFATLVAGIDAADEQLAEA*
+>NZ_CP033200.1_305
+MTNSNEESGSDFNSMVAAEVRAWLARSGKRQADLAAALGVSQSGISHRLRARVAFTLEEL
+ATIAEVFDITLAELLGPVILQARRSPHTDMVGAGASARLPRLDSNQQPFD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002019.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002019.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8dee52351d11f5083b22f89818eb1982db5fd03c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002019.fa
@@ -0,0 +1,11 @@
+>NZ_CP042169.1_591
+MTMIKEPGVSPTAGLGPAAALFHGFSDPTRLAILRHLATGEHKVRELTEHLGLAQSTVSA
+HLACLTGCGLVSSRPVGRASLYSLAAEPELLEVLAAAERLLTVTGHAVELCPHSGPAATG
+ALPHDAGH*
+>NZ_CP033200.1_1729
+MSPAAGLGPAAALFHGFSDPTRLAILRHLATGEHKVRELTEHLGLAQSTVSAHLACLAGC
+GLVASRPVGRASLYALAAEPELLQVLAAAERLLTVTGHAVELCPHSGTPGPDGPAAA*
+>NZ_CP083691.1_687
+MIQEKGATLDEVATVAYAHLFQAFAEPTRLAIVQHLASGEHRVRDLVEHMGLAQSTVSKH
+VGFLVECGLATMRPEGRSTWYSLAQSELLRTLIAAAERLLDATGTQALLCTHLRLPHTHH
+ASDTDKK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002020.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91816ceb6eb9025bb1e1a886e6588e1dccb083e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002020.fa
@@ -0,0 +1,39 @@
+>NZ_CP042169.1_679
+MHRLGPELQGILAWCRSRGVPTAFWNKEDPVHFNTFLTAAGEFDAVFTTDLDCVPRYKRE
+LGHENVHFLPFAAQTAQSNPVEVFDRVEGCAFAGAYYAKYPERLADLRELSAELSADGRR
+FDIYDRNHGRATSGYTFPEDYQRYIVGGALTPGLLDVPYKGYTVNLNLNSVKQSQSMFAR
+RVFELLASNTLTVSNFSRGLRLMFGDLVVSTDSGRQMRRRLEAIEAQPNGNERLRAVALR
+KVLREHTYTERLEFVASRSGVTLPDAAVERPLMVVPSTLGRDAAAVVELVRRWAGQTWND
+WVLAVQGKVEEFAPMPLELQDPRVVLFDELADLDGLARTRGCTLAGMLDPNDWYGPHYLE
+DMVLTLRWADVKTCGHVEHYAVDSVDGSLERRELGTAWRLQDKILPCRSLSRLDWAQVAD
+CNGVARQLDAAQLSGLAVSPLEYCAGGATSEEPALAPASSLDVYEGLTLTEIRQHADDLV
+FAESSDDMPVMDLGTIFEGMKSFDEMTLTWEDGVPRVTSSLGAGRHQYWINSLARPVEFH
+QNGNDQPVYFDVSVGLDIMLVAYWLDADGQRFGHAMIPARQYTTVKIPEQARAMRWGLRV
+SGSGSAVVHRVVNGPYVAPSVPMLAGSSDVLITNIYPAYDNLYRNGFVHSRLRRYREMGH
+RLETILVGEGDGPRFREFEDVDVAVLRVQDLIATLATGEVKTLVVHCLLPETWNVLKATS
+DLPPTTVWVHGFEIQPWWRRRFNYATEEELDAAKMLTEQRLAMWREVFDSSPDNMHFIFV
+SRWFAETVFEDVGIRLPDHRYSVIHNPIDDTVFPYQEKTAQHRLRVLSIRPYHSHVYAND
+LAVAAVLELSNEPWFNELDFTFIGDGPLFEETLAPLWDFENVLIRKGFLTHAEIASEHAR
+HGVLLVPTRSDTQGVSRDEAMSSGLVPITSAVAAIPEFVDEEVAFLAPPEDHRALADAVR
+TLRAEPARYLRMSAAAARRVRRQSGADHVLDAELRLAFRTDGDHSAPSVRPHPEREAHRP
+*
+>NZ_CP042169.1_861
+MLRAVFDTLPQDSDAVRRLRAAAAPPRRRRTSPPRPAAPAGAHGDTPGYRGYLHLADVGD
+TYTAQEASTLLQLENAALKRRLFAEPAPPLPPTGHEDEDLAAAPRRVADHLARADAADQL
+GDDAPRHLVVVGVYPTLENPYGNGFVHRRVKYFQAAGVRVDVAVIDRSAEPRSYEYDGVH
+VLVGRGAEAAEMLRTRHYESVAAHFLVRSLWEPIQDALAGHRFFVFMHGFESRRWIRTVR
+NHRTQGQVDDAIVDTLERQRFWREVLEHPHGPERFVFVSRWWRRAAQEDMELVFPGQRTA
+IVHNVIDTDLFRFVPKDPEQRFRVLWVRSAANLNYGADLAVRALERLRDTPLWDRMQVTV
+IGDGKHFGLFEAAFADDANVTVERRYAVQEEIAALHREHGVFLVPTRLDSQGVSRDEAMA
+SGLVPVTNDAGAVREFVDEDCAMIAGVEDVAGLADGLRRLMEDPDLFLRMSQAAAARVRA
+QTSPEHTVDHEMALMGLAAGPGGRGEENA*
+>NZ_CP033200.1_592
+MLRAVFDTLPQDSDAVRRLRAAAAPPRRRRTSPPRPAAPAGAHGDTPGYRGYLHLADVGD
+TYTAQEASTLLQLENAALKRRLFAEPAPPLPPTGHEDEDLAAAPRRVADHLARADAADQL
+GDDAPRHLVVVGVYPTLENPYGNGFVHRRVKYFQAAGVRVDVAVIDRSAEPRSYEYDGVH
+VLVGRGAEAAEMLRTRHYESVAAHFLVRSLWEPIQDALAGHRFFVFMHGFESRRWIRTVR
+NHRTQGQVDDAIVDTLERQRFWREVLEHPHGPERFVFVSRWWRRAAQEDMELVFPGQRTA
+IVHNVIDTDLFRFVPKDPEQRFRVLWVRSAANLNYGADLAVRALERLRDTPLWDRMQVTV
+IGDGKHFGLFEAAFADDANVTVERRYAVQEEIAALHREHGVFLVPTRLDSQGVSRDEAMA
+SGLVPVTNDAGAVREFVDEDCAMIAGVEDVAGLADGLRRLMEDPDLFLRMSQAAAARVRA
+QTSPEHTVDHEMALMGLAAGPGGRGEENA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002022.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002022.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f971a6bf7b851568ae5b86b48998809fac655ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002022.fa
@@ -0,0 +1,11 @@
+>NZ_CP042169.1_783
+MTDSPIAADRDGIRYLSGAIPAADDVRALYDAVGWSAYTADMDTLMGGLQGSATVVTAFD
+GGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIASELLRRVFARFGQVRQHVLLTDTEE
+RQRAFYEAHGFRESHDVEGDELRAFVRFQSRDG*
+>NZ_CP033200.1_524
+MTDSPIAADRDGIRYLSGVIPAADGGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIAS
+ELLRRVFARFGQVRQHVLLTDTEERQRAFYEAHGFRESRDVEGDELRAFVRFQSRDG*
+>NZ_CP097650.1_751
+MTDSPIAADRDGIRYLSGAIPAADDVRALYDAVGWSAYTADMDTLMGGLQGSATVVTAFD
+GGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIASELLRRVFARFGQVRQHVLLTDTEE
+RQRAFYEAHGFRESRDVEGDELRAFVRFQSRDG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002024.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002024.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95ca9c029c24cc1b97f0e395212a046186f1122e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002024.fa
@@ -0,0 +1,14 @@
+>NZ_CP042169.1_858
+MSGNVFTAASADVAEDAVLGDGTKVWHLAQVREQARLGERCIVGRAAYIGTGVELGDDCK
+VQNLALVYEPARLGRGVFIGPGVVLTNDTYPRAVNPDLSQKSGDDWEAVGVDIGDGAAIG
+ARSVCVAPVRIGEWALVAAGSVVTRDVPDFGLVAGVPAKRIGWVGRTGRRLEEKDGVWVC
+PDTGETFIERDGALRPAEPAQEEENHG*
+>NZ_CP033200.1_589
+MSGNVFTAASADVAEDAVLGDGTKVWHLAQVREQARLGERCIVGRAAYIGTGVELGDDCK
+VQNLALVYEPARLGRGVFIGPGVVLTNDTYPRAVNPDLSQKSGDDWEAVGVDIGDGAAIG
+ARSVCVAPVRIGEWALVAAGSVVTRDVPDFGLVAGVPAKRIGWVGRTGRRLEEKDGVWVC
+PDTGETFIERDGALRPAEPAQEEENHG*
+>NZ_CP040019.1_1193
+MSKLRMLSRMPKKGRFMFIISGGDRARYMSRKGLVRGMGENVWFQPRALPNDPNLIRFHN
+NIVVASGVTFVAHDVINLMIGRKNGVRLPVNEDCIEVMDDVFIGSGSVILPGVGIGPRAI
+IAAGTVVTKDVPPDSIVRGVPAKRLGDFSVLEAQRLADAGRFDGMTRAQIDDVLWE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002030.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..719397b280f9fa543b06677edced597452b72155
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002030.fa
@@ -0,0 +1,9 @@
+>NZ_CP042169.1_1001
+MARHGRDEDEAHEAPAGAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVIGCA
+MMGFALGIAWMYVERGRDGRDR*
+>NZ_CP033200.1_724
+MARHGRDEDEAHEAPAGAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVIGCA
+MMGFALGIAWMYVERGRDGRDR*
+>NZ_CP097650.1_942
+MARHGRDEDEAHEAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVLGCAMMGF
+ALGIAWMYVERGRDGRDR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002034.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002034.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5a65a000bad524794052df5f933494271289e8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002034.fa
@@ -0,0 +1,9 @@
+>NZ_CP042169.1_1271
+MTRARLEGAVMDLLWDHAEGLTAAEVRTLLHREGAPPALTTVHTALTRLAAKGRVRPAEG
+GRPRRFRAAVTREAHTAELLRDLLGSAPDREAVLAAFVGGISETDSAALRRLLD*
+>NZ_CP040019.1_1552
+MTRARLEGAVMDLLWDHAEGLTAAEVRTLLHREGAPPALTTVHTALTRLAAKGRVRPAEG
+GRPRRFRAAVTREAHTAELLRDLLGSAPDREAVLAAFVGGISETDSAALRRLLD*
+>NZ_CP083691.1_1446
+MARARLEGAVLDALWDHPDGLTAQELRVRLEREDGAPAVTTVLTALSRLTAKGHVRRVGA
+RRPQVFAAARTREQHAAGLLQDILGSSPDHEAVLAAFVGGISDADAAALRRLLT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002041.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..706eb7fe090d4412d5c8f780c6885c35a09c147d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002041.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_1544
+MTDSPLHLDRPDAPRIIVLGATGYAGSLVVDALVAQGARPVLAGRNRDSLQHAARRHDGL
+EVAVADAGDPASLRALVTEGDVLVSTVGPFERYGRPVARAAAERGAHYVDSTGEVGFVKD
+LKADLDATARRTGATLLPALGFDYAPGMLAGGLALAQAGGRARSLQIGYFADGELDPRVD
+LSHGTRQTMVDALTERTITWRGGRLATTGPASRSAVFRVDGQDRRGVLFGGTESLFLPRM
+QPGLDEVEVFNGWFPARPTQIGAAALGAVGWLPGVARGVQALLRPLAGDPGGPDAADRAR
+TGSRVGAIARDAAGRVVADVHLRGPNAYTLTGDLMAWGARQLAAGRALEAGVVSPIQAFG
+LDDFETACAAVGLVRA*
+>NZ_CP033200.1_1267
+MTDSPLHLDHPDAPRIIVLGATGYAGSLVVDALVAQGARPVLAGRNRDSLQHAARRHDGL
+EVAVADAGDPASLRALVTEGDVLVSTVGPFERYGRPVARAAAERGAHYVDSTGEVGFVKD
+LKADLDATARRTGATLLPALGFDYAPGMLAGGLALAEAGGRARSLQIGYFADGELDPRVD
+LSHGTRQTMVGALTERTITWRGGRLATTGPASRSAVFRVDGQDRRGVLFGGTESLFLPRM
+QPGLDEVEVFNGWFPARPTQIGAAALGAVGWLPGVARGVQALLRPLAGDPGGPDAADRAR
+TGSRVGAIARDAAGRIVADVHLSGPNAYTLTGDLMAWGARQLAAGQAREAGVVSPIQAFG
+LDDFETACTAAGLVRA*
+>NZ_CP097650.1_1471
+MTDSPLHLDHPDAPRIIVLGATGYAGSLVVDALVAQGARPVLAGRNRDSLQHAARRHDGL
+EVAVADAGDPASLRALVTEGDVLVSTVGPFERYGRPVARAAAERGAHYVDSTGEIGFVKD
+LKADLDATARRTGATLLPALGFEYAPGMLAGGLALAQAGGRARSLQIGYFADGELDPRVD
+LSHGTRQTMVDALTERTITWRGGRLATTGPASRSAVFRVDGQDRRGVLFGGTESLFLPRM
+QPGLDEVEVFNGWFPARPTQIGAAALGAVGWLPGVARGVQALLRPLAGDPGGPDAADRAR
+TGSRVGAIARDAAGRVVADVHLRGPNAYTLTGDLMAWGARQLVAGRAREAGVVSPIQAFG
+LDDFETACAAVGLVRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002043.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7148a6d3c912dffee7441cff9d2c4205954d966c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002043.fa
@@ -0,0 +1,8 @@
+>NZ_CP042169.1_1566
+MRLVWDRSAWEDYTHWQTTDRKVLNRINTLIDAALRDPFEGIGKPEQLKYGAAGAWSRRI
+TEEHRLVYLVDGEDLIILQARYHY*
+>NZ_CP033200.1_1287
+MRLVWDRSAWEDYTHWQTTDRKVLTRVNTLIDAALRDPFEGIGKPEQLKYGAAGAWSRRI
+TEEHRLVYLVDGEDLIILQARYHY*
+>NZ_CP083691.1_1165
+MTRKPSGPFGPPLAPASAAAIARRAAGAWSRRITAEHRLVYLVDGEDLIILQARYHY*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002047.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b64383050ed17e9c04697575b3e6260cab6175eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002047.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_1573
+MKTPVLSATDMRIVEQVLDMGDGYVLDFSNRTFADFFADLDVEIEPEDSGLSKAKRLRAF
+FRSASTSECARVLHALLEYRGEQDGDDESASIDKYRAIVSRLEGVAVPLSAAPVAPEVLT
+LAYVRELSDKAERRLAASDLEGAITVSRTLVEAVLEQLEIRLTGQSGNYAGDLQRQYKAV
+AKILRIDDKDDQVDEGFKQIARGLVQIVNGLAAIRNMASDGHARHVQPQARHARVAVNSA
+KTVASFLVEVYLAKRTGPTSPAAVRSGG*
+>NZ_CP033200.1_356
+MASTSPTLLPFRIDSLATSLFAKETGFSGPHLHDFFARYTDMLGPYRWNGSPSRWQIFQT
+GLHSLPLPQQRAVLLELCSYDGEFKNGRPPEGELTRLRGMLLSAGTPGAHAAQESLQKLE
+DWEAVNRSWQAALTKVQDDPDGAITATRTTIESVCKHICDERGVKYEDGWDLARLYKATS
+SAMQVAPDQHSEQIIKQILSGAATLVGGLAAMRNALSDAHGRGKRSVGPAPRHAKLAVNA
+GFAIAGFLIDTHVEKPPVSS*
+>NZ_CP083691.1_2155
+MASTSPTLLPFRIDSLATSLFAKETGFSGPQLHDFFARYTDVLGPYRWNGSPSRWQIFQT
+GLHSLPLPQQRAVLLELCSYDGEFKNGRPPEGELTRLRAMLLSAGTPGAQAAQESLQKLE
+DWEAVNRSWQAALTKVQDDPDGAITATRTTIESVCKHICDERGVKYEDGWDLARLYKATS
+SAMQVAPDQHSEQIIKQILSGAATLVGGLAAMRNALSDAHGRGKRSVGPAPRHAKLAVNA
+GFAIAGFLIDTHVEKPPVSS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002051.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002051.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9616fbabd995ffa1928e48ece64ecc8194fa0185
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002051.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_1906
+MAHASTHPAHPLPPVAPRRLLLAQRLLRGEGSVEVTAFRAGETLTTAVHGVSADGRLVVA
+HVPNLLGSLGAFHTPAPLDVRVDVLRDALDLTLPTRLASAHLLGTLRWCRDSAEVAALKL
+RGRVADLVADVGPRVRVGVVETQRILLHDVDGVAVFCRHTLPLTSRGLVDQAELADLADD
+VLGTAPEVLADLADAVALGLLPGESTPLQVDAEPLPEPPAHALDADEAGVTLLRVRDGET
+TAVHVALPGAGRLDHSPRHAWRRLLDAIPARVAHP*
+>NZ_CP033200.1_1611
+MAHASTHPAHPLPPVAPRRLLLAQRLLRGEGSVEVTAFRAGETLTTAVHGVSADGRLVVA
+HVPNLLGSLGAFHTLAPLDVRVDVLRDALDLTLPTRLASVHLLGTLRWCRDSAEVAELKL
+RGRVADLVADVGPRVRVGVVETQRILLHDVDGVAVFCCHTLPLTSRGLVDQAELADLADD
+VLGTAPEVLADLADAVALGLLPGESTPLQVDTEPLSESPAHALDVDEAGVTLLRVRDGET
+TAVHVALPGAGRLDHSPRHAWRRLLDAIPARVAHP*
+>NZ_CP097650.1_1833
+MAHASTHPAHPLPPVAPRRLLLAQRLLRGEGSVEVTAFRAGETLMTAVHGVSADGRLVVA
+HAPNLLGSLGAFHTLAPLDVRVDVLRDALDLTVPTRLASVHLLGTLRWCRDSAEVAELGL
+RGRVADLVADVGPRVRVGVIETQRILLHDVDGVAVFCRHTLPLTSRGLIDQAELADLADD
+VLGTAPEVLADLADAVALGLLPGESTPLQVGTGPLPESPAHALDADEAGVTLLRVRDGEA
+TAVHVALPGAGRLDHSPRHAWRRLLDAIPARVAHP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002052.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d1810f90da875256bf46cb950b431b2e482daa1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002052.fa
@@ -0,0 +1,9 @@
+>NZ_CP042169.1_1907
+MTTAVRTCAASACAFNAETSCSALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH
+RLECTYNADLACTAEGIEVTDVATCATYTID*
+>NZ_CP033200.1_1612
+MTTAVRTCAASACAFNAETSCNALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH
+RLECTYNVDLACTAEGIEVTDVATCATYTID*
+>NZ_CP097650.1_1834
+MTTAVRTCAASACAFNAETSCNALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH
+RLECTYNADLACTAEGIEVTDVATCATYTID*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002054.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1dc406bbcc3c8d1f38f1d815a1edfa3adfcf71a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002054.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_1910
+MTEQYDILIVGGGNAGVSLAAALRRKRQGRVAIADGQQLHRYRPMLNYAAGGQADMARFE
+RPMRAVIPDGVEWIPDHVVAVDAEERTAVTSTGLTVGFRHLVLCPGLTPWWGAIDGLREA
+YAAGWAASAHVPEHVDAARALLSRVAAGDRVVANVPAEPSSCGGTVLKALFLACAAWERT
+GILPDVDVHLVTPYGRILDRQTIDPALAEAVARYGIHVHAGAEVNAVDHEAREVVLNTGE
+RITDVAAAYITPVVRAPEFIAEAGLADDGEAGLAAVDPATLRHPVHPHVWALGDAAALGT
+RPSGGALRRQVKILTQNIQAADAGKPLQKYDGYTVIPVMVSRDELVLDEHVRDGSEDRSI
+PGVDLTKPRKSTAAFDRLGQPRIYWHRLLKGKV*
+>NZ_CP033200.1_1614
+MTEQYDILIVGGGNAGVSLAAALRRKRQGRVAIADGQQLHRYRPMLNYAAGGQADMARFE
+RPMRAVIPDGVEWIPDHVVAVDAEERTAVTTTGLTVGFRHLVLCPGLTPWWGAIDGLREA
+YAAGWAASAHVPEHVDAARALLSRVAAGDRVVANVPAEPSSCGGTVLKALFLACAAWERT
+GILPDVDVHLVTPYGRILDRQTIDPALAEAVARYGIHVHAGAEVNAVDHEAREVVLNTGE
+RITDVAAAYITPVVRAPEFIAEAGLADDGEAGLAAVDPATLRHPVHPHVWALGDAAALGT
+RPSGGALRRQVKILTQNIQAADAGKPLQKYDGYTVIPVMVSRDELVLDEHVRDGSEDRSI
+PGVDLTKPRKSTAAFDRFGQPRIYWHRLLKGKV*
+>NZ_CP097650.1_1837
+MTEHYDILIVGGGNAGVSLAAALRRKRQGRVAIADGQQLHRYRPMLNYAAGGQADMARFE
+RPMRAVIPDGVEWIPDHVVAVDAEERTAVTTTGLTVGFRHLVLCPGLTPWWGAIDGLREA
+YAAGWAASAHVPEHVDAARALLSRVAAGDRVVANVPAEPSSCGGTVLKALFLACAAWERT
+GILPDVDVRLVTPYGRILDRQTIDPALAEAVARYGIHVHAGAEVNAVDHEAREVVLNTGE
+RITDVAAAYITPVVRAPEFIAEAGLADDGEAGLAAADPATLRHPVHPHVWALGDAAALGT
+RPSGGALRRQVKILAQNIQAADAGKPLQKYDGYTVIPVMVSRDELVLDEHVRDGSEDRSI
+PGVDLTKPRKSTAAFDRFGQPRIYWHRLLKGKV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002057.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002057.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8353ff6157d4279af0db682cabffd0fb329b68f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002057.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_1987
+MSEPIGLRDAAIEWLKMRSLDGQVPLTREDIGDFRWNGEPFPLISTQNGIRKPAGFDAAL
+SFYTVYRPKGHARPYEDEIGDDGLMRYKWQGTNPRLPANQGLFRAYERGLPLIWFVGVGM
+SPARFQVVAPVYVVGREDERHQIVFAPMEPEDYSPELMHESVLEASLKRYLRREVKIRVH
+QPHFRSTVLAAYDNHCAVCNFAHPELLDAAHIVPDREVHGLPTVVNGLAMCRIHHGAFDN
+HFLGITPDFTVEIRQDLLDEVDGPMLRHGLQDLHGRKLMKLPTRRADRPCRENLAWAYER
+FREATVADVA*
+>NZ_CP040019.1_758
+MVEPAGLRNDAIRWLAERTLDGQLSVTREDLADYRWDGEKFPLISTMQGIRRPAGWSATL
+SIRTAFRRSGETRPYEDEIGDDGLIRYKWRGDNPQQPENVGLRNAMHQRLPIIWFIGISM
+NPAQYQVISPVYILGEEPERQQFVMAPFAEEDYVPDLMTGSVMESSLKRYLKRETTVRLH
+QPLFRSTVLAAYGNHCSVCNFAHPELLDAAHIVPDREVHGLPTVTNGIALCKIHHAAFDR
+RFLGLRPTQGRPVVEIQQDLLDEVDGPMLRHGLQDLHGKPVMTMPKRRVDYPSNENLAWA
+YAEFTRAGRAA*
+>NZ_CP083691.1_725
+MVEPDGLRETAIQWLIERTLDRQVSLTREDIADFRFQGEPFRLIPSYQGIWKPARFEATL
+SIVTTYRAPGQERPYNDALGEDGLHRYKWRGDNPNHPENVGLRRAMERQLPIMWFTGVGG
+KPPQYQVTAPVYIVNEERDRQQFVLAPLEDASEIPERGEGSEMVTALRRYMKRETVVRLH
+QPVFRSTVLVAYEDHCAVCNFAHSELLDAAHIVPDSEEEGVPDVTNGMALCKIHHAAFDR
+RFLGIRPTKDVPVVEIRQDLLDEVDGPMLRHGLQELHGKPLMKVPSRRADRPGTDKLVWA
+YERFLNATAADVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002059.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e4706ad53e4c47f65e86766174abbf08f4a6f245
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002059.fa
@@ -0,0 +1,14 @@
+>NZ_CP042169.1_2040
+MGGASATLRTRGLGRHGRNARVLASHNPLIYRARLLGDRAVNGTPLERHYRLGG*
+>NZ_CP083691.1_580
+MTTTTDRTDTISRPADVGTADSGVPTTAHPADRPQFLAARARLAPVFAWLAETAAERDRE
+RVTDREATDRLAAAGFPGLRVPEDAGGAGLTFPEAARLYVELAEADSNVLQALRVHVVNV
+ETVLGSPDGPRRERWLHRFATGETVANATTEIGNRTGHYETRLTTRPDGSAVVNGRKAYS
+TGTLYADWTIVVVEDEDGAERAATVRSDAPGVTLHDDWDGFGQRLSASGTTEFTDVVVDP
+EELTPVGQSLDDGSSIFASQAIFQFVHLVGLTGIARAVVRDAAAYVAGRTRGFSHGAAPR
+PGDDPQVLQVVGELEAAAFGAQAALDAVVGPLDRALRAEAAGAPLAEAEVDAVYTAVYAA
+QQVIARAALDAATRLFEVGGASATLRTRGLDRHWRNARVLASHNPLIYRARLLGDRAVNG
+TPLERHYRLGG*
+>NZ_CP097650.1_1981
+MRLIHNKDCCGWFAIRRGASARHTGGADGAPPSREPARDALERAATRLFEVGGASATLRT
+RGLDRHGRNARVLASHNPLIYRARLLGDRAVNDTPLERHYRLGG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002065.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002065.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d7b01ac2c3da329a5d6cad8a7be508c730e47b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002065.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_2148
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA*
+>NZ_CP033200.1_1873
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA*
+>NZ_CP097650.1_2093
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002066.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6255339d417c6354197a3215e591264f5c86cde0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002066.fa
@@ -0,0 +1,9 @@
+>NZ_CP042169.1_2149
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETRLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR*
+>NZ_CP033200.1_1874
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETPLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR*
+>NZ_CP097650.1_2094
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETRLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002069.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee956937875c3075c70b9d95d352f574eff0a0aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002069.fa
@@ -0,0 +1,22 @@
+>NZ_CP042169.1_2156
+MVGIKDVARMAGVSTATASRALTGSGPVAAATRTRVQEAVATLGYVADSAASSLASGRTR
+NIGLVTPSVHRWFFAAVLEGAADELVRHGYDLTLYDVGQDPERRSTVISDLLPRRRLDAL
+ITLSFRLSVFEFAGLERLGRPVIAIGGRLPAGETLPDWFTAVQVDHARAARMATEHLLEL
+GHRDIAYVGRVDEDIEFQVSTERTRGFLHALAATGVRTPADWMVPADFTIGGTYHQARAL
+LADPRRRPTAVMCISDEMAMGTWMAAHSLGLRVPEDVSVMGLDGHPEAARLGISTVDQNP
+LEQGRRAVRLALGALDGAAHPHRIMHHLALRPRASTAPP*
+>NZ_CP033200.1_1881
+MVGIKDVARMAGVSTATASRALTGSGPVAVATRTRVQEAVATLGYVADSAASSLASGRTR
+NIGLVTPSAHRWFFAAVLEGAADELVRHGYDLTLYDVGQDPERRSTVISDLLPRRRLDAL
+ITLSFRLSMFELAGLERLGLPVIAVGGRLPAGETLPDWFTAVQVDHARAARMATEHLLEL
+GHRDIAYVGRVDEDIEFQVSTERTRGFLHALAATGVRTPADWMVPADFTIGGTYHQARAL
+LADPRRRPTAVMCISDEMAMGTWMAAHSLGLRVPEDVSVMGLDGHPEAARLGISTVDQNP
+LEQGRRAVRLALGALDGAAHPHRIMHHLALRPRASTAPP*
+>NZ_CP040019.1_516
+MVGIKDVARMAGVSAATASRALTGSGPVASSTRTRVQEAVAALGYVPDAAASSLASGRTR
+NIGLVTPSVHRWFFAAVLEGAADELVRRRYDLTLYDVGQDHDRRSAVLTDLLPRRRLDAL
+VTLSFRLSPFELDGLARLGRPVVAVGGRLPSGEALPEWFTAVQVDDARAARMATGHLIEL
+GHREIAYMGRVADDIEFQVSTERTRSFLDALAAAGLRTPADWMLPADFTIGDAYHRARAL
+LADPEHRPTAVLCISDEMAMGTLMAAQSLGLRVPEDVSVMGLDGHPDAARLGISTVDQTP
+VDQGRRAVRLALGALDGTPTRPASSTTWPCNPGRAPRRRERRAGSRPRRRRPPSTPPSPR
+IVGHVPARERTPPWPP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002070.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002070.fa
new file mode 100644
index 0000000000000000000000000000000000000000..511a2318aba725e724523812383391c403289fad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002070.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_2161
+MMQSSEGAWVDPVEGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSIA
+ELAEAFDLDVSTVHRQVAAAMKAGLVERVVDPDGGSARLHRPTEEGRARLAAELSSRADN
+VAQIVSSWPAEDVVEFSRLLRRFNEGAEERRGHPWPRPQTGPGAEDPRL*
+>NZ_CP033200.1_1886
+MMQTSEGAWADPVRGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSVA
+ELAEAFDLDVSTVHRQVAAAMKAGLVERVADPDGGSARLHRPTEEGRARLAAELSSRADN
+VAQIVASWPAEDVVEFSRLLRRFNEGAEERRGHPWPRPQTGPGAEDPRP*
+>NZ_CP097650.1_2101
+MMQSSEGAWVDPVEGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSIA
+ELAEAFDLDVSTVHRQVAAAMKAGLVERVADPDGGSARLHRPTEEGRARLAAELSSRADN
+VAQIVSSWPAEDVVEFSRLLRRFNEGAEARRGHPWPRPQTGPGAEDPRL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002071.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002071.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dccb2fee6a59f7b61bbde7877906a640328e0129
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002071.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_2186
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL*
+>NZ_CP033200.1_1900
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL*
+>NZ_CP097650.1_2120
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002076.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002076.fa
new file mode 100644
index 0000000000000000000000000000000000000000..079eb90d529fc3ac04d2de7b30e1b3089aee0cb2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002076.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_2211
+MDITVGAVGRASLSDWEQECCGDPIAVGEVHELILLPSRGVSQAGPLASAGWVVTHHDDG
+SPAGSIPLRRVRAVVRAAHEVWPSGRLAEIDRVPGHADLTILEPEEATGLGLGEVVYVGA
+YEPVLPETPRPDEWLLDLEILEDLGPHTW*
+>NZ_CP040019.1_452
+MDITVGAVGRASLSDWEQECCGDPIAVGEVHELIVLPSRGMSQAGPLASAGWVVTYHDDG
+SPAGSIPLRRVRAVVRAAHEVWPSGRLAEIDRVPGHADLTILEPEEATGLGLGEVVYVGA
+CEPVLPETPRPDEWLLDLEILEDLGPHTW*
+>NZ_CP097650.1_2145
+MDITVGAVGRASLSDWEQECCGDPIAVGEVHELILLPSRGVSQAGPLASAGWVVTHHDDG
+SPAGSIPLRRVRAVVRAAHEVWPSGRLAEIDRVPGHADLTILEPEEATGLGLGEVVYVGA
+YEPVLPETPRPDEWLLDLEILEDLGPRTW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002077.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fee4f3373bff647d55937a449ecc20151a694fe8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002077.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_2213
+MGTIFLYEIAGTAILLLLGVGVVANVVLSKTKGNGGGWLLISFGWGLGVFAGVYVAAATG
+AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQTET
+DQGAILGTFATGPEIRNPLWNMVTELIATFVLVFVVLLFGSTPSGLGPLAVALLVVAIGA
+SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV
+*
+>NZ_CP033200.1_1918
+MGTIFLHEIAGTAILLLLGVGVVANVVLTKTKGNGGGWLLISFGWGLGVFAGVYVAAATG
+AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQAET
+DQGAILGTFATGPEIRNPLWNMITEVIATFVLVFVILLFGSTPSGLGPLAVALLVVAIGA
+SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV
+*
+>NZ_CP097650.1_2147
+MGTIFLYEIAGTAILLLLGVGVVANVVLTKTKGNGGGWLLISFGWGLGVFAGVYVAAATG
+AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQAET
+DQGAILGTFATGPEIRNPLWNMVTEVIATFVLVFVILLFGSTPSGLGPLAVALLVVAIGA
+SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002079.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..432660c4bf74f78e110d84ee4bb1cd27ac1f7cca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002079.fa
@@ -0,0 +1,24 @@
+>NZ_CP033200.1_90
+MTTIPIHEAQVRHQPLHAYVEEHAQVSPDRTAIVCGGSQLTFGQLQSQVEQLSAYLSEQG
+VSHGDTVALFMQNSPQFVVSLLAVQRLGATAGPCNPMFKQWELEYQLNDLDTKVLITFDD
+LVPVFEKTDTGVQTVVLTRWSDVIEDVSQVPVEDGAEPVQQTKAPHTVRYAQIIGGERTV
+PPAAEIDLAQDPALIIYTSGTTGQPKGAMLSYRNVEFKTACTVQTYGFTSDDVFCAVMPI
+FHIAGMTVCMNSPLMVGGTMVIEPRFEPGTMIRDLERHAVTVTYTTPPMNLALLDHPAMA
+EADLSAVRLSPGTSFGIKITREISDRWEEVTGAPLFEWAYGMSETHTGDTQMPPEAIRYG
+SHGKPTFDTDVRISDPEDPSREMPQGELGEILVSSPSVFLGYRGREEATQKTMHRHWYRS
+GDLGRIDSEGYLHFEGRNKDLIKSSGYSVFPEEVERMLVRHEAVAQAAVVGYPDPQRGES
+VRAFVILEEGQSVTPKELIEWSRERMAAYKYPRDVRIIQELPTTTTGKLQYAKLRDLD*
+>NZ_CP033200.1_2247
+MNTTVSGARIPIRPDDVVLAVLPFFHVYGLTSVLNICVRHACTMVLLPRFDAAAALDLVE
+RHGITRISAVPTMLIGMVEDPDTGRDLSSVSQVVSGGSALPQEVLRRFEAKFPRATILEG
+YGLSESTSSVAVNVSREERRVMSIGKPLWGTECRVVDAEGHLLGPGEDQVGELLFRGPTI
+MKGYYRNPEATAATLVDGWLRTGDMGYRDEDGFIYVVDRKKELILRGGYNVYPREVEEVI
+ATHPAVSEVAVVGRPHPSLGSEVVAVVSTRPGMSVTPAGVIEHAKVSLAAYKYPREVVVV
+DSLPKTATGKIRKRDLATTLAEPASPESHSATP*
+>NZ_CP097650.1_275
+MNTTVSGARIPIRPDDVVLAVLPFFHVYGLTSVLNICVRHACTMVLLPRFDAAAALDLVE
+RHGITRISAVPTMLIGMVEDPDTGRDLSSVSQVVSGGSALPQEVLRRFEAKFPRATILEG
+YGLSESTSSVAVNVSREERRVMSIGKPLWGTECRVVDAEGHLLGPGEDQVGELLFRGPTI
+MKGYYRNPEATAATLVDGWLRTGDMGYRDEDGFIYVVDRKKELILRGGYNVYPREVEEVI
+ATHPAVSEVAVVGRPHPSLGSEVVAVVSTRPGMSVTPAGVIEHAKVSLAAYKYPREVVVV
+DSLPKTATGKIRKRDLATTLAEPASPESHSATP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002080.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002080.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6bfac06cd099cb195fe4ba13a467f7ef10aa459
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002080.fa
@@ -0,0 +1,16 @@
+>NZ_CP033200.1_222
+MHHHGGAFTGIKKHHHAWAPLIEEMQEDVDAWVTGYRVPRSSEAAYFHGPLGRDVRKNFS
+LLLGFSGKIVRPGSPLTSEWLAEVERRLDYYGSLLAQAPGNIYGDNPGYPVPWTRIGSQV
+FEPLTLKYREHIRIDPRLKPQLWGHR*
+>NZ_CP040019.1_2383
+MALNAARRAKHQVWTLRKVSAQQARELLDTTAQRLRPLSFNPHRYPLHRFLRFDAPMQET
+LPAPERIFVLWTGLNEMPAIRAANLGRIRTIVGVPVEFVTPATLHEWTVEHHPLHPAYPH
+LSLTHSSDYLRAYLLHHHGGGYMDLKAPAGSWADMFTRLNGDPEAWVLGYPEDSKGRIPP
+YGGHMERDLRIHFARVMGTMAMIARPRSPFTAEWFHEVERRLDYFLPLLRDHPGGVRDEI
+DLYPVGWTQILADIAYPLPLKHHDHIRLEKGFTPPDEAYR*
+>NZ_CP083691.1_2263
+MRLMYSARQAKHAAFVANKRTRRVLGAGKWRALTMVTPALSRVWPFRYDAQRYTGPNRGK
+EGHDLSFLQLPPPIDAASSELPRRVFVLWTGNNPLPPNRSRNLAHLRKVIAVPVVLVTPQ
+TLGGWLIPGHPLHPAYEHLSLVHRSDYLRAYLMHHHGGGYIDLKAPVGSWAPAFDRMERD
+PSAWLSGYGEINANASARFPGPMGRDIATHWKSLVGTAAMIVRSHTPFTGEWIREVDRRM
+DALAPRLAASPGLVRLGGPGYPVSWTDLLGKVYQPLQLKYFEHIRVDDDLLVNFTDYQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002082.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002082.fa
new file mode 100644
index 0000000000000000000000000000000000000000..799c376580c28ee0cb4d395f1635449db49d9feb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002082.fa
@@ -0,0 +1,9 @@
+>NZ_CP033200.1_311
+MPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRWVCQHRVDAGLKD
+GPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR*
+>NZ_CP040019.1_2228
+MPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRWVCQHRVDAGLKD
+GPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR*
+>NZ_CP083691.1_1790
+MPLPFEFERMLFMPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRW
+VCQHRVDAGLKDGPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002084.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002084.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c791ff609ba963bdd0a76ce33b83818901d6d9c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002084.fa
@@ -0,0 +1,15 @@
+>NZ_CP033200.1_345
+MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTKSLAARMGTTAPNVTETVKRLAAQGLV
+EYQPYKPVTLTGKGCEHAIAMVRRHRLLESFLAASLGYSWDEVHAEAERLEHAASDELIE
+RIDQMLGHPTHDPHGDPIPTPVGQRERPAHAVRLDAAEPGFYRVLRISDADPQRLIRFQQ
+AGIVPDSVVEVAEAGHFRLRVVAVGPVELIETDAAAIWLVPSSTRG*
+>NZ_CP083691.1_656
+MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTNSLAARMGTTAPNVTETVKRLAAQGLV
+EYQPYKPVTLTGKGREHAIAMVRRHRLLESFLAATLGYSWDEVHAEAERLEHAASDELIE
+RIDQMLGRPTRDPHGDPIPTPEGQRAQPAHAVRLDVAEPGFYRVLRISDADPQRLVRFQQ
+AGLVPGTVVEVTEAGHSRLRVVAVGPVELIETDAAAIWLVPSATRG*
+>NZ_CP097650.1_1957
+MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTNSLAARMGTTAPNVTETVKRLAAQGLV
+EYQPYKPVTLTGKGREHAIAMVRRHRLLESFLAATLGYSWDEVHAEAERLEHAASDELIE
+RIDQMLGRPTRDPHGDPIPTPEGQRAQPAHAVRLDVAEPGFYRVLRISDADPQRLVRFQQ
+AGLVPGTVVEVTEAGHSRLRVVAVGPVELIETDAAAIWLVPSATRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002085.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b44b3b9995c9f599129de76a603be3a552212e53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002085.fa
@@ -0,0 +1,20 @@
+>NZ_CP033200.1_353
+MTRISPLSAAGTDFDGTRLTVARRLRRKTKATLAREVGVTPTAIAQFEKNLSKPTQSVLA
+RLCLQLGLPREFFGAGRPLALLPASGAHFRSLRSTSATSREQALAYGELCLELVDLIGAY
+VDLPPVSLPELELPEELTDEAIVEAARLTRSTWGIAPGPLPSVVQTLEAHGIIALRLPVE
+TDAAVDAFSTYSGARPLVFLSPTKDDKARSRFDAAHELGHLVLHPDTEPGSKLVEQQAHQ
+FAAEFLMPRDEIIEDLPRRINWPAFHELKRHWGVSLRALVYRAHSLGRLSEASYRRANQQ
+LSAWGHPEPGPLGPAESPQVLGIARQLITDGGYDFEGIMAAGRIAPEVAEAVMDAASTVR
+PKLRFVI*
+>NZ_CP083691.1_307
+MTMMHELGHVIYDRDVSTPWRSTKSPEEERAFRFAGAMLIPANVMKKRVTESLTLHGYLA
+IKADYGVSVGALVKRAESLGIISKSRARSLYIQISSQGWRYNEPVPVAAERSLLIQQATA
+RAFGENLEGVAQSTGVPHRLVEHWTGFKRDLRAPMADVIPLRR*
+>NZ_CP097650.1_164
+MSLEPSRIVRARRRAGISKKRLADLIGATPRTISNYETRGAPDALAATLADVLNVDPTFF
+SMPATSPLEEDRVFFRARRRTSAAVRHAASEAGRTGVEFYSLIAEHFKLPEVDLPDLVGM
+GPAIAARQLRAHWKVGAGPLPNLIQLAESRGLRVMSLPGTTDEVDAFSVWEKGVPYIFLS
+QRKTAERSRFDLAHEIGHLVLHSGLGNGDSVERDAEREADAFASEFLLPGEVLRGAMPRQ
+PSTEAVLKAKVSFGVSAMAMAYALFRNGLLSEWAHRQMCIDLTRRGYRSSEPGGIHRETS
+RVFGLTLSLARQRLGLGTEEIAQALGVCPQEIHELTFGHAVTPVASVGGSSAAPEPGPRP
+SLRVV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002091.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002091.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f970e45e6477b19554550dbb06d693abd3f5a339
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002091.fa
@@ -0,0 +1,10 @@
+>NZ_CP033200.1_1609
+MKISDRVRAMRKELLLTQQQLADLAGVSDATVRQIERGTGKSTLKSVLSVMEVLGLELEV
+TG*
+>NZ_CP083691.1_195
+MSRQPASVPLTSALDTAPFGREMRALRRGAGLTQAQAADRMGVSLRWLKYLEAGTRRPRL
+QDVGRVAVMDPLTGRMATSVLQTLTPAGKITPSGPRLSLAHLARLAGWPLEPMDPSVSDA
+VTPEALAVVADVLDAAHALLDQADPHMEDLEALAATRNVSAVVHRLDHVYAALAAEDAR*
+>NZ_CP083691.1_818
+MAQPHPSPLVPVGERVRAARREMGLTQQELADLAGVSDATVRQIEHGTGKGTLGSLMAVL
+EVLGLHLEVNG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002095.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002095.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9157f40a62704e5dd3b41d28f43bce1b4e49b059
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002095.fa
@@ -0,0 +1,18 @@
+>NZ_CP033200.1_1666
+MSIAAQAKDDDTFDSAHVLDPAATRDSQGQISEEIAAVHAQAQGETQPRLDFPPYRSSVF
+RHPTKSLVHADPETVELWSPAFGHRDVHPLEADLTVGQNGEPIGERIKVRGRVLDDDGRP
+VRHQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGIGRTLTGADGTYEFTTIKPAPYPWKN
+HRNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFPLDPIYQGITDQAARDRLVATYDHS
+VTSHEWNTGYWWDIVLTGSHRTWMEDEEGDH*
+>NZ_CP040019.1_826
+MSDPVQKQDDDTFDNARVLDPAATQDSQEQISEEMAAVHGQASGETQPRLDFPPYRSSVF
+RHPTKSMAHADPESIELWSPAFGHRDVHQLESDLTVGQNGEPIGERIKVRGRVLDGQGRP
+VRGQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGVGRTITDDRGFYEFTTIKPAPYPWKN
+HHNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFSLDPIYQGITDQKARDRLVATYDHS
+VSEHEWNTGYYWDIVLTGSHRTWTEDEEGDH*
+>NZ_CP097650.1_1883
+MSIAAQAKDDDTFDSAHVLDPAATRDSQGQISEEIAAVHAQAQGETQPRLDFPPYRSSVF
+RHPTKSLVHADPETVELWSPAFGHRDVHPLEADLTVGQNGEPIGERIKVRGRVLDDDGRP
+VRHQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGIGRTLTGADGTYEFTTIKPAPYPWKN
+HRNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFPLDPIYQGITDQAARDRLVATYDHS
+VTSHEWNTGYWWDIVLTGSHRTWMEDEEGDH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002098.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002098.fa
new file mode 100644
index 0000000000000000000000000000000000000000..891b21c0e46b7cd99d67c0b1c1f12157393e2470
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002098.fa
@@ -0,0 +1,23 @@
+>NZ_CP033200.1_1704
+MAHQAMQRGRRRMVHLTGLFAGIGGIEQGFHNALGSKVETDLLCESWAPAQIVLKNRFPG
+AELHPDVRELASLPEATDILSAGFPCQDLSQAGRTAGIRGEQSGLVTHLFELLRRRISAG
+RRLPTLLIENVPNMLALDKGAAMEFLVQEMETLGYSWAYRVVDTRFTGLPQRRRRVIVVA
+SVNLNPSEVLFADEAASRPDDHYSSDAFGFYWTEGKGGLGWAPDAIPTLKGGSTIGIASP
+PAIWVRGAEDATRALVVPREAEMESLQGFPRGWTDLDFGLSAARTRGTRSKLLGNAVSVR
+VAEWVARRVFAPGEVVCPSVDWGSSRQWPNAAAGMGGKRWRVEASEFPTLEPYEHLLEHV
+DVSSAPALSRRAVSGFRSRLLQGNLGRYPGFREAVAEADRALTEDQLITKLEA*
+>NZ_CP040019.1_2167
+MALTSVEVCAGAGGQALGLEAAGFKHLACVEYDKHACTTLRTNRPQWNTVEADLLEWSGA
+AYAGKTDLFAGGVPCPPFSKAGKQLGEADERNLFPRALDLIEEIGPRAVMLENVRGLLDP
+QFQEFRDGVDARLESMGYVPSWRLLNASDYGVSQLRPRVILVALKEPWAQHFTWPEPNKK
+PAPSVGELLAPLMAANGWEGAKAWAARADRIAPTLVGGSHKHGGPDLGPTRARAAWAALG
+VEGRTIAAEAPEPGFEGMPRITVQMGGMVQGFPADWQFTGAKTHGWRQVGNAFPPPVAAA
+VGKQIRKALKAAN*
+>NZ_CP097650.1_1921
+MAHQAMQRGRRRMVHLTGLFAGIGGIEQGFHNALGSKVETDLLCESWAPAQIVLKNRFPG
+AELHPDVRELASLPEATDILSAGFPCQDLSQAGRTAGIRGEQSGLVTHLFELLRRRISAG
+RRLPTLLIENVPNMLALDKGAAMEFLVQEMETLGYSWAYRVVDTRFTGLPQRRRRVIVVA
+SVNLNPSEVLFADEAASRPDDHYSSDAFGFYWTEGKGGLGWAPDAIPTLKGGSTIGIASP
+PAIWVRGAEDATRALVVPREAEMESLQGFPRGWTDLDFGLSAARTRGTRSKLLGNAVSVR
+VAEWVARRVFAPGEVVCPSVDWGSSRQWPNAAAGMGGKRWRVEASEFPTLEPYEHLLEHV
+DVSSAPALSRRAVSGFRSRLLQGNLGRYPGFREAVAEADRALTEDQLITKLEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002103.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002103.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5fa1f8358f4fa736f36fec992001eb37e766d068
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002103.fa
@@ -0,0 +1,7 @@
+>NZ_CP033200.1_1810
+MGMKQRISKVGAGVAVAGPLAVSGAVPAQALTDSGRQDCSAGLLLSGTYGYCYYPY*
+>NZ_CP083691.1_533
+MGMKQRISKVGADVAVAGLLAVSGAVPGQALTDSGRQDCSAGGGYVGARGEQQRYGDRMS
+FDVGGRTTKVVNRYTYGFDSGLRMSQNWRVSSESLLLSGTYGYCYYPY*
+>NZ_CP097650.1_2029
+MGMKQRISKVGAGVAVAGPLAVSGAVPAQALTDSGRQDCSAGLLLSGTYGYCYYPY*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002104.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002104.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee357c79d0dbd2cb100ae0657b0c853401458f48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002104.fa
@@ -0,0 +1,9 @@
+>NZ_CP033200.1_1884
+MSQNDLTVYGADWCRDCLRTKRQLDELGVAYDYVDLVADPAQADAAERISGRKNIPVVVF
+PDGDHQVEPTNEETAAKLTALGLI*
+>NZ_CP040019.1_510
+MTQNAPALTVYGADWCRDCLRTKRQLDELGVAYDYVDLVADPAQADVAERISGRKNIPVV
+VFPDGEHQVEPTNEETAQKLTALGLL*
+>NZ_CP097650.1_2099
+MSQNVLTVYGADWCRDCLRTKRQLDELGVAYDYVDLVADPAQADAAERISGRKNIPVVVF
+PDGDHQVEPTNEETAAKLTALGLI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002108.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002108.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9118873be96062ad9498fd2343f3cc7ac219da2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002108.fa
@@ -0,0 +1,24 @@
+>NZ_CP033200.1_2252
+MSETRSGVLPDHDIYLLDDELTEEQREVRDRVRAFVDAELMPVINDYWERAEFPFELVPK
+LAELNVAGTVIEGYGCPGMSRMAGALVSMELARGDGSFNTFFGVHSGLAMGSINAFGSDE
+QKERWLPRMARMEMIGAFALTEPDHGSDSVALETTARREGDTWVLDGAKRWIGNASYAHV
+IVIYARDVADGQVKAFVLEREPDTEFPAGFEPTVITGKIGKRAILQPDIVISGLRIPEAD
+RLPGCSSFKDVNRVLSTTRGGVAVETLGHAVAAYEAAVAYAGQRVQFGKPIAGHQLVQGQ
+LATMLADVTNIKLTCFRLLELQDQGRLTGPMASLAKMSAARQARRVTSMARDILGGNGLL
+LENHVARHLTDMEVVYTYEGTDSMQSLIVGRAITGVSAFA*
+>NZ_CP040019.1_793
+MADRPAVIDHPDYFLLDSDLTDAQRALRDRVRDFGREQVLPIINEWWEKAEFPEPLLPGL
+ADLGIIGTYIEGYGCPGMSRIEAGLVAREMGRIDGSVNTFLGVHSNLCMGSIYILGSDEQ
+RQRWLPAMAKLEKTGAFALTEPKHGSDSVSLETSARRDGDEWVITGHKRWIGNGHAADVV
+VLYARDEADGEVKAFVVEKQEDGSFPAGYNPTVITGKVGKRAILQADIVIENLRVKEENR
+LVNCESFAGVNRVLKATRGGASWEAVGHGMAAFEIAAAYALEREQFGAQIGGYQLVQERL
+ATMLTDLTTMQLMCVRMAELQERDELTLAMASMVKMHTSRKALDMTRTARDIVAGNGLLL
+ERHIGRHLTDMEVVSTYEGTDSMQALIVGRDITGISAFTRSRRKS*
+>NZ_CP097650.1_280
+MSETRSGVLPDHDIYLLDDELTEEQREVRDRVRAFVDAELMPVINDYWERAEFPFELVPK
+LAELNVAGTVIEGYGCPGMSRMAGALVSMELARGDGSFNTFFGVHSGLAMGSINAFGSDE
+QKERWLPRMARMEMIGAFALTEPDHGSDSVALETTARREGDTWVLDGAKRWIGNASYAHV
+IVIYARDVADGQVKAFVLEREPDTEFPAGFEPTVITGKIGKRAILQPDIVISGLRIPEAD
+RLPGCSSFKDVNRVLSTTRGGVAVETLGHAVAAYEAAVAYAGQRVQFGKPIAGHQLVQGQ
+LATMLADVTNIKLTCFRLLELQDQGRLTGPMASLAKMSAARQARRVTSMARDILGGNGLL
+LENHVARHLTDMEVVYTYEGTDSMQSLIVGRAITGVSAFA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002112.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002112.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6afd20b8d9253b51fcfb513160d3b500379d2ff1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002112.fa
@@ -0,0 +1,26 @@
+>NZ_CP040019.1_745
+MTLAHPASRPMPATSPATPGATPPDPAARLVPLRGADHAAVLAEAVRVRASGGIPVVGDE
+RWPAALMAAQVEHAAATLRDLAVRDPRAAAEIAWAAFTSGSTSRPRVVLRTEASWRAGHR
+VAADWLGLRPGEELLVAVHPVSSMAVHAASLCGALGARLRVTARARLSAADLAGPVVLDA
+TPSQLVDALDLLDDGAPSTLRVALIGGDRLPAGARDRAAAHGIRVAHFYGSAEASFVAVD
+LDGAGLRPLPDVRLRIADGADDAGPAGPNTPDPNTPRARTGLLELRSDQLAAPDDSRLSS
+GAPRWREDGWLTTGDRATWDPDAGVLEVHGRADDVILTAGATVAAADVEAELAAARDGSG
+RPVASGVLVVGVPDRRLGERVCAVVEPARGQDPEAALQMLKTAARAGLSPAARPRRWVLV
+DRLERTGSGKIRRALPAATRHAAGRQDHA*
+>NZ_CP083691.1_707
+MSPLAPVPDPAARLAFLADADHAAVLAEAVAVRARGGVPVVGDERWPADLRAAQREHAVV
+QLRRLAARDPDLAARVGWAAFTSGSTSRPRVVLRTDDSWRAGHPHVAAWLGLAPGEAMLT
+AVHPVSSMALHAAAWCAATGHRLAVSPHARLTAADLTGPAALTATPSQLTDALDLLDDGA
+PSTLRVALVGGDRLPAGARERAAAHGLRTVHYYGAAEASFVAVDLDGSGLRPLPGVELEV
+AEPDVLADADGPRTGVLRVASPQLAVPDDSRLASGAPRWDAEGRLTTGDRVTWDPAAGIL
+TVHGRADEVVLTAGATVSAADVEAELAAVAGPDGRPVAAGVLVLGVPDPRLGQRVAAAVE
+PAPGVAPEDALAALQGVARARLSPAARPRRWVAVGRLERTGSGKIRRVTPPELRP*
+>NZ_CP097650.1_1938
+MIPPVRLPPSDDDVAPAVSRLAPLRGADHEAVLRRALEARTAGLVPLVGDERWSVAQWQA
+GVGHAEALLAELTARAPDRAARIGWAAFTSGTTGRPRVILRTADSWRTGHRLVEDWLGLE
+PGESLLVPVHPVSSMAVNAADLCAHVGARLLVPSRARLRAADVTGGAAAVHCTPAQLADL
+CDLLAAVRAASAPAGPRVVLVGGDRLPGQLRERAAALGLRVVHYYGSAEASFVAVDPDGS
+GLRALPGVRLEIREGVLHVRSDQLAEPDGTRLTDGTPRWGADGWLCTGDRAQIDDDGVLH
+LRGRADDAILTGGATVIPAEVEAELLRATVRRESTASGGDSAPHAVPVCTAVLVQGEPAP
+RLGSLVVAHVEPAPGLPADVVLAALKEHARTHLPPAARPRRWQVVDRLERTGSGKIRRMA
+PDVAAIPDPPGGSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002116.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..033576e0075e1d75371bfccbc647403193b4b0e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002116.fa
@@ -0,0 +1,36 @@
+>NZ_CP040019.1_1059
+MTTATPRQPLIEDHAYLSNQHSGALLTREGDVTWLCLPRFDAPSVFTSLLGEPEHGRWSL
+RIADGEVRERAYLPGTLVLRTRWRGPDGEAEVLDFMPLTSHRGSGRAHDDDAGALADEGE
+AARADLVRLVRCTSGSVSVDQCLQFRMDYGEVVPWVSRQTDPADESFLAVVAGGDALAVH
+GPDLRPDSTAHRGRTRLEAGQSAAWTLAWYPSWSMAPAAPDPERALEATVTDWVEWLGEP
+LATGPRADRVARSLLVLKGLTHRDTGGIVAAPTASLPEDFGGVRNWDYRYVWLRDTALTL
+EALMAHNHTDDACAWRDWLLRAIAGDPRDVQIMYTLSGERRMPERDLEHLPGYEGSRPVH
+VGNGAADQWQADVIGTVMLALGRLRDAGVDEDRWSWTLQKRLVERVLEHRDTKEHGLWEM
+RGEPAYFTHGRVMMWAALDQALHAARDHGLPAEDEELAAWEQARDELREEILTEGVGPSG
+GFRQTYGSEETDASLLQIPHTGFLPHDDPRMLATVADVERDLVTETGLVMRYRASGMDGL
+PGEEAPFMMCGFWLVEQYARSGRLADAERLMARLDECSNDLFLMAEEYDDGRDRMAGNFP
+QAFSHLGLIRAVDALEEARGAAGGEG*
+>NZ_CP083691.1_993
+MTAQTAPASPLIEDHAYLSNQHSGALVTRAGDVTWLCLPRFDGPSVFTSLLGAPEHGQWS
+LGIADGEVVERAYLPGTLVLRTRWRGPEGEADVLDFMPLADHAGSGVVDADDVGILMGEG
+EGPLRRADLVRLVRCTSGTVEVDQWIRARLDYGEVTPWVSRQEDPAGEEFLAVVAGGDAL
+AVHGPDLRPDGMRHRGSTRLEEGRSQAWTLAWYPAWTTAPAAPDAEHALEKTVTGWVEWL
+GDPRARGPRAERVARSLLVLKGLTHENTGGIVAAPTASLPEDIGGVRNWDYRYVWLRDTS
+LTLEALMAHNHTDDAAQWRDWLLRAIAGEPKDNIQIMYTLSGERRMPERELGHLPGYEGS
+TPVNVGNGAADQWQADVIGTVMLALDRLRDAGVDEDQWSWPLQKRLVERVLAHRDTKEHG
+LWEMRGEPAYFTHGRVMMWAALDRALHGVREHGLDATEEETAEWERVRDELREEILTEGV
+QEDGAFRQTYGSDETDASLLQIPHTGFLPHDDPHMLATVAQVERDLTTETGLVRRYRATG
+MDGLPGEEAPFMMCAFWLVEQYARSGRVEDAERLMARLDDCANDLFLMAEEYDDDRGRMA
+GNFPQAFSHLGLIRAVDALEECAEDARAAE*
+>NZ_CP097650.1_1665
+MSAQPRIDDHAFLSHQLSGALVSREGAITWLCLPRFDSASVFTSLLGTREHGEWSLGIED
+GEVAERAYLPGTLVLRTLWRSPSGVAEVLDFMPLLDADGVGDAQGDDGGPDGTGASEAAP
+RADVMRLVRCLAGRVRVTQSVFARLDYGEVEPWVSRQEDADGESFLAVVAGGDALAVHGP
+DLEPVDGHHEGTTELVAGESAQWCLTWYPAWGMAPSAPRAEDVLEATVRRWRGWLEESTR
+QAPRADDPLADRVQRSLLVLKGLTHRATGGIVAAPTTSLPEDIGGVRNWDYRYVWLRDTA
+LALEALLAYGHVEVATAWRDWLLRAIAGEPHEVQVMYTLSGERYMPERELEHLPGHADSR
+PVVVGNGAADQWQADVIGTVMMALCALRDAGVPEDEWSWPLQKRLVERVVAHREDPDHGL
+WEMRGEPAFFTHSRVKMWAALDRALHAVATHGVPATEAETAAWERHRDELREEILTRGVH
+ADGHFTQAYGSDAVDASLLQIPHTGFLPPDDPRMLATVRRIEEELVTDTGLVLRYRPDGS
+DGLPGEEAPFLACAFWLVEQYARTGRLDDADALMERLDACANDLDLMAEEYDDGQDRMAG
+NFPQAFSHLALLRAADALALVRAGDGAGEAGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002117.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002117.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df2d7592808d21e687032f5eeb99c211852f40c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002117.fa
@@ -0,0 +1,16 @@
+>NZ_CP040019.1_1275
+MSSPTGGSTAADASPRNRAPGGLLNRFLNVIEWSGNKLPDPIIIFAALCALTLAASAVAG
+LSGWSAVHPGTGETLVATNLLSTEGMRVVIGDAAKTFGAFAPLGQVLIIMLGIGVAERSG
+WFEVGLTQSMTSAPKGLIIPAIALIGLLGNIAGDAAPIVLPPLAALIFLKLGWHPIAGIA
+LAYAAATGGFAANLMIGMSDALVQGFTQEAAVIIDPDIETTVPMNWWFIAASVVVLLPVL
+WLVTSKIAIPRLGSYQATDDVEAGDMEVTDVQRRANRWALVALALFAALVVAACIPQGSF
+LRNAETGSLTTDAPLMNGIGLILAVAFFLPGLVYGVRAKTITGSSDVARMMVESMATMAS
+FIVVVFFASQLLSYVSASNMGAILAIRGAELLQGQDGIVLILGIIAISAVVNLFVGSASA
+KWAILAPIFIPMMMLLGYHPAFTQMVYRIGDAVTNPITPMFPYFALVLTYAQRYDKKLGI
+GTFISTLVPYSLAMGLVWTVMMVVWYLLGWPMGPDGPIHLPTP*
+>NZ_CP083691.1_1183
+MTSPTGGSTAADASPRKHTPGGLLNRFLNVIEWSGNKLPDPIIIFAALCALTLAASAVAG
+LSGWSAVHPGTGETLVATDLLSTEGMRVVIGDAAKTFGAFAPLGQVLIIMLGIGVAERSG
+WTICAATTWCGTTRPAPRWSRSCARTCSRAR*
+>NZ_CP097650.1_587
+MGIGSLIATMLPSSIAFLLAWTGMVIGWMWLALPLGPNAPVQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002120.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e4f617b5c8bdfeb80100606736c0382d7277907
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002120.fa
@@ -0,0 +1,17 @@
+>NZ_CP040019.1_2385
+MSQPTAAGFRFYDAFNGSAADPSPHFNVARYRAHYPGPPTPGQAGCAISHFRVLESFASS
+LGHEDGVALVSEDDVLMPPETEAVLEGILKDDSFEIAVLADRGPTNPSLAFQRLLMTEAE
+LSLLSRPIVCGGRIRRLGRFEGNPYMAALYLVTRSGARKLASGLVDDAGGPWTIADDWPL
+FRDRYGLDIRVLRPGLVTYMGGSTTRDAESLARDALSAAGDGRPLTRLKTAVGLRSRSRA
+ARLVVRATLRDIATR*
+>NZ_CP083691.1_2226
+MPDIVDYRVIALADSTRLEGFLAQPLGRRFRPFEAVDARKGYGPEDFDAEGFEVRFGRPP
+LNGEVGCTLSHMSVLREFAVEDGAVTDVLVVAEDDARFSRFTSEVLNRLLETSAVRGLVV
+LADPYGPVDMRGRLGAPTLEDKLQQSLLRRRLRPLAGAPRFAVGRWSRGLVGTGFYLVSR
+DAAKYDIAWRLRHRRGGAR*
+>NZ_CP083691.1_2262
+MGQITDRYVISLEGSPRREAFFSQPGVADFVVWDAFDGRTGAGRDRFDVVAFERRAGRPP
+EGGEIGCTLSHAGLLADFAAGLGRPDDLMLVAEDDVVFTPDFEAVLGRVARTRGWGWTLL
+AQGLEDPFRDPFWAKSRDRAPQSLLAKPVGPPSSPWRYRLGNWDGELWGTGLYLVTREAA
+RALTDHATREGLSWAADDYVTWHAAAGVKVWILLPTIAGWVGESEINATTRPHLQIQSYA
+AHPMGRQAWSRRVSRFRAGARIAWKEMRGDTRPWAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002124.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002124.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b4e060de5cf96be2473c2f3291c23002733e325
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002124.fa
@@ -0,0 +1,8 @@
+>NZ_CP042169.1_164
+MDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEFERRR
+IKERQAEGIALAKARGKYVQAPKLSDTDVEQARVMIEMGIPKAEVARTFEVSRQTLYTSL
+RRVVSS*
+>NZ_CP040019.1_2285
+MKYVREGDLVKVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDGLM
+LGILAAFAEFERRRIKERQAEGIALAKARGKYVQAPKLSDTDVEQARVMIQMGIPKAEVA
+RTFGVSRQTLYTSLRRQASD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002132.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002132.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b649f18abd548b756c970e7d35896e5b34c6f0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002132.fa
@@ -0,0 +1,6 @@
+>NZ_CP042169.1_480
+MADYHGFYRDELGIDVLAVRPNLAGWEGESSIQDDEHVGWRAANDAEIPPVGVADFLREW
+RHRALRKARSTKFDLHWRLRMSQQR*
+>NZ_CP097650.1_479
+MADYHGFYRDELGIDVLAVRPNLAGWEGESSIQDDEHVGWRAANDAEIPPVGVADFLREW
+RHRALRKARSTKFDLHWRLRMSQQR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002140.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002140.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f97080e5a72960921f1f37728a08e532377a8a4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002140.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_579
+MIPVKDLIKAREDWDFEREVALDEQSSVERELASANGHLSRLKEALIERGLASLLWGAQH
+EDVASVPDLVQDTSEAVLAAQMYLADWLVLPDSAVRHLEDIDTAPEAYNWGNKAWRGFRA
+LAAYAQDRASGWDKGGFWEWCASGPVLGWPATSKKLSMTESEGVQTSGKFKGTRDFKVDP
+AVDSSGEITMLAHLKISEGGGNLAPRVYFYDDTNGATKKVHIGLVGPHYLVPNKSTN*
+>NZ_CP097650.1_180
+MAVGYRAIFAVSPREDALAIARESVHSWLVDKLNRARPEVRQQALELDFNAPFAVQLSDE
+IHVSNTRAHGDNGQLQQLIRLDESSAPGETWRVNITADRNDVGGVRQQTIMVELDPLHLD
+AETAVMRAAPPRFVREMLTQHVLRSGTTVLTATPKALRGSEGGREAYRAVIDPLRQAQAV
+IAAQPPGSDMTIWQAAVASLTRQAMGITTALTLDKDALDQFNRRLPRNLQLQPGEVRTFA
+PHVDLDDPADSLRHRSLGPGTFARHIKPRVKDGVTVPEVDPTFASVHARRARMYALEQPL
+PDSIRSMRQQVRTGELREERDRAAGLVTGFSTVRVRPAAPAPAASPHRPGAGKRPSPTPT
+SGRLGASGAIPVPRPLPPSQEKVAEASSATPVAPAEAPQASAPSSITPVPAWQKTLVQLV
+WSTLGTEEITKEAIELLAEQLAASGRREQVADEQIANAVREAEIAAAQHDDLRARLEDAE
+LAAAAEQEERESLAREVEHLRRKAIEAERYEDLVVPEATDEEAKPSTFDDLIERIQSERF
+TTHEYVVFTGDMKKVNEVEAIDIVGRHLSSCWEFVLTLEGYARAKKDGFNGGVHQYLTSG
+EVDGKRCSPGKHASLESESVKSNAAQRRERLLPVPKNVDRSGAVHMWAHFKCSKDGTKSP
+RMHYYDDTDNTGKIYIGYIGPHLTNRQTSSM*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002141.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002141.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d82aa03ebc38d8c050d8569434877931abf714a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002141.fa
@@ -0,0 +1,6 @@
+>NZ_CP042169.1_808
+MVSMSRPPEPRPAPAPTARAAAARPATPPGVQGRWARRAAGGLIGVSVLLAAWSFALPFV
+FGLGPRQVPWWREVFGLIRIQGVVGV*
+>NZ_CP033200.1_549
+MSRPPEPRPAPAPTARAAAARPATPPGVQGRWARRAAGGLIGVSVLLAAWSFALPFVFGL
+GPRQVPWWREVFDVNHEANLTAWWSSGLLLLGAAGFTTVGLVRRALGRTGGGACSRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002148.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002148.fa
new file mode 100644
index 0000000000000000000000000000000000000000..338c31a1720da68059d9b961824b37d8b12a579a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002148.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_919
+MANTSAIEWTEVTWNPVTGCDRVAAGCDNCYALTLAKRLKAMGAEKYQNDGNPVTSGPGF
+GVTLHPKALGQPRSWKAPRVVFVNSMSDLFHAKVPLGFIRDIFDVMRETPQHTYQALTKR
+SLRMARLADRLDWPANLWMGVSVEDETVTGRIDHLREVPAAVRFLSCEPLIGPLRDLDLA
+GIDWVIAGGESGANHRPMDQAWVEDIRDQCVSADVAFFFKQWGGRTPKANGRLLEGRTWD
+EMPTSRAALAG*
+>NZ_CP040019.1_2062
+MAQTSAIEWTEVTWNPVTGCDRVAAGCDNCYALTLAKRLKAMGAAKYQQDGNPATSGPGF
+GVTLHRQALDQPRSWKTPRVVFVNSMSDLFHAKVPLEFIQDIFDVIRETPQHTYQALTKR
+SLRMARLADQLDWPPNLWMGVSVEDASVTNRIEHLRRVPAAVRFLSCEPLIGPVGALDLD
+GIDWVIAGGESGANHRPMDEEWVTDIRDQCVAAGVAFFFKQWGGRTPKANGRVLAGRTWD
+EMPNQPASMAV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002158.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002158.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f82163567d848967ef6f2a3a10317e9a4f01cd89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002158.fa
@@ -0,0 +1,9 @@
+>NZ_CP042169.1_1445
+MTTTTPKTARQLRAEWQAEIARREAEIVAAERAEARRIDEALRRAGRARVAAVETLYEML
+GIDEQTKTRTRRDGSVQTVRADLDEAERAERLVAAVAALLEGAAGTRSAPAGGAEAVPDE
+AAQMVPEEPSGALAPLPPAAGGESAEPDPEEDEAHASDDAEEPVSDEGDEAAREEDAYAE
+EPAYGTVSDDLHEAGWQA*
+>NZ_CP040019.1_2157
+MTTTKTARQLRAEWQAEIARREAEIAAAEREEDRRTDEALRRAGRARVAAVEILYELLGV
+DEQTTTRTRRDGSIQTVRVDRDETERAERLVDAVRALLAHCDGLRSAPAESAPTSAPLPS
+PAGLDATVSGREQTAHAESESTSDEGWAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002163.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002163.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1ec6e0efe1062a1cb80d29a23382fe1833c8999
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002163.fa
@@ -0,0 +1,8 @@
+>NZ_CP042169.1_1461
+MTTPQFSVDRTRRPVATYRAISTKDAASTQRDGEAVLEVRELSSRSGQREAEVLFHDGQW
+QLCDPEHDLVPGFTFDAFPEHPFLAEAYGETWNGWDTPVVRREVLADILTALELSHRWEG
+DVTVLEVDDYEDRIVPRLDGLYDLQQAGWTVQQVELG*
+>NZ_CP040019.1_2170
+MTTTPPPVDRTRRPVATYRAISSRDASSTQRDGEAVLEVRRFAARDGHAEAEVLFGDGQW
+QLCDPERDLIPAFEFDAFPDHPFLAVEYGEDWNGWATPVVTRETLADVLAALELAHRWEG
+STAVLEIEDYEDRIEARADGLYDLAQAGWTVQQVEL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002164.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78c091213d2a9f3666c18663edde393479a43fce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002164.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_1556
+MMHDERPTGRLGLALGGGGARGLCHIGVWRVLEELDIRPDVLAGTSMGGLLGALIAAGHD
+AASLEKIERSVDWPRLINWGLTGGILSSERLRAWLRELLPDTFEELQIPLVLTAADVVEG
+QTRYLHTGDLITAIQATTAYPGALEPVTVGDSVLVDGGILNQIPVDGVRFLGAQRVIAVD
+ATTLEPLERPEPGARTRTRRSPATSLRQAMRAIDVMQAQLTTVRLSLYRPDVLISPPIEG
+MTVADFRSSGVAIAAGEEATRARAEKLVELSRGRMA*
+>NZ_CP033200.1_1279
+MHDERPTGRLGLALGGGGARGLCHIGVWRVLEELDIRPDVLAGTSMGGLLGALIAAGHDA
+ASLEKIERSVDWPRLINWGLTGGILSSERLRAWLRELLPDTFEELQIPLVLTAADVVEGQ
+TRYLHTGDLITAIQATTAYPGALEPVTVGDSVLVDGGILNQIPVDGVRFLGAQRVIAVDA
+TTLEPLERPEPGARTRTRRSPATSLRQAMRAIDVMQAQLTTVRLSLYRPDVLISPPIEGM
+TVADFRSSGVAIAAGEEATRARAGKLVELSRGRMA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002168.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002168.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db38b4ac24569968e7e517b6fbc8960e311fd675
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002168.fa
@@ -0,0 +1,7 @@
+>NZ_CP042169.1_1564
+MSGNAFQDLPFPVSGPILGSVGERFRLETASDEGTATFSAGGTEGGTYSCGAGQTLLIGD
+SALLCRAVGENSLDFTISRPR*
+>NZ_CP040019.1_1254
+MRTRVTTSLLGLGLTAAALVGCQTQTWISMCFTDATLRSCEVSVSGNAFQDLPFPVSGPI
+LGGVGDRFRLETASVEGTATFSAGGTYSCGAGQTLLIGDSALLCRAVGENSLDFTISRTR
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002171.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3857236ad7c0cfb6dd11b895c61377145989438
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002171.fa
@@ -0,0 +1,8 @@
+>NZ_CP042169.1_1736
+MTAQATDGRHAEDFTVGEECDLGTYEVTEQEVIAFASHWDPQDIHIDPGHAETGGRYGGL
+IASGLHTLAILQRLQVLGRREHWNVIAGQGIDRLRFRRPVRPGDVLSGHSRVIDVRLEPE
+WRRGLVVFDVRALNQEGKEVLTMEMAAYLEMRSEATAGRRA*
+>NZ_CP040019.1_1069
+MTAQATDGRHAEDFTVGEECDLGTYEVTEQEVIAFASHWDPQDIHIDPGHAETGGRYGGL
+IASGLHTLAILQRLQVLGRREHWNVIAGQGIDRLRFRRPVRPGDVLSGHSRVIDVRLEPE
+WRRGLVVFDVRALNQEGKEVLTMEMAAYLEMRSEAPAGRRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002172.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002172.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a108447a4dc289bb1cf5fa1b9df619622b37806f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002172.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1739
+MATLPSVLATTARRVPQHPALKWGDSSLTYADLDATVDRLAGELISRGLRPGDRVVLVAG
+NTPEFVIGLYGALRAGAIVAPVNPRSARPELEHFLADTEARMLLVDPTVGEGVQALAAAD
+SGSAQLLALGALDGFDDVLAAADGRPEGAVAHPDLAEDDDALIIYTSGTTGRPKGALFDH
+HRVLWVGQNMIMGLGMRVGETMVHVAPLYHSAALNLLLFSGVMLGATHVLLPAFDPDEVI
+ATLERERATIFFGVPTMLAYMLRSPRLAASDLSHLRGILYGAAPMPASTAEALVAALPHV
+HIIQACGQTEGGPGGILLTHEEVMAKPHTSGRMAMPNTEVRVVDADGRDVGPGEVGEMIM
+RGETMMKGYWRNPEATAVTVVDGWVHTGDLTRVDEEGFLTVVDRLKDLIITGGRNVYSAE
+VENALAGCPGVAELAIIGRPHPDYGESIVAVVAPMPGATVSLEALRDYGEGRLSHYKLPH
+ELVLREIPRNLSGKILKHRLRADLTEPGVPA*
+>NZ_CP040019.1_1066
+MATLPSVLATTARRVPQHPALKWGDSSLTYADLDATVDRLAGELISRGLRPGDRVVLVAG
+NTPEFVIGLYGALRAGAIVAPVNPRSARPELEHFLADTEARMLLVDPTVGEGVQALAAAD
+SGPAQLLALGALDGFDDVLAAADGRPEGAVAHPDLAEDDDALNIYTSGTTGRPKGALFDH
+HRVLWVGQNMIMGLGMRVGETMVHVAPLYHSAALNLLLFSGVMLGATHVLLPAFDPDEVI
+ATLERERATIFFGVPTMLAYMLRSPRMAASDLSHLRGILYGAAPMPASTAEALVAALPHV
+HIIQACGQTEGGPGGILLTHEEVMAKPHTSGRMAMPNTEVRVVDADGRDVGPGEVGEMIM
+RGETMMKGYWRNPEATAVTVVDGWVHTGDLTRVDEEGFLTVVDRLKDLIITGGRNVYSAE
+VENSLAGCPGVAELAIIGRPHPDYGESIVAVVAPMPGATVSLEALRDYGEGRLSHYKLPH
+ELVVREIPRNLSGKILKHRLRADLTEPGDPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002177.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..887f4df83c5e70c2e17a6c74e5a8a3c457783dd3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002177.fa
@@ -0,0 +1,14 @@
+>NZ_CP042169.1_1894
+MVPASSIHTAATARTGTTYSGPMPVSAQGPRVTVVGDSSALGSTSLMNLEMPGITVDAKE
+DRTFAEGLTRLGQLKAAGRLRDIVVLGLGVNTGGTAAAQARQAMDLVGPDRELVLVTASG
+PVAWRAFTEQAMRDLAARYPGRVAVTDWEAASRYVTDFRADRIHPRAQGLSVDAQLVRLA
+ADRATGARTVTVQAGQTLSGIAVAYAVPGGWSAISRATGVPLAQLPSLNGPTLSTVLHPG
+QVLRIRCPLT*
+>NZ_CP097650.1_680
+MNRSTLGTRLGASVLVVAALVSAAPAAPAVTSASGTTTTTATTGLAPGTYLAQSGDTWAY
+IAPRVGVELADLLRANGATTSTAIRAGQPLVLPAVSKHLPATSRTGTPYSGPMAPSSAGR
+RVTVVGDSIALGAASLMNLEMPGLTIDAREGRTFAQGLTRLAELKQAGRLGDVVVLGLGV
+NDGGATATQVRRAMDLVGTGRTLVLVTASGPVAWETSTNTAMRNLAATYPSRVVVADWKR
+ASAYVTDFREDRIHPRGQGASVYARLVRLAVDTAPVLRSTTPRTVTVQAGDTLSLIATRY
+GVTGGWQALATLNKISDPHMIRVGQTLLLPATSTTTTPATYTVLPGQGWYAVSRATGVPV
+TQLLSLNGATLSTEIHPGQRLRLR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002179.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002179.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c1750f4fa0810510b95a04c6983bf76a551b925
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002179.fa
@@ -0,0 +1,8 @@
+>NZ_CP042169.1_1946
+MTRLPGLRPPRFLDPWRRPLAPRLPWHVVLAASIAGALTIATLSLGEDLASVPLLVGAFG
+SSCVLVFLVPHGPHSHPANVLVGHVVSAACGIAVISVLPLAWYSLAAGMGLAMAVMAGLR
+VIHAPAGATALAVMLSNADWHYLVTPVLAGALVLTACALLYRRLMWRVIGPAE*
+>NZ_CP040019.1_831
+MSRLSRAPGLRRPRLLDPWRRPLLPRLPWHVILAASLAGAATIATLSIGQDLTSVPLLVG
+AFGSSCVLVFLVPHGPHSHPANVLVGHVAAAACGIAVSSVLPLAWYSLAAGMGLAMAVMA
+GLRVIHAPAGATALSVMLVEAGWDYLLAPILSGALVLTACALLYRRLMWRVIGPPPPPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002180.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002180.fa
new file mode 100644
index 0000000000000000000000000000000000000000..948dc95f0701a15971a81042485eb8d61a4f0bc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002180.fa
@@ -0,0 +1,8 @@
+>NZ_CP042169.1_2003
+MNQPSMATLSSGKITLRDARRGTTRDVELEPFEMAVHPLHDRSTGRPLTPLTWFETINLC
+NELSNAEELQPAYTRAGDGRSVTWNTSADGYRLPTEAEWEYACRAGTTSPAYGPLEDIAW
+TGLDHLEGPQPVVRSENP*
+>NZ_CP083691.1_2170
+MTPPAAEGHFSRATLTDLLCEKFIACRVKSSLHLDSDARRGTTRDVELEPFEMAVHPLHD
+RSTGRPLTPLTWFETINLCNELSNAEELQPAYTRAGDGRSVTWNTSADGYRLPTEAEWEY
+ACRAGTTSPAYGPLEDIAWTGLDHLEGPQPVVRSENP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002183.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002183.fa
new file mode 100644
index 0000000000000000000000000000000000000000..503b6fcc89a4d340b7986701e60cee886edba265
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002183.fa
@@ -0,0 +1,13 @@
+>NZ_CP042169.1_2159
+MLRPRLARPTALLTAGLAALALLTGCSVDGDAAAGSSAGSPSAASSSSGASSSGRVSDGA
+APSSSRAAGSSSAVASASRAVESSQAAEASRAAAASREAEKSAAAAAAEASRSAEAEAEA
+VAEAEREAEASAEVEVGAAEEESAASAGGDGLSAEGQQAVRQAQSYLSFTAFSRSGLIDQ
+LEFEGFSNADATAAVDSLDVDYAAQAVKQAQSYLTHTAFSRTGLIDQLEFEGYSNADATA
+AVDGLGIDYNEQAAKQAQSYLSHSAFSRAGLIDQLMFEGYSASQAEYGVDAAGL*
+>NZ_CP040019.1_513
+MLRPRHTRPALLLTAGLTSLALLTGCADGDPAPGAAATTAAATTAAATSSAPTTQAASSS
+PASSPRTSSAAASSSAKASDAAAAASSSAAAASASEAAESSRAAEAEAEASREAEAEAEA
+ARAREAEESAAAEAEREAEAAATVEEDSSTTAGEGTVSSGQAVRAAKNYLEVLPFSRDGL
+VHQLVAGDGYSDADAAAAVDSLTVDYEAQARRAAQNYLDVLPFSRDGLVHQLIAGDEYSD
+ADAAAAVDSLTVDYQEQAARAAQNYLDVMPFSRDGLIRQLMDGDDYSASQAEYGVDAVGL
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002190.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a889a6fd5e9cb6cfa9be02b9ce8fceb908b8a1d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002190.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_2194
+MTWISANLDFILSLTWRHIAIASPVVLLSLLISVPLGRLANATGWGRRLIVGGSSLLYAI
+PSLAVFVILPGLVGTKILDPLNVVIALTLYGVALLTRSASEAFDAVDDELLTAATAQGHS
+AWQRFWRVELPLAGESLLAGTRVVSASTLSLVSVGALIGVQSLGTLFTEGYARSFVTEIV
+VGIVGTVILAVVFDLVLVALAALLMPWTRRAKVRKASGRRRSSQDTTTTALATVPDLAVQ
+EGRR*
+>NZ_CP083691.1_441
+MTWIAENLDLILDLTLRHVALAVPAILLSVLIAVPLGRAANVSRWGRRLAVGGSSLLYAI
+PSLAVFVILPGLIGTRILDPLNVVIALTLYGAALLTRSASEAFDALDPDVLHAATAQGHS
+PSQRFWGVELPLAGESLLAGTRVVSASTLSLVSVGALIGVPSLGTLFTEGYARAFLTEIL
+VGIAGTVLLAVLFDAALVALAAALMPWTRRGRRTVPAPEDARHDAALTDAVTDPVTAPAE
+GVTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002194.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002194.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e91856f6883b6d1d506c169198f4acdf35f2c39
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002194.fa
@@ -0,0 +1,16 @@
+>NZ_CP033200.1_17
+MATPRKLPRGITLNPSGRYRVKLYAQDREFSLGTFAALADAKAALAVAQGEVARGTFIPP
+AERRRALKAEAEAASARAAAESRTVRQLADAFLAWKEGAGLAWGSVYTYRRHLEGHFLPE
+FGDRAVGAVTTVDLNAWLDRLESDHGASVAPEVHGTVTALFKFAAGQARDLPRGFTPWIT
+ASPVPALTRTRRREHRQVTILAPSELARLSELMTYPEDRALILTAGWCALRIGEALALRR
+RHVVTDDAGRLMLRIETQVQARGRGLYEAPPKSEAGRRTIYVPALAREALTAHLAQHVGA
+TAEALLFSRRGGGNRLNNPNTIGKRLKSAVDLLNREREDAGAEPLGRFTFHGLRHTGLTR
+MGQQGATEAELMAFAGHSDPKAVRIYQHAERNRLAALADRMTGEDA*
+>NZ_CP040019.1_28
+MPKPQRLPRGVDRLPGGGYRARLTVDGYQHTIGSFATLGDARAALDIARGEKARGTFVPP
+AVTRARLKAEKEARRAQAAADSRTVRDMAEAWLSWQTERGLKLGSVYTYRRHLEAHFLPT
+FGDRPVGEVTALDLNAWLDALEESKGHAGAAQIHRVVAALFKWATGDAAELPRTFTPWLL
+TSPVPPLAARRLRRPNLPQRNRETLTDAELSALADLMPEADRLAVLLSGWCALRIGEVLA
+LRRRHVTTDPDGTAWVRVESQVQARGSGVREESPKSDAGRREVPVPPVIAADLAAHLDTH
+AAPGPDGLLFPRVGGGNGLNNPNTVRKRFNAALAALNAQRAEAGENPVENFTWHGLRHTA
+LTRLGQAGATTAELKAYAGHSDGKSVEVYQHAERRRLAALIQDV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002195.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002195.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9409bba3f770a8de843cd1d0bae3ee1fe5938cab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002195.fa
@@ -0,0 +1,16 @@
+>NZ_CP033200.1_82
+MSDRLRDLVLAFAGGTASASQVDLILEAGGLDDDLVQAVSRLRQEGRLARRQREAARILV
+DAATLITGARDMDEILELICRRTRLLLDSDMAYVSLNDVDQGQTYIRTTDGVLTSAYRNL
+RMPLGTGILGQAAGGATVSQTGDYLDDTSFPHIPAVDEAVRGEGVVSILAATLRVRGRRI
+GALLVADRRPRTYTPDEVDLITQTAGLSAVALSRNEEMRDLQTALDDLTVAREEIESKNV
+LLSRLGRLDQELFSVLREEASPADLAEVIGQAIGTEVKALFPADLPAHRTPAAPVVSEHP
+CQDSPNGMATLVRAFTGHRELGALEAHGSLDRDERFLFERGATALTALLLAQERGWATQM
+QQQHRLVKDLENASTETWRSVAGRLAPHRLQEGGTVRVLAVRTEQLQDTRMALRELLARR
+GGVSSIRYEVLRVISPNLTGRELHELLVSRDRSAAVCEQEALLMPEDIRVSLQGVQRTVR
+AMAALNITGVADPRWDLGLTGLAVAQLPPATVDRLVYRALEPLLSYDRQQGTELTHTAWS
+FLECDGRVSVAAERLHIHPNTLRQRIGRIGTLLGEDWHQGSHRTDLHLALRLHRVQSASR
+TG*
+>NZ_CP083691.1_819
+MAFLGPGEHFRDLPGAFRTLENALAVSRVAGGLHAVDASTVGAVGMVLAGAGEASKDVTA
+RPLAPLRDLPPQRASALRETALAYLDAGTNVAETSRRLFLHRNTVLQRLEQLGAVLGPDW
+HTPPRSLDLHLALLSAARDDGGAPGAPPVRSQPRRRAEELRRPRSPAARC*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002196.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002196.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0efa8ee7ab0d4b092e9c5fdd93d8aa99680556f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002196.fa
@@ -0,0 +1,14 @@
+>NZ_CP033200.1_226
+MPSPLDLARQAKHRLFLLRRAREVVRQAAAVRGSERFAREYALASAGFDLPGLPAMSGPC
+AVAMVRDEADVIERSVRHLADQGIPHIVVVDNGSKDATPDILRRLAGEIPGLVVGADREP
+AYVQSAKMTRLADLASAAGATWVVPFDADELWFGAEGTLAEALAAADAPVLRAVMHNAFP
+AADGSGPLLDTIAHFNVKVAFRPRSGAVVEMGNHEVLRPGVRADGLRILHLPWRSFEQFA
+RKSRTGAQAIALADTPEDKAYHWRRLGALDDDALRAAWEALLAGQPLTDAAWYPRGTLRP
+LRSDTPTRWDEV*
+>NZ_CP040019.1_2388
+MDLLSPARALKHRAFLARKDAELRAEARRLRADPVFRAQYSAAEAGLKVPPLEDHPGPWA
+IAMVRNEADVIETAVRHLVRQGVDHLLIVDNLSEDDTPQVLARLAQEFPHLHVGTDHEPA
+YYQSAKMTRLADLVSAAGARWIIPFDADELWFAPQGRLVDALTRSGVPVRRAHLYNLFPT
+PDGQQWHLDTARHFDDKVAFRAWDGAVVVMGNHEVSRPGPRDGEGLRILHLPWRSFEQFA
+RKTRIGAAAVAQAELNEGEAYHWRWLGSASEDELRAVWRRLLSGEAVANAAWYPRGTLRP
+IGDTLPSSWADVQALLGPGPAEGNALSR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002198.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002198.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c85f6811eda82f647f0323e65ad0080b6c5e20a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002198.fa
@@ -0,0 +1,14 @@
+>NZ_CP033200.1_286
+MSAALDRLKQQNAQSGSQQQLDSPETMEALTSILAAVEAQNARLDRLAEQQKKLAGFVKV
+MDEETTRRLERITASASTSSPSSDASARIASIESRLNEIASTLGEFAQSLNGESLNAASQ
+SLVAEAQRNHAATASAIEGLKAQAAANQKLVSQVGGAVQRIEKRTEERVVKAVEQVAGEA
+SATIAANLDASNERAERIIAATAKLEARQLWSAAAAMCLALLPVVVVVAGLWMGIAGLIT
+GAQWALDVDGSVWLGIGRWLVIAAGLAAAGYGVFASVRWVAGLVETWKGRGMPTWPNWRR
+*
+>NZ_CP040019.1_2321
+MSAALDRLKQQNAHEQPPQQLGSPATMEVLTSILTAVEAQNARLDRLAEQQKKLAGFVKV
+MDEETTRRLERIAAPASTSSPSSDVSARIASIESRQNEIASTLGEFARSLNGESLNAASR
+SLVAEAQKNHAATASAIEGLKAQAAANQKLVSQVGGAVQRIEKRTEERVEKAVEQVTGEA
+SATMTANLDASNERAERIIAATAKLETRQLWSAAAAMCLALLPVVVVIAGLWMGIAGLIT
+GAQWALDVNGSVWLGIGRWLVVGVGLAGASYGLFASVRWVAGLVETWKDRGLPKWPRWRK
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002201.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002201.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a53b141b38e4fe976d0347b1823bb9891ac63715
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002201.fa
@@ -0,0 +1,5 @@
+>NZ_CP033200.1_289
+MSANSAAFDHLTGFRWRQGDPSLADAEAQLYDLGVLRSVLERPSRSPSPTPEPMG*
+>NZ_CP040019.1_2324
+MSANSAAFDHVNGFRWRLGDPTLADAEAHLYDLGVLRSVLEEAVEIAVADARADGVTWAR
+IGDALGVTHQAVIKRYRRGGAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002202.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002202.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3b4a0241983309e136aa4ca09f3a4131eb32a43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002202.fa
@@ -0,0 +1,6 @@
+>NZ_CP033200.1_291
+MTRKHLGFLNFGHWIHRPGAEPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQRMFSSP
+FPILAAMAARTERISLGTGVIDLR*
+>NZ_CP040019.1_2316
+MTKKHLGFLNFGHWIHRDPVGGRPAEPDATAALDDVVQMAVDAEAAGLDGAWIRIHHFQR
+MFSSPFPILTAMAARTQRIHLGTGVIDLR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002203.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002203.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2f5ccc55432388070f0e93b1d34c41d85c216da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002203.fa
@@ -0,0 +1,11 @@
+>NZ_CP033200.1_312
+MSTLTLSSKPLTDDRRAVLHRRIRWIVAGTITYNVIEAAIALAAGTVASSSALIGFGLDS
+IVEVLSAAAVAWQFATPDPHRREKVALRLIAFSFFGLAAFITVDAVRTLFGAGQPEHSTV
+GIVLAAVSLAIMPFVSWFERRTGRELGSASAVADSKQTLICTYLSAVLLVGLVLNSTLGW
+TWADPVAALVIAAVALKEGVEAWRGDACCTPASALIAGDQNEKDGDGCGADCACCAHSAC
+LQYRRTGW*
+>NZ_CP097650.1_1951
+MSTLTLSSKPLTDDRRAVLHRRIRWIVAGTITYNVIEAAIALAAGTVASSSALIGFGLDS
+IVEVLSAAAVAWQFATPDPHRREKVALRLIAFSFFGLAAFITVDAVRTLFGAGQPEHSTV
+GIVLAAVSLAIMPFLSWFERRTGRELGSASAVADSKQTLICTYLSAVLLVGLVLNSTLGW
+TWADPVAALVIAAVALKEGVEAWRGDACCTPASALIAGDQNEKDGDGCGADCACCAH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002207.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002207.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25a3d65c19f84ba3f9b9f47f6e09d30ae89f2a6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002207.fa
@@ -0,0 +1,6 @@
+>NZ_CP033200.1_361
+MSVTKGLLVRLEALPGKEDEVQEFLGIGRGLVEEEPATVAWFAIRLGPSSFGIFDVFPDD
+AGRDAHLSGAVAKALGEQTGKLFSEPTIEKLDVLASKLPA*
+>NZ_CP083691.1_1188
+MSVTKGLLVRFDALPGKEDDVKDFLDSGRALVAEEPATIAWFAIRLGPSSFGIFDVLPED
+AGRDAHLSGPVAVALGGQTGAGALFSEPTIEKLDVLGSKLPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002210.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002210.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a7fd73a758ac94a909328182b17a8fa519e0b98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002210.fa
@@ -0,0 +1,24 @@
+>NZ_CP033200.1_740
+MTPVPPSSPSRLDALTAPTARHAHRLLVAKAIREFTHERLLTPVRGERVDDAGRHAYTLT
+LGGVRWTFTARALPLEHLGVDPDSVCRAGDPDAVAVDRFVLDAAEVLGLAGEALDVYLEE
+LASTFAARCHTLAGERPSAADLVDADYTAVEAAMSEGHPGFVATNGRIGWGATEYAMFAP
+EGGRALHPVWLAFPSELGGRWTWPKTASAGAAVPAPPPPITEAVAGLWAERAAALDVDPE
+AYTLIPVHPWQWEHRIQVAFAPDLAVGRLVHVGEDPDAFTAMQAVRTLFNASDPHAPQLK
+TALSVQNMGFVRGLSPAYMSVTPAINAVVADLVDSDPLLARWGFGVLREYASAGYTGDAF
+HAVGSKGPHTKMLAALWRESPLPRLAEGERVMTMAALLHRDGGGRSVAGALVERSGLTAA
+QWLHGVVTAYVTPLVHLAAAYSTVFMPHGENIVLRLREGRVTGAFLKDIGEEVVVGADGV
+PLTEQTRRIRIDLTDEDLSLSFFTDMLDGVLRHLADVMDADALLPAEEFYAVVGRVLAEY
+TALGLADVERLGLDAEDFAHSCLNRLQLRNATQMVDLTDPSGSLLYAGRLANPVSAPLRR
+ALAELRQDAAA*
+>NZ_CP097650.1_957
+MTPVPPSRLDALTAPTARHAHRLLVAKAIREFTHERLLTPVRGERVDDAGRHAYTLTLGG
+VRWTFTARALPLEHLGVDPDSVCRAGDPDAVAVDRFVLDAAEVLGLAGEALDVYLEELAS
+TFAARCHTLAGERPSAADLVDADYTAVEAAMSEGHPGFVATNGRIGWGATEYAMFAPEGG
+RALHPVWLAFPSELGGRWTWPKTASAGAAVPAPPPPITEAVAGLWAERAAALDVDPEAYT
+LIPVHPWQWEHRIQVAFAPDLAAGRLVHVGEDPDAFTAMQAVRTLFNASDPHAPQLKTAL
+SVQNMGFVRGLSPAYMSVTPAINAVVADLVDSDPLLARWGFGVLREYASAGYTGDAFHAV
+GSKGPHTKMLAALWRESPLPRLAEGERVMTMAALLHRDGGGRSVAGALVERSGLTAAQWL
+HGVVTAYVTPLVHLAAAYSTVFMPHGENIVLRLREGRVTGAFLKDIGEEVVVGADGVPLT
+EQTRRIRIDLTDEDLSLSFFTDMLDGVLRHLADVMDADALLPAEEFYAVVGRVLAEYTAL
+GLADVERLGLDAEDFAHSCLNRLQLRNATQMVDLTDPSGSLLYAGRLANPVAAPLRRALA
+ELRQDAAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002221.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..327a15898a1d288c23281ac71367e5ea3d34fe3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002221.fa
@@ -0,0 +1,8 @@
+>NZ_CP033200.1_1738
+MADDLAQCYLMSYPPDVAASDLDEAREEMNATFRGDYGKLRADASTTAWVGGRLAGAIMV
+VTHSIWDEHLTGPFIIDLFIDPHARGKGIGRALVQHAIATCCDAGDHTLSLRFGQGTSDA
+AMRIYQRLGFRPVG*
+>NZ_CP083691.1_1272
+MSTDLLTLRLPAAHAADHVRGDFEFRGLDTGTTDDLARCYLMGYPPGVAASGLAEAREEM
+DATFRGDYGELRADASATAWVDGRLAGAIMVVTRSIWDADLAGPFIIDLFTDPAVRGKGV
+GRALVQHAVDTCSAAGDAAVSLRFGEGTSEAAMGIYRRLGFRPRTGTQRGG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002223.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002223.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f202dc4546db10019b5ca0b0e42105e8bfed444
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002223.fa
@@ -0,0 +1,10 @@
+>NZ_CP033200.1_1909
+MTTLQRLRAEVARRYAALGLPAWPDPHPDGAPPREEEYSRVTDPQRYRIAAARARVWAEV
+LAEAGAVVVPDPVRGIPLDEAGRADLAAPVDRALRVAPPAGVDGASPWWLLETDVPQDDD
+GGVLPVIRVAVGAPRQVHALLPDCGCDACDPGSDELLEAVDQAVVRADGTAEALGRVPGW
+SFEALTDACRDLAAGGRPRLPRGTRRWCGRAK*
+>NZ_CP083691.1_417
+MTARARVWAEVLAETGAVVVPDPVRGIPLDEAGRADLTVPVDRALRVAPPAGVDGASPWW
+LLETDVPQDDDGGVLPVIRVAVGAPGQVHALLPDCGCDACGPGSDELLEAVDQAVASAVG
+TGVNLRGRHGLRRRDWHVHWRSDGTAEGQGRVPGWPFEALKDACRDLAAGGRPRLPRGTE
+ATVRAGWFPEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002231.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002231.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d89efaf366fc33316ba73e81f4ee3aae1d3466b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002231.fa
@@ -0,0 +1,6 @@
+>NZ_CP033200.1_2173
+MYSVYAQHWQRDTEAAASARVYQVSRLRHDAAPAPGVSIFRHGRPVLTLTPDDARRIADG
+LHDAAERAERVPTTPTRKEHHS*
+>NZ_CP040019.1_36
+MTRRTFITNRDRWTRDLTTATKSRANAILREHPDGGTVPGVMIFRDRLPVLTMTPDQART
+LADQLHDAADTCLEAANG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002234.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002234.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa2cb91e8fa5225379aeee27aee27e06d9cc2f13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002234.fa
@@ -0,0 +1,6 @@
+>NZ_CP033200.1_2178
+MNGPTCRHCADWAYGYAEGYAQGHASGLAAGRVQGAAEGPAHPAIADSVARMFAGWDGAE
+AAHARSAAGFRDWYAQARQEENAHDIAA*
+>NZ_CP040019.1_31
+MSTLETVAERVAADRALYAAAYAQGHADGLAEGLAQGAAHPAITDSVARVFAGWGGAEAA
+HARSVAAFRAWHTAARAELKEAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002244.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002244.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5013f8ae8869ad65e20e125c6510b2c9ba0477ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002244.fa
@@ -0,0 +1,21 @@
+>NZ_CP040019.1_83
+MGESRSGGIIRYAHLQEPHCVYGGWIQEDFTARQVLDSLTSQNEQGEVVPWIARAWEVSD
+DGLAWTFHLREGVHFTDGTPLDAQVVVDNFQYWADGGNSTAAVHLGGFFESAEVADAHTV
+RVHLLRPNGVLPSTLSQTYFGLQSPTALRTRSKEDNCRQPIGSGPFTVTEFQRGSHISYA
+RNPDYQWAPADARHQGPAYVDGIRWSFVPDNTSRYGALLSGEADAIGEVPAVNVAEAQER
+FAYQQYVTPGRPVVMSLNTREGIFTDVRVRKAFAHATDRESIVRSAFLGTVPFEPNGFIS
+RTTPGYDPTLADALPYDADAANRLLDEAGWTGRDPDGVRTKDGRRLQSRIVYGAGSILNP
+DGATAVASVAEQARAVGFDLGIRPATQSELFGGLFATPETRGIEVGYWTSPHAGILHINY
+RPSTPEEPNGANTSFLDSPETYSTVVDALSARSEEQRNALFAQAQHELNDLVPAIGLYDQ
+TNSVATSRGLTGVWLEGSQGAPVFHDAYFVAPAAPDGPPADARRTDQKD*
+>NZ_CP083691.1_125
+MSRPPHPARRRRRALRVSVAAAAALVLASGAAAVALPTGPDGPSDGQVLRVALGSDQGCL
+DPQQVSSNDSIYVARQVADSLTDQDPETGQIVPWLAERWEVSEDARAYTFTLRDGVTFSD
+GTPVDSEAVAANLDSLAEGLGPRASLATGYLAGYAETDVHDARTFTVRFHRPTVQFLQAT
+STVSLAVVSPASIAAGAEQRCAGVVGSGPFVVDAYSPGAGSTLSRRDDYAWGSSLWKETG
+RAGVDRVEFSIVQESGVRAGLLQSDQVDLIGSIAPQDEDPLAASGARLLQRANPGTPFGL
+LLNHEHEPFTDPRVRQAVSAALDRQEIVDVAFFRDSQPATSMVSRTTPGYADLSGRLQHD
+PQRAAAALQEAGYTRDPDGYWTKDGTPLTFTVTWSAVSPHNAPALEMLQQQLDDAGIRVR
+LREISTDQAGQILAESDFDAFWTNTTRADVDILRTSYHTGLANRSNAAASPTDGLLEQID
+ATTDSAARDRLAARAQDELLTSLPVIPVAELDTQLAARPEVSGVLFDSGSRLILHDARVD
+AEQKEQKEQEEH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002247.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002247.fa
new file mode 100644
index 0000000000000000000000000000000000000000..226515236bac34429f1c2abbd180c181cec1f84f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002247.fa
@@ -0,0 +1,11 @@
+>NZ_CP040019.1_107
+MTPTSALSSRAPGLAACLALGLAALGTATAVRPWAPALSPLLLAILAGLAWRNLAPVSER
+LAPGVAFAATSVLRAGIVLLGLQLLLSDVLALGPGVIALVVGVVGVTFAATLALGRVLRL
+PWDLTVLVASGFSICGAAAVAAADSVVRARREMVATAIGLVVLFGTLMIPVMPLLTGALG
+FEEQAAGLWIGAATHEVAQVVAAGGLVGGTALSVAVTAKLARVVMLAPVMTGLAWWQRHR
+DALEPATLDDGAPTAVERPPLVPWFVVGFLLAVLVRATGWLPAGVLDAAALVQQLLLATA
+MAALGLGVHLRSIAAVGPRPLVLGAASTAVVVVVGGFGATLLA*
+>NZ_CP083691.1_75
+MPARLEPGIAVAAKPVLRAGIVLLGLQLLLSDVLALGWGAVGLVVGVVALTFAAALALGR
+ALRLPWDLTALVASGFSICGAAAVAAADGVVRARREMAATAIGLVVLFGTLMIPLLPALT
+GALGLGERAAGLWIGASTHEVAQVVAAGGPRPLVLGAGSTAVALAAGRAGAALLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002249.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61fc3ef5e3dfc2194a3f79bf7a648545ab5c47ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002249.fa
@@ -0,0 +1,14 @@
+>NZ_CP040019.1_140
+MTAQTPATAPADDAPLEVPVLDLSGMRRPDGSFDPDFLARLRHAAHHVGFFQIVDYGAAP
+GQVDDLFRVTAEFFARPEAEKLALHNQDSPHWRGYSAVAAERTQGRPDSREQLDFSPDRA
+PVPAERIGEGEEYWHLQGPNRWPADMPELERSAMAWTALMDRVGEDLLKALSVAIGLEED
+HFAEAFDGDRAWMAKLAHYVGGVAEAGTQGVGLHADYGFITLLLQDEVGGLEVRPHGQDA
+WLPVEPIPGALVVNLGEMLEVATDGYLMATIHRVQSPPEGVDRYSVPFFYSPRLDAVIEQ
+VELSAELAADARGASDDPDNPMLASFGSNMLKGFVRAHPKVTERFHPELLDR*
+>NZ_CP083691.1_98
+MTAPSPDSATPARVVPVLDLSIMRRPDGSFDPDFLDALRHAAHHVGFFQIVDYGAAPGQV
+DELFRATAEFFALPEEQKQALHNQNSPHYRGWSAIAAERTQGRPDSREQLDFSPDREPVP
+VERIGEGQEYWHLQGRNQWPAQMPELERIAMDWTALMDRVGEDLLKALSVSIGLDEDHFS
+AAFDGDRAWMAKLAHYVGGVAEAGAQGVGLHADYGFITLLLQDQVGGLEVRPYGQDEWLP
+VEPIPGALVVNLGEMLEVATDGYLMATIHRVQSPPEGVDRYSVPFFFSPRLDAVIEEVTL
+PDEYAAEARGVSDDPTNPMLASFGSNMLKGFARAHPTVTKKFHPELLPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002251.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002251.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7f395840555b68cef06ef935671c68f673a138c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002251.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_215
+MTDEQDAVDGRAGVPSWRVIADRISAEHRAADDGPIDEVDPADFDLDEDCCLGGCCAKGI
+AYLDAVEQAAARRARRTRA*
+>NZ_CP097650.1_165
+MTDEQDAADGRAGVPSWRAIADRISAEHRAGDDGPIDEVDPADFDLDEDCCLGGCCAKGL
+AYLDAVERAAARRARRTRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002254.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002254.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97530ed44d5c816211cf2492307a963b47aa9ff4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002254.fa
@@ -0,0 +1,18 @@
+>NZ_CP040019.1_327
+MSAEEKNLPHGEESTTVGEMNDTVATGLPEEPRTEEGADAPQGARAENPQSDAAAGQCPV
+AHGGAALPHPTSGDANQQWWPNRLNLKILAKDQPVQSPHEADFDYPAAFEALDLAEVKET
+IAEVLTTSKDWWPADFGNYGPFMIRMAWHSAGTYRVTDGRGGAGEGQQRFAPLNSWPDNA
+SLDKARRLLWPVKKKYGQSLSWADLIVLAGNVAHEIMGMPTFGFSGGRIDAYEPADDVYW
+GPETEWTNGGAERYKGERDLDNPLAAVEMGLIYVNPEGPEGEPDPLKSAKDIHETFSRMG
+MDAEETVALIGGGHTFGKTHGAGPVEPHIGPEPEAADLEQMGLGWKNTYGQGKGRDTITS
+GLEVTWTYHPTRWDNEFFHILYAYEWELMESPAGAKQWRPVNGGGSDMVPESDFQGRREP
+RMLTSDLALRFDPVFGEISRRFKDDFAAFQDAYSRAWFKLTHRDMGPRPRHRGVEVPQEE
+LLWMDPVPAPESVPGDAEVKAVKDAVAQAGLSVTDVVKTAWAAASSFRSSDFRGGANGGR
+IRLEPQRSWEVNEPAVTGPVIDALEKIAQEAGVSFADTVVIAGNWAVEKAAADGGVQVTV
+PFTPGRGDATAEQTDVTSFGHLEPKVDGFRNWDPRGSKTFPAEFALVDRANLLGVSAPEM
+TVLVAGLRVLGAVHGDSQDGVWTDRVGVLSQDFLTAVTDIDTQWEKVAEGRYRGVTADGR
+ELTGTRNDLVFGSNPELRTLAEVYAADDAREKFVQDFVRAWAKVMDADRFDAK*
+>NZ_CP083691.1_267
+MHGKGASLPHPTSGDANQQWWPNRLNLKILAKEQQVINAHDADFDYPTAFAALDLDEVKK
+TIAEVLTTSKDWWPADVGNYGPFMIRMAWHSAGTYRSGDGRGGAGTGQPLTARPAADDGR
+PPHRVGARSAFPPGAGPCLQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002260.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002260.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad6fb1f3f51837c54cf0891a6efbf4ef7d19fe3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002260.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_380
+MWVHHLDVSYRAVKSRPASARALRDTILIEELKRIHAENYGVYGVRKMHHAMRRAGWEIG
+RDQVARLMKLASVEGVRRGRKPIITRPAGEPDARPDLVERCFTAERPNQLWGLP*
+>NZ_CP083691.1_647
+MSYRAAKTRPASTRALRDEILIKEIRRVHAENYCVYGVRKMHHAMRRAGWEIGRDQVRRP
+GGSGRIHCPRRSLRRACLFRFPQIAIEHHWPVRERE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002261.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc1324262d55a4d2c7a0ec562d7920ff190ada69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002261.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_381
+MIAFIDEHRDQFGVEAICRTLRATECGFITST*
+>NZ_CP083691.1_648
+MIAFIDEHRERFGVEAICRVLSATECGFITST*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002262.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002262.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f5e505f9a3752bb4471e8acb2c1e4c1d8782d65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002262.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_382
+MPKKYTPELRERAARMVLERQAAQGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEITQA
+PAGEDLQQENKRLKRELAEARRANEILKAASAFFARELDRPTTR*
+>NZ_CP083691.1_296
+MPKKYTPELRERAVRMVLERQVAEGGPRSHSIRAVAPQLRVGEETLRMWCNRHGHEITQA
+PAGEDLQQENKRLKRELAEARRANEILKAASAFFAADAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002265.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002265.fa
new file mode 100644
index 0000000000000000000000000000000000000000..288bb1c2d3d3a06978f5751d30364418debc6d51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002265.fa
@@ -0,0 +1,12 @@
+>NZ_CP040019.1_468
+MVTHTDLMTIGEFSSLSRLSVRMLRHYDAHGVLVPEHVDAHSGYRRYAPAQLRDAADIRN
+LRDVGLGVSAITALLAARGTSTWTDALALQRCTLVEELHAARERLSLIDRMLTPGEIPMT
+IQLNRTAVPAMTVVALRGTVPSYSDEGRLWERLMPALQQQGIRPVGPCGVIEHDDEYREA
+DVDLSVYCPVAPGTRAEGPLVVLQLPERDCLVAHVIGPYTQISQAHDLIVQRMEAEGLAA
+RQDGTLASNVFNRYLVTPDQAAPEDLVTEVCRPLA*
+>NZ_CP040019.1_2629
+MSRRMLRHWEQEGLLSPALVDPVTGYRRFQATQLGRIRAIAELRDLGFSLSEIRQLLDPQ
+IAHSSLERILMQQADRLRDQITEASARLAQVQHRVDTIQKKAQEISMNLSLTPLPELSLQ
+GASTTVLDETDIGSAVARLRDLVPHDQGDLILLFDGTSPDQITVTAATADGATTPGLQPV
+SAPLAPQGATVTFPTPPSSVADAWVLIDAELEKRGLASGGVYRQIISPDGSTTLQAAVHA
+RD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002271.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002271.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b90c51ec778460eb1484ba9a2762450442983918
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002271.fa
@@ -0,0 +1,10 @@
+>NZ_CP040019.1_501
+MTSVLFVVSAADAWTLKDGTTHPTGFWAEELATPHRLFREAGWDIVFATPGGVPPTVDRA
+SLGEAAGSEEERAALTAHLESIRAELDAPLRLEDVDDREFDVVFYPGGHGPMEDLAADPV
+SGALLSRRVTAGDPVALLCHAPAAALAAKDADGANVFAGRRMTAFSDEEERAGGLAEQAP
+WLLETELKEAGVVYEKADEPMAPKVVVDGAVYTGQNPASSAELAERLIADLG*
+>NZ_CP083691.1_450
+MTKVLFVVSAADQWTLKDGTVHPTGFWAEEFVVPHQTFTEAGWHVDIATPGGRVPTVDQL
+SLGMMAGSPAKREQLRAALDRLRPALERPLVLADVDDSAYDLVFYPGGHGPMEDLAYDPV
+SGALIARRLLDEAPLALLCHAPAAVFAAKRADGTIVAEGRRMTAFSDLEEKLNPFARKAK
+WTLEAQLKHGGVQYEKARFPMQSHVVADGALYTGQNPQSSAALAERLVHDLSARVER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002281.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002281.fa
new file mode 100644
index 0000000000000000000000000000000000000000..773793e54c1f4b9de992830820ee5f6aaf07d89a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002281.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_628
+MSGGAQSVSVRVHGDSILGQECLKSMMWPWSVERLGLPCVGLSWGVPGETFKVQGAYARE
+PVRYEDLNFQEIGLVGEDFGRGRPAWPDRCFSLELFPEYSPEVAWLRLRVVEEAGAQVFR
+AQVTLRPRSEGRGCEADLDWWESRLGALPAQMREWARS*
+>NZ_CP083691.1_2175
+MSGGAQSVSVRVHGDSILGQECLKSMMWPWSVERLGLPCVGLSWGVPGETFKVQGAYAQE
+PVRYEDLNFQEIGLVGEDFGRGRPAWPDRCFSLELFPEYSPEVAWLRLRVVEEAGAQEFR
+AQVTLRPRSQGRGCQADLDWWESRLGALPAQMREWARS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002285.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de0528bcf296bf6de4146ea4b638e1f0d10c58cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002285.fa
@@ -0,0 +1,10 @@
+>NZ_CP040019.1_697
+MTQRRTRWRSAASQDAEYRAHWKAAASADVGTPDALTWAVLGDSAAVGVGAARVEESYVA
+QVAAGVAERTGRPVRVLNLAVSGATAAHVLADQLPLLPADGVDAVTCVVGGNDVAWPVRF
+RVDRFAAPLEKIAQRLPAGATLGTVPVFRIPPYESRVECANAAVRVIAARHGLGVADVHA
+ATRRTSLRHQVSMLSHDLFHPNGAGYRDWARAVLPEVLRQVRGEAPTR*
+>NZ_CP097650.1_1977
+MPSPSGWQAQHDADYRAHWHALAARADPDALTWVVLGDSAAVGIGAESVERTYVAQVAER
+VAAETGRPVRVVNLAVSGAMAKDVLADQLPLMPASGVDAVTCVVGGNDVTWAWRFREAAF
+EEPLEAIARALPAGATLGLVPTFRIPPFEARVRRANTVVRRVAARHGLGVADVHAATWRR
+NLRHQVSRLARDLFHPNGAGYEDWAAAVAPEVLRQVRGQAPAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002287.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002287.fa
new file mode 100644
index 0000000000000000000000000000000000000000..600833aeab1c25e73b75c2211d514895f9060d73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002287.fa
@@ -0,0 +1,10 @@
+>NZ_CP040019.1_738
+MSSAKNSDQRRQDRAAVLQAHWAAEAKAARKQKVLWGAGGVTAVALVGALVTVAVVTDPP
+PPTRQDIEIAGLETFEDLDAMHVNSPVDYEQDPPVGGDHASTWLNCGVYTEKVPKENAVH
+SLEHGAVWAAYDPSALSEEEITALQEALPDTHAVVSPYEGLESPITLSAWGAQVAVETPD
+DERIEEFVAKYWQSPEAPEPGAACTGGLDGPGRVA*
+>NZ_CP083691.1_2141
+MSTKLMADPEAKAERRRKVLVGAGALTAIAVVGGLVTLAVIQNPPPQAREDIEIAGLQTF
+EGLSANHVSTPVDYEQSPPVGGDHASAWLNCGVYTEPVPNENAVHALEHGAAWVAYDSEA
+LSQEQVDALRTALPAAYVVLAPYEGLDSPIVLSAWQAQVAVDSPEDERIEQFVAEYWQSP
+DAPEPGAACTGGLDAPGRIA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002291.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..276c375f477a7d872e317d8618a63d35067e43c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002291.fa
@@ -0,0 +1,15 @@
+>NZ_CP040019.1_811
+MATPAGAVGKGPNHNPRSTVNTSILATHAELVAQLQKEDARQDAMELTVIGQSVKGRDIH
+LASWISDPENPTILFLTQQHGNEQLTTEGAMAFIKSLGTGKMRSVLDDVNVLVVPMANPD
+GAMGDVDFSLEDYIASGDRNLTRYNANEVDLNRDHVAKTQPETRALHENVLGAYDIDYMI
+DLHHQGTRSAVDGELVSGSILYPTSPNVAPDVVEDSQRLGSVVYDAVEQYGWGNLGRYVG
+GTAETIARNGVAAEYGIATLLFEMRGMSDHEYESYVLGQRSNGYLIKQTVVTLEATTKAI
+ADGSIETADIGLWNTLPEQRTLPLAAE*
+>NZ_CP040019.1_1969
+MSPLTSPSLSRRGALGVLASAVALPLVAAPPAQAAGSMPTPSDTPPLAAIRDLADMLREL
+RKLERTSRGAIRVTTLAEVGTAEAHSEQGRDLYVALVGHGPRHVWLQGRIHGNEPYGLEA
+TLDVLASLGGNGSPAYRRMREEFTVHVIPMYNPDGSEANTRGTTLWDREADAPLLVGRGR
+PRTVDLNRDWGVGRFQARESRAWYEYWTMVKPEFALDIHHQWLKQDWVTGEDVTLSLGVS
+LAPGGPTLPGIRGGEYDRLARQLAGHVWLETLHRGHISTDRYDVGENTVIDIHGGVVSAM
+MMGLDWNGLNPTGHSNVAIFFETSGNTNSLGHKARGKLVQQNVLAVTAALDGMATGAVQR
+VDPAVWDRIPHTPVKYYSTDYAGLIPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002297.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002297.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6aa71b1afc7fa2cd40357cf0f9fe4230cad1174c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002297.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_892
+MDGVRGTWAPGTVRGVLHASGVGAATGYPGVVLATPAATEHPAAQIADVPAQLLVSVDLP
+DHWDRLDAFEGAGYRRVPAVVALDDDAVRPAYLYELVPDAVPPSA*
+>NZ_CP097650.1_1814
+MALTGVPELGGWRVTPSPTPAGTTPPELTITYATDDFATALALANRIGEAAEAADHHPDL
+TVSYGRLTVGMHSHDVRALTSRDVRLARTVARLASEVLAPHALAAYGTLAPGRSNAHVMD
+GVRGTWIPGTLRGTLHASGIGAATGYPGVVLAGTAPAHATTDVPAQVLVSADLPDHWDRL
+DAFEGAGYRRVPGVVALEDDDAVRPAFVYELVPDAVPPSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002300.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002300.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31f7a37f653853f354747fe89835e6d0d14b739d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002300.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_927
+MSEPERTRPETTPDGHHIVVDGRKWRAQDPHIPEALAGELVKGLMAARRLVRTDPTTARP
+RVQDAKVALGERGDPWWEPTPEGTRERLAAAMRTLLRQRDEGKTICPSDAARVAGGEAWR
+DLMDEARAVAAELHAAGAVEVRQRGERVDSAAARGPIRLAAGPQLG*
+>NZ_CP083691.1_1202
+MTGEPITPSDPEHSGPERTGPEHTPDGHFIIVDGRRWRATDPDIPEALRAELVKELMAAR
+RLVKSRGDAARVRVQDAKVALGERGDPWWEPTEQGRRDRLAAAMRTLLRQRGEDRTICPS
+DAARVVGGEDWRDLMPVAREVAGTLAEEGVVVVTRKGAAVDVATARGPVRIAAGPALET*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002303.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002303.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2dbe691e26eaddd5e9f7811ebc1674e750c68102
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002303.fa
@@ -0,0 +1,9 @@
+>NZ_CP040019.1_960
+MGPGQHAKLTMEGIAARAGVSKQTVYRWWKTKVDVLVEAVGAGYLVIPLPVIPDTGDLRE
+DLAHWLREMQEEIDGGGATHLSQSLVAAIATADSQSRQIHGMLVAPVREQLHARFRSARL
+GDGVDREMLAETVGAQLVMRVLFAEPTDEEWVRRLLDLVAPEGS*
+>NZ_CP083691.1_923
+MTSLTPPRAGTIRPGGRTARVRAEVLRATRELLTQQGASAMRMELIAERSGVHRSTLYRR
+WKRPAGIIADLADDIAGTIAVPDTGDLGQDLRQLAGRLAHQLDGDGGALVRALLGWPDQE
+VQQHLEDFWRDRRADVGLVLQHHGIDADPALVTRLLASPLHYRSLIERHPVDDETITAAV
+ESTILAVLRTPRTSHR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002305.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002305.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f688c1a8e040ec841919349a4bfd4399720ac172
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002305.fa
@@ -0,0 +1,13 @@
+>NZ_CP040019.1_993
+MTDAGPQGPAVPVRTRRVAHPGRVTAVVLVVAALVAAAFLAGRFFQPPSTAADNEAAATP
+IDVWAHAEERVIDDGSSYVATVAAGRTRTVTVAADGPAVVLRQAAEVGEMVRPGDAAGEV
+SGVAYVFLPEPLALYRDLTEGDRGEDVASLQRALRQTGRWTATDGVFGDSTARALRETFR
+GAGSPLPEDEPVTVGWRQFIPVSDDGAVVTAAATYGATLTEDRPLLELQVSAPTIRFTAD
+VTQATALEKGQEVEVSGAFGSLHGTIAKIGEFAAAEGSERAGHPVTVAFDATAEDAPPVG
+QSVTVSTTAAEDVPAMLTVPQTAVRVEGASSYVVVQVPASAREGSASSAPAERRVPVTVE
+RTGGGYAAVSGDLAPGDRVKVS*
+>NZ_CP083691.1_935
+MLVLALLAASFVAGRFFQPPTTADPAAVARPIDVWAAVEQRAVDTTASFAGTVAAGKTRS
+VAVQAEGPAVVLRQTAKPGESVRPGDVAGEVSGVTYVFLAEPLALYRDLTEGDEGEDVAS
+LQRALQKAGHATDTDGVLDSGTARALRELFAEAGDPLPEDAPVTVSWHQFIPLGKDGAQV
+TAAAGVVSALYPAWVASRQRPADALRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002307.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b1f3baf664c1374b8499e3369a59bdd996c0ba6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002307.fa
@@ -0,0 +1,10 @@
+>NZ_CP040019.1_1021
+MTKIAIITGSTRPNRLNRQVADWVLERANGRGDAAEYELVDIADFDLPLLDEPMPAAWQQ
+YANEHTKAWSAKIAEFDGFVFVTPEYNHSLAPALANALSYLNAEWANKAAGIVGYGSAMG
+VRATEHLRAILSELQVAHVQKHGMFSLFTDFKDFAEFQPTELQAASVDPMFDQLLSWTEA
+MKTVRQG*
+>NZ_CP040019.1_1299
+MRLGIVIGSVREGRFGAQVGAWVEEVARGLDTGGRDAEWDVLDVAAFDLPIMTDEGWAQD
+EDGPAEVHRWRDAVAACDGFVFISPEYNRNIPGAFKNAFDLLSAQWKDKALALVAYGGLG
+GVRATEAWRFTVAAYNMHVVGDSVQLVRRADFPDETFARTEHHDKTLSRVLTRLVDLTEA
+TAALRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002317.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002317.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbdd8dab350ddc58af66081a85a1fafbdb33a217
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002317.fa
@@ -0,0 +1,11 @@
+>NZ_CP040019.1_1889
+MTDLAAEHPRTDAVDSVSTRTHDEPFAVVGPWKDDPAAAGTAEKVKVTDEMLELVEAVRP
+TLLADGMFLVGLDIVGDKLMEVNVFSPGGLGSCQSLYGVDFAPAIIEDLERKVSVRKHYK
+GQIGNANLATI*
+>NZ_CP083691.1_1837
+MKIGFVVNDVATEKPVYTTTRLAMAALQAGHEAYLVGAGDVAYEPDGSLSVLAHGTQKKH
+RSLERLLEEVQDPANAAQMPVDELDVVMLRNDPADDATERPWAPTAAVSFGQLIAAAGVL
+VVNDPHTLANALSKAYFQHFPELVRPTTLISRDEALISEFIDERGGKAVLKPLQGSGGSG
+VFLVDRKESPNLSQIVEAIARDGYVVAQEYLPEAKNGDVRMFVMNGRPLEVDGRIAAFRR
+RSSSDDVRSNMSAGGTAEKVDVTDEMLALVEAVRPKLLADGMFLVGLDIVGDKLMEVNVF
+SPGGLGSCQSLYGVDFAPAIIQDLERKVATKDHYLGRIDNTRLAAL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002320.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6065f1eca720ef6d4bdfb8c69defbeaf9a3c330a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002320.fa
@@ -0,0 +1,13 @@
+>NZ_CP040019.1_2233
+MADAVQVCAFNSTYTASQGPAVPCSSSAREREDALLDALDVDPPGSWWSRAAELARPRTV
+VAGDPPREDWLAVPLRRDGPLATTGDLGRAAAVGLVIREDGPLWDEDLVRTLTPPPICPK
+VLEVRTPADWLRLVEAWPEAASKATAEILARHTGLDGRWLVPRWTAVAEQWDAVHLSIGA
+WARSAGVVQPVGEGSAWTMCAGWDPDATFWLTAQPTVASEQVLPTLTPAEALDGLAG*
+>NZ_CP083691.1_1268
+MKASVQDLLPGPRGRRLCLEAARMLSHRVADLVFWLGYELDPDRGISSLVMWPPGGGALE
+AGARPAVSIDQVAQALADLDLSGLTDGVVQAALVGSVMSARYWQEPDGEDVLAGHPDIHA
+ALEAVAAGVLGSAAARHWGSPRAAAQWVIDWRAFEDPAPVPRDARRVLAAWAREERRQEV
+RAAAEHPVDPTANFSGTWWSIPQGAVVSVGQIPTGLDLVEDDIGAEAATVIPVRGAGRTY
+EVRGPGDWIRLCRRFPLEVSASRRHDWYRVTGRSGRWVIPDWEQVASEWDAVHLTTLGYL
+SAATRALPVEAGVATVLAGWDPDTTVWLADAVRESEEPRQCWQRVSGDDGWARCVPVRDV
+GSEGPARGRGASPPVEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002326.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002326.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6684a4fbf5fa21e9d3625acec7f823cd8c5d82c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002326.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_2588
+MLLAGVYFYAAAICTTIINDGGPGWLYLLVLVFVWNAFKFLWIGPVSLIQLISVRAGERR
+ERQPVPSSR*
+>NZ_CP083691.1_1736
+MLMFRLIWIASIHTRDLLHRYMPTNIVLGKLRTRRGLKWGVPAMLLTIPYLAVANILTIL
+IDRGAPGWFHLLVLLFIWNAFKFLVTGPVSVVLLVRARTVERRDRRLLSRSPAPTV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002328.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002328.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ada6ea39ab4d84417216eca6df1840e4cfb205e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002328.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_2619
+MCRAVTCKTCGKTTWAGCGQHIAEVKRTVPAGQWCPGHDKEKEKAAATSGFFARLFGR*
+>NZ_CP083691.1_526
+MCRPATCDVCGKTTWAGCGQHVDSVKASVPAGQWCDGRHTPAEQAAARKDAPARGGLLAT
+LFGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002330.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002330.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35c247dfbef46a79fd6d93f5a17a56af40a4b376
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002330.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_1
+MRSFTRQDQNNNPSEKGRLLSQDPTVCQHQHATTNHMLSNPKAYSHPAGTTTGTIH*
+>NZ_CP083691.1_1355
+MRSFTRQDQNNNPSEKGRLLSQDPTVCQHQHVATNHMLSNPKAYSHPAGTTTGTIH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002331.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2431b8d7b7dd3051307b3bb1566492cb5c7918d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002331.fa
@@ -0,0 +1,10 @@
+>NZ_CP083691.1_43
+MAAVPDSLKLEGARFVGRSLRGARFIDSDLSHVRARGVMLDGADFDSPWLLDGEGSLVVN
+GVDVAPLVEVELNRRFPGRAQRRAEDAEGLRGAWGAVEASWRQATDRASALPDGAVDVSV
+EGEWSFSQTLRHLVFATDAWLSRGIQGAEEPFHPLGQPRAGAEDDGVDLAFFASTPPPYE
+QVLAVRSERLAQVREFLASVDDAGLDEERRHPWSPEYPETVRSCLHVILEEEWEHLRYAL
+RDLDALDDAAAQGR*
+>NZ_CP083691.1_1185
+MPALSAGACGTQRRAEDAEGLRGAWGAVEASWRQATDRASALPDGAVDVSVEGEWSFSQT
+LRHLVFATDAWLSRGIQGAEEPFHPLGQPRAGAEDDGVDLAFFASTPPPYEQVLAVRSER
+LAQVREFLESVDDAAAQGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002334.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002334.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cec8a36c0a5c894efb09b134a02656552bb7d48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002334.fa
@@ -0,0 +1,10 @@
+>NZ_CP083691.1_293
+MSDQNAVLVEYVDPDAVSLPLRVRARSEVWLPAFVVAVVLWVLFVMILLGLPPVLFEDPS
+AMLVLFRWLAVVGFIPLSVYVAYTWMAWRRPRHLMVDEEAVWTDSWRVAWSDVEAIWLNP
+THGLAPDKKTQVGFAVHERAWTDELRRGNRWDSGFPFGLGGMKPRDGMIMTQFATEPPIQ
+SLLPLFERLRARAHGQPPEREKLWPGQEPWDGWVGPWS*
+>NZ_CP083691.1_321
+MTVSDQNAVLVEYVDPDAVSLPLRVRARSEVWWPAFVVAVVLWVLFVMILLGLPPVLFED
+PSAMLVLFRWLAVVGFIPLSVYVAYTWMAWRRPRHLMVDEEAVWTDSWRVAWSDVEEIWL
+NPTHGEAPDKKTQVGFMVHERAWTDELRRGNRWDSGFPFGLGGMKPRHRVIQTQFATDPP
+IQSLLPLFERLRARAHGQPPEREKLWPGQEPWDGWVGPWS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002335.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002335.fa
new file mode 100644
index 0000000000000000000000000000000000000000..518fb70b4260e49b6519deccc32ccbc36214d251
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002335.fa
@@ -0,0 +1,12 @@
+>NZ_CP083691.1_294
+MRQDAGAQTVGNVVSTIAVSAGTGALAGSVLPGLGNVVGFAAGVVSGVAMAVPVADTDGD
+GQKDSVAEMAGDVAEGAWNWIRGK*
+>NZ_CP083691.1_322
+MTTSYVTKVGMSEWESADSMDQLAHGVTVAASSLAEVVSDQDATWQSLGNHYEGDGEGDL
+VNGFFVPVENAARVVLAAEALDKAFLDFSNALRGLWADRRVFETEVDTYNSMYGAQAIET
+LPPGVDSWRAALASMPADLERRYQQAASTCASAVRTIDIEALDLDSVSEGRPGQLGREIV
+AEAAKNALPLDPENPSTSALGLLDVARVREPWLRFDDVIPETWQARFMGLNVGPLGASVY
+AGGAAMVRAAQTRSWAPLRNVPLAMSMTMRNYSNDMAALALRYEDPRKFRRPTWPAFKSQ
+FLDGLPVTGFIRSTVPLWGKRTPATVGAPAPAMAGAYRVESRGAFRLNAGVKGLGAAGTL
+VGAGLTYRDEYDQQLRENQAETPGASREEVESEARQDAGAQTAGNVLSTIAVSAGTGALA
+GSVLPGPGNVVGFAAGVVSGVAMAVPVKDTDGDGQKDSVAEVAGDLAEGAWNWIRGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002337.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002337.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe52b30e3b6c2804e9fa63823ec639dab5dc1282
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002337.fa
@@ -0,0 +1,8 @@
+>NZ_CP083691.1_311
+MPEYDFETYPTTPDAMAKYLQEREAAGNPMTGEEALAYSDWSRERGRAIQAKIDARKTPE
+EREEFRRFAEEFERQCLEDEKRFAEEAAREAAEDAERAAQGKRPIKRERDIVTPKGFSGI
+GVTPRGW*
+>NZ_CP083691.1_331
+MTKYNFEAYPTEPESMAKYLHEREAAGKPITRAEGEAYIEWSLAKEQEITERKERMSPAE
+RAGHEGFQREEEPMGAIFDLEDARSEVEALVEAAEDAERAAAGKRPLKRERDIVTPEGFS
+GMGVTPRGW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002339.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002339.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8011c6c0a3f46ab4ec1f7a0e16b8eee9f2be182c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002339.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_319
+MGAIDQSTDNDADYDVIEQTWLDAGQTVKELVDRARTLMEENDDIAAGAHQKAGNHMGLV
+HV*
+>NZ_CP083691.1_324
+MTIQYDSAAAAAYEDEVLRIASRIETILGDREQQKRFVADNYQSTDNDADYDVIEQTWLE
+AGQTVKELVDRARTLMEENDEIAAGAHQKAGNHIAGMRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002340.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002340.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9864e909dcf47b12c7a6bd7809e8cca55f81e289
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002340.fa
@@ -0,0 +1,12 @@
+>NZ_CP083691.1_332
+METFWGLTTPAWTAIYTLLTAGLLVAAIVAGLYAKRQWETARDAQVEATRPYVLVTLEPG
+ERSMAMVDFVIRNIGVRPAYNVTISIEPHLLRAREEGGNEMAAMRLLHEPTAMIPPGQVT
+RMFYDRMSDRSGRDDLPVHHTAVVSYVDSSGREWTDTFDLDLRVLEGGMFHSYDDLHTVS
+QTLKKMARTLDRSRVLKEGEMDVVAVTENRADHQVRTLLEEYHRQVEIANLHRGKPGYVD
+RVRSFDARAESIAEQLRALGVSVQGAPQD*
+>NZ_CP097650.1_1101
+MDDTFWGMSATGWTAYYTLLTAGLLLVAIAAALYARNQVQIARAAQREATRPYIIVTAEP
+SPIGWRVMDLVIRNIGQRPAYNVKVSLTPEPVRANETPGAPISEVQWLREPIPMLAPGQE
+LRTFYDAMEERLNSGRSDLPTSHDYSVEYDEGTVAAKKGKRDHRDSGVVDLNAMAGAMQP
+DVYNIHHVASALRDIKKEVAKMNRSGTYIQPASEVRDILDQRGPRTKPRSTVPGPLPAER
+SALRRLYDRFTGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002341.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002341.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4769505c99655c73f41e03c7757c326c72aa278
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002341.fa
@@ -0,0 +1,20 @@
+>NZ_CP083691.1_409
+MGKVRGDQAVQSLQPHKVLDSDSSHGRLIRQQGERVPTDGDFTLSDRAQKEIVKLFIASE
+SSLEGRTIGEWFSEDFFESNFWTYWATMFAFETWHSLAEMRRYLLRFVHAIDGLADFSAL
+KFNRYDQYDSMVKPLLAYLEPHGVDFRYSTTVRDVRVETADGKVRAERLLLTVDGVQQEQ
+EVGEDDLVSVTNGSITESTTYGDHHTPAPSTTEPGGSWTLWENLAEQSPLFGRPGVFYRG
+LPERSWFVSATATVESREVEEHIERLTQRPLHDGKVNTGGIVTATDSPWMLSFTVHRQPH
+FPTQRPDQTIVWIHALYSDTEGAYVKKPVTECTGEEITQEWLYHLGVPEDRIPEPAAQES
+VNTVLVYMPFITSYFMPRRAGDRPAVMPEGSMNLAFIGNFAESPTRDTVFTTEYSVRTAM
+EAVYTLFDVERGVPEVFASATDLRELI*
+>NZ_CP083691.1_1163
+MQYTAGNYEAFARPRPAQHAQETKAYIVGSGLAGLAAAVFLIRDAGVPGANVTILEKGEI
+AGGALDGLDVPEKGFVIRGGRELENHMECLWDMMRSIPSLELEDASVLDEFYWLNKDDPN
+YSLRRATVRRGEDAGHEGRFDLPKRAQKDLLKIFLAERAEMEGKRIDEVMGREFLDSPFW
+MYWRTMFAFEEWHSALEFKLYLHRFIHHIGGLPDFTALKFTKYNQYESFVLPLMHYLTEH
+GVVFRSGTEVLDVDFAHRNGEIRATAIRCRRDGAEETIELGEHDLALMTIGSLVDNSDEG
+DHHTPAALNEGPAPAWDLWKRIAKKDPAFGRPEVFCSSIEETKWESATVTTLDERIPAYI
+ERIAQRDPFSGRVVTGGIVTAEDSSWLLSWTVNRQPHFKKQPKDQIVVWVYGLFVDVDGD
+YVKKPLAQCTGEEITQEWLYHLGVPVEEIPELAATGARCVPVMMPYVTSFFMPRRAGDRP
+QVVPEGAANFAFLGQFAETGRDTIFTTEYSVRTGMEAVYELLDVERGVPETWGSTYDVRD
+LLEASARMRDGKKVEMPGPAALRGYLRGKLEHGEIGQLLEEHGLI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002342.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002342.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af0c0ff33aeeee185ec180c831b92fb233c3e203
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002342.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_604
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVISEPADQ*
+>NZ_CP097650.1_976
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRM*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002346.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002346.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa8fd23d382e44da3067721dbe40f9b8096f4710
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002346.fa
@@ -0,0 +1,28 @@
+>NZ_CP083691.1_620
+MNFSVDLNIGDRVLTDAGPARVKSMWALGVELETINEPAKLVPWTDLIIRPTIDGQAQAV
+DAALHPWWDQLPEKVQQDAIFKMECVLEILTGFRSGLASLAQPHEPVVPFGPFSQASVSA
+QCEAMARLVSFEKSADRELMRRVQDGELDSPGVTPRAVHHWVRRWQASGLRGLVDGRALR
+SAQGFGALDPRFLKIAEQEFARFDGSASATNRQEIHRRIQVRMHAEGITDAHLPQRLVSD
+YLSHRFAQLGKTTRAHRSRRHRKISSTASAALHHLGHCATDVTRADNLVYDEFTGKPMSV
+EIATIMSVPARVIVAVRVFPKSVSATEVALLLYDAMRPQSMLIDQDGASDWRWCGVPTSL
+QLPEQASPLANDPASGLGEHAIPAMTPTHLRMDNGSIFRSEQLRRLALHWSITLSHSRGT
+RPTDNPHIERFHETLQRFYQQLPGYKGRNVSERGSWTGVVAEAPLLTAADLERRLRQFIA
+LDYHRRPHTGLTLPGAPEVNISPLEMFDWILATTGRIHVPQHPDLIYQFLPTRWLTPGHA
+GVEYKNMTYDAAVLDEFRSKIPGRFRDEDAKVPFHYDPRDATRLWFRHPDTDRIHEIPWR
+NRHLLHAPLTDVVRDEARRRIRARGGPKALTGALIDRQLIEEIGHLAHTRADETWTTTMA
+ASRMRFDQARRDHDEAALAHRLTTPEAPTDLEHGGRHLRLVPPDAMPDRTATNGLAGLFE
+PWPDYAQEI*
+>NZ_CP097650.1_2164
+MRAQMSAPIQAGDSILTEHGPVEVIAPQSTGLLVRAPGGQETLITHAQVIPRRFQNGTIA
+GVMASLYPLWDQLDQAVRDDALFKLECVNEVNTGYRRGVASLALEGEPFYPFGPGWGVSL
+RARYQAMARLVSLEKRVDRVLMRRVYDGEVQRPEIGLRTLQSWGESFEEHGLRGLIDGRA
+LRKVQDFGVIDVRYRQAADEVFGQFDGEISAVNQQEIQRRIYALLRQRGQSDVQVPDRLE
+SDFLRHYYRRLGKGTRAHRSRSLRKIATTSSAALHHPGYCASDVTRADNLVTDEYTGKPI
+SVEICTIISVPTRVVVALRVFPRSVTSFELGLVLYDAMRPFSMVAADGAIDDWRWCGVPT
+GLQMSAPQCPRHVKEDEGPLGVHYIPAVTPVEMHTDHGSTYISDQFRTLLQQFGITLSLT
+RGGRPTDNPHIERFHETLQRAYQQLPGYKGRNVSERGSVVGVQADEPLLTARQLEAYLRA
+FVAVDYHRRPHTGLIWPGTEEQALTPLEMFDAMLASTGRLHYPQHPDLIYQFLPIRWLTI
+RHAGVEYKNMAYDAEVLDEFRDCRAGAFRDKDAAAPFHYDPRDTTRLWFRHPETDRIHEI
+PWRGRHLLYAPMVEIVRDQALAQIRRRAGRRHSAKVSMLELIDEIGQLATAPRDETWAHK
+LSAARMRWDQGQRDHDEVAHARALQQAHVPKPRTSRAGRDHLLSLPGGRTEDTPPAGFGL
+ADLSEPWPDYPEEHDELA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002349.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002349.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d8a72740476e5d2a48c9b65cdc43390a4594a13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002349.fa
@@ -0,0 +1,10 @@
+>NZ_CP083691.1_650
+MSAEPDGMRPHSPSAQEAYAARAVEYADLLGRMDAVADADKRLVEAWAQRTGGVLADVGC
+GPAHWTAYLHSLGHDVRGIEPVEEFVAHARRAHPEVRVERGSFETLPTAAVDGILAWYSI
+IHTPPAEMPHLFEHAHRSLRPGGSMLLGFFAGDEVEPFDHAVTTTWHWPVDALSRLLTTA
+EFTVVDRGTRQDPGARLHGWIEADRE*
+>NZ_CP083691.1_919
+MEAGTLDAEGGTTITADDVHGENISSCAAYGARAAEYAELLGTMAAVADDDRLLVEAWAH
+ETGGSLADVGCGPAHWTAHLAALGHDIVGVEPVDEFVAHARRVHPGVRVETGSFRTLPAS
+TFDGILAWYSMIHTPPPEATLLLEHAHEALRPGGSLLLGFFAGDRVEPFDHAVTTAWYWP
+LDDLTSVLTAAGFTVTDRGTRLDPGTRRHGWMRAHRN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002350.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002350.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e76da8a6b15a0c64e186012612ece54934ae7be8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002350.fa
@@ -0,0 +1,10 @@
+>NZ_CP083691.1_651
+MDLAPSSSPTIELSWHADLTPGQLDDLNRLFAAEYLEDFGEWDPDQPYGYAPHDMHVIAT
+LDAQTVGHIGWARRSITVGDHHVTIAGVGGVLVTPSGRGHHLGQRLMRAAVDSMRAHSDA
+EFGYLGCHESVVPFYVSCGWRRIVAAERYIGLNGQPSESAQGDPLLVMPLRNAKQPWSAG
+EIDLQGRPW*
+>NZ_CP083691.1_683
+MDLVPSSSLKIELTWHTDLTPGQLDDLNRLFAAEYREDYGEWDPDQPYGYAPHDMHVIAT
+LDAQTVGHIGWARRSIAVGARPVTIAGVGGVLVAPSGRGHHVGQRLMRSAVDSMRVHSDA
+EFGYLGCDESVVPFYVSCGWQRIVAAERSIGRGGQPTQSTQGEPLLVMPLRGTEQLWPAG
+EIDLRGRPW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002353.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002353.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11e13e37ab8c0954a70e30f54ff7e0421297255f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002353.fa
@@ -0,0 +1,13 @@
+>NZ_CP083691.1_657
+MTRMSVLEAWTWINEYGSAIGAVAGVVAALVAIIALISAALDSKARSQPMIAAEFRPAVD
+SDSSIDFIITNLGPTPARDITVTFNPPIVIPDDSDRLLAPYLVKRYERPIPVLNPGQILS
+NTWWAGRAGTGNELTNHEPTPDEVNVTKIYAAAHRARTVFYTPEVSATMRALQEDLRHDM
+IRTERCIEEHLVLHGGHVDHAHGPNPSLLELIIIDESERLTGNAIEWLRDQYDRTGIAMI
+LIGMPGIEKQFTHYPQLYSRLGFAHQYRPLGHDELLFVLERQWRKLGKTLDPDDFTDAQA
+IAAVERITRGNFRLLERLLPQIQRVLKINELDVITNDVVEAARSTLVIGTT*
+>NZ_CP083691.1_661
+MTSQFIVTKEHRRFAEFADAVRKQNTIGVCFGPAGVGKTLSARRYAHWDSIGPFIARWAA
+RSEDDTKIYAAAHRARTVFYTPEVSATMRALQEDLRHDMIRTERCIEEHLVLHGGHVDHA
+HGPNPSLLELIIIDESERLTGNAIEWLRDQYDRTGIAMILIGMPGIEKQFTHYPQLYSRL
+GFAHQYRPLGHDELLFVLERQWRKLGKTLDPDDFTDAQAIAAVERITRGNFRLLERLLPQ
+IQRVLKINELDVITNDVVEAARSTLVIGTT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002355.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002355.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c3f319416ad6bd13239de283d63522075f739c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002355.fa
@@ -0,0 +1,9 @@
+>NZ_CP083691.1_719
+MTKSLISSAVVVLLILLVTVLTDASTWLVGLLSGLACLAGAWCAPLFQSGSPYGGTFFGG
+WQSRWDGPKAVQLLAAGAAVAVSVVLNLFGGGVPAVVGIIVALLVGALIPVPGDPAGGGH
+GADPEDARPA*
+>NZ_CP083691.1_721
+MRMTPARVASAAVLAVLTLVCLLLMLDTWSFMGALLVSLIGAVLFVAGAWFAPLARSGDA
+LGGTPLRPWQAGFDGPKTTQVAGGGLVALLVALVTGGAPLVGPILGVVAAVIGGRFLRIP
+SHAQVVAAVGPEVAEASEHLPGEHHDAAPADSVADPDTDPVPVPATEAADSEKPRHEHAA
+DVSPETAPVPVIHPADAEHPHGSHAAMAHPDPVDDVPGDGEPTTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002356.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf2178492545748b6643a740e997e93dbbc1de5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002356.fa
@@ -0,0 +1,7 @@
+>NZ_CP083691.1_920
+MHGEERSTRAALERAGHVGLASRIGLDGTLVPPDGRAGPGAPDAAGVGYASRVPEQRIIA
+RRSLGNAPTRPDGLRLASLAALGEEQFSTHMLAASGGDPFDTSTEESALEDLLEIIEGAG
+DHFDPHAWYVVGDGEGEIGVVLPQPLPDKPGTGTVFYVAVLPSRRGRGKGRQLHQFGLSE
+LARRGCTEYVGSTSVDNAPMVAVFQANGCELEH*
+>NZ_CP083691.1_1271
+MAVLPSRRGQGMGRRLHALGLAELARRGARKYIGSTGRKKAAMVAVSRANDCIVEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002363.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002363.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83e8d59c8e1b0d6e954bcd250ec051e5a988b719
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002363.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_1754
+MNIYPDFGAFGDNTTLHTVIGALLTFVLVTAVLTMLISGITWAIATANGNHTTATKARTG
+LLVALGTATLAGAGITWLNWLINLGDQL*
+>NZ_CP083691.1_1756
+MLDLMTSVLPTLPMMLPMEVDITPNDDGLPGIAQLRNIVAAVMTIGLILSVLALIISAIV
+WGFGANSSNPHLAGRGKVGVLVSCGAAIICGAAVTLINFFWNVGQSV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002364.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002364.fa
new file mode 100644
index 0000000000000000000000000000000000000000..501e2c5f33c13f12322c8ddf8fc8fbe258262b73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002364.fa
@@ -0,0 +1,14 @@
+>NZ_CP083691.1_1787
+MEGLERVGSVLGMMLQVCVNGARDIAEHPALSADPVRVAAECAEAVAAGADAVHVHPKDA
+HGQDSLQNPDVGRWVREVRARCAGVPVGVTTGAWALPSVEDRRQAIVGWQTLPDFASVNW
+HEPGADQIAATLLDRGIGVEAGIWHQEGLTAWLASPLRSRCLRVLIEVQDIPAEEVESEA
+LVLVQGVRRAEPAMPLLLHGEERSAWPALKLAGRLGLDTRAGLEDMVTFADGRPAPGNAE
+LITVASHLRGRSLEEEPTVMKPYSVPLAEARTAFLAALDAFEEGASSLDDLTLLGVSHVH
+GWSRLDCLVHVRLGLQEMLAGLAARTDDTPDVDAASYWTTYEPEKDPVPGILMTRRTASA
+YARPRNALEHLNQVSAGLRHAADTLIEESIAFQGHVLTAGDMLATWAVELAVHHHDLALP
+AGAPAPAPAAVHIGRLTAEALGSTSGARAGAEDDLAVMLAGFGRR*
+>NZ_CP083691.1_1832
+MSVAGEAERFAQQAHQFAEAASGLDDLALLDPSLCRGWSRLDLVVHVRLGLEEMAAGLGV
+RADDAPDHDDVTYWSSFAADEQDPVPGHMWLRRTASAYARPTDATAHLRDAAERACAASA
+LQDPRPVRFQGKVLSVMDFLRTWSVELALHLVQLDVGVVPSAAGLARRTLEALTGAPLPV
+RLTDHSALRVALGADPWPADEPGGGAYPLGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002368.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9cc55733dbd01914e234b6c9571c788abba7cac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002368.fa
@@ -0,0 +1,12 @@
+>NZ_CP083691.1_2264
+MNTRCLVLTSGRAADGPYGIDQLGQFGYDLVEVEPARTRVHRKLRDVVEHRSGRPMDKTV
+RSVRQAWQADLVLAFLEKEALAASWAKRRGVAPFAGRPLVMIACWLADELQRMSPAQRTA
+VVTSYSGVDLIIVLSRNQVEILVEAGFDASRIEAVSFGYNPDQFPVAAFEERRGIVSVGA
+DRGRDFPTLLQAVEGSDLQLHLYTGEGHLNDVELPAEAVLHGRVPFERYQEVIATASMVA
+IPTHVMAYPSGQTVALEAAGTGACLILTDTPAMREYFTDETAVFVPPGDADGWRTALTEL
+TSDAEARRRLGRNAAAMVADHFTYADMWRQVDEAIRRRGWSAQ*
+>NZ_CP097650.1_498
+MEGVDRLLMFSSNQVRIFTDAGIDPKRLHPVLFGVDERFYHPSKEPRRFQVLAAGVDRGR
+DWQTLVEAARLLPHIRFELYTRPETVAPLAVPSNMTVHAPVGIDEHRHNLQSSDLVVVPT
+HDLAYPTGQSVMLEAMASGACVAVTATEAMADYQDDGVSTLALPLHDPEGVASVIEMPIE
+DAALRRQIAESGRAAIEERFTFTRMWDEIRQVVRDVARDGASTASAFR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002372.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002372.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80bf648b39f3801608f9fb7c2d0b9570577812dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002372.fa
@@ -0,0 +1,9 @@
+>NZ_CP042169.1_33
+MTGQWEWTTLREVLVPQPNKKPLQQGWSPKCIPSPSPDSETWGVLKTTAIQPGRFDETQN
+KELPATLAPRPAIEVQQGDLLMTCAGPRSRCGIPALVRSTRPRLMMSGKMYRFRPVEGVD
+SAFLEKWLLSAEAQARIDAMKTGISDSGLNLTQDRFLALPVPMPGMEEQRRIVDIVEEHF
+ARLDVAEGSLDVADKRLEGLVESAIQLCLDWGSVRQVELRSLLAEPLANGRSVPTREDGF
+PVIRLTAIRDGWVDPLQRKGGDWSRNDAKKWLIRPGDFLLSRGNGSLGLVGRGGLVLDDP
+GEVAFPDTIVRLRPNREKIDLDYLSMLWNSRLVRRQIESRVRTTAGIYKINQEALKSIEI
+PVPSLEVQGRLASSIGGVRLAGRRIAGVVEAERRRTAALRRAILTAAFAGRLSGRSTDTE
+VIEELVASR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002376.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002376.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ff796da7e089ecf784fd61e10b7ed4c0e118c66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002376.fa
@@ -0,0 +1,11 @@
+>NZ_CP042169.1_387
+MEVEGWTHVSPSLGEYRYLSGGEGQRVTAFDVTVPDSAAHLVLQGHAWKPEFPVRVNGAP
+MVLRHVHPLDTPVAPFSPDTRVRVWDFVQHVPVSPGTASIEGVVHASLPTEKSTALLTVG
+FLDEAGRPLPGPSDLPQNPTFGPFVQLRGAAEGPLETQFQIAVPSQARWVRIQGRRGWGN
+SDVMMQAEVDVTEVRSSAAEIDAFLAEIPEGDTLLVIDTTAPPLGHETLSLRPNNLARAF
+ERAGVWVVFLPFSSLQEFPARVSDRILQVARKDFGRLVRGLTTRRRSMGDTYICSSFPSI
+GAVALGTQLKTLGWQVVYECRDDMEEFNRVGYSKWYSPALERQMLIVADKVVSVSTALDA
+KLVSMWPALRDHAVIPNAVNRHVIDQSEGLRTEESFDRREHLRVAGYVGHLTPSWFDWPL
+IAEAARRMPETVFEIIGHGAPQGMSLPSNVHLLGPRSHEQLADIVTGWKAGLIPFLDIPL
+TRSVDPNKIYEYFAWGLRCVTAPMGSVETYPSTWVHRGVDEFVEKLDEALSTPWAPGERE
+AMESFVQSSDWDDRAERLLSYYGITTEGRD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002380.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002380.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93356d5ad6991f877d49751fcd9a3eca49e27b70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002380.fa
@@ -0,0 +1,8 @@
+>NZ_CP042169.1_496
+MKILVYGAVHQQPNIGVSALAAGAEAVLSRAFPDADIRFRSTGPLGDGPMNLSHTAPLLK
+EMVVNRRGLRGWTRSFDLLCDIRGGDSFTDIYTSKMFFKLSAFPLYAQALRVPVVMLPQT
+IGPFENRASRILAKRFMRGCRLVMARDPRSSDFAAELGRPVDLTATDVVFAIERPEPSLK
+HRDVVLNTSGLLWHAGNRHVDSDAYRAGIRGVIDILLAEGRQITLLAHVVGRTDTGADND
+RAALAALREDYGDRLEYVVPSGLDEVRSLMASANVVVGARMHACLNALSIGVPAVPMAYS
+RKFAPLLDQLGWHHTVDLNASGEQIATAVLEEIHAVEGEDLTPVLRTARARIDAAVEALR
+QLSD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002393.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002393.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2743f3551431dc04b136aa1bdddc3c17c273633a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002393.fa
@@ -0,0 +1,3 @@
+>NZ_CP042169.1_600
+MMSSQKDTATLKVQDVHQLQAIAEAAARIAEQLAGEGAAESVRDAIRAVDDQLGDYAGHW
+DEYAAVNDWSSTIKGGLGNHVKAVPATDLF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002395.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002395.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef005aa98761f2b8c3ba39cc17317f8e6a82986f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002395.fa
@@ -0,0 +1,13 @@
+>NZ_CP042169.1_680
+MTARIAVVGSALTRSALVADPRLSVPAGHFLARVSMAGLGTPPVEDADLTGVASDFRREL
+VRRDVDRMLVADLVRLDPDAIVVDVADERFALDVLPSGAVVTVSPEYLESAPPQDGRRRV
+PSGDDEHFALWVAGWRTFLSTLDAVGLRERLILHHGGMAVRTADGTAARHEAAILAAARY
+ADRLADRAAQDLDPARVVRVDDAIRHAALADDGTADPLALAPAAAAALAAGVVAVLDGRD
+PWEVDGLVDVSPDAEPVEPAAPQAPAEPAAPEPSAEPAAPEPSAPYRDVVESDYANYGVD
+PVRWGSVEEFAASGFGPGLHILPLPDGNHLDLIIRGDLGGVGERESVVVFLTGAMSQRNS
+VAPPFFAGRRLSYELGIPWVAVSDPSMQLADDLLLGWYTGSPGSQAHATLLATLRALADG
+LGRDLLLVGGSGGGFAALRLNEELEGRSSVFAWNPQTDLLDYHPPTVRDYLRTLFPGKEL
+DPVAEREAVEARLAEEGIGHRVGTLDAGRRVVVFQNAGDHHVEGHLLPLVHRTPGMTGGP
+RRFATDAEHQVRIATWGAGHAALPAHVTARAVDAMRRGHSASTVATDIDALLAHERGDDS
+DGPDVLVTAEPGGLSRVDWAAFPGEADDGHACTLSRMHGEDVVDQVEHIGPPVVLPRLDD
+GEHWRLEAFDARGRRVHEIHVDGRGDPVLFGGTGGSARPRRARQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002396.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002396.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8654150804afe9c9f650f8a780228bee000433ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002396.fa
@@ -0,0 +1,7 @@
+>NZ_CP042169.1_812
+MNRRALLLALLQVAVAAGILGWVVLLFGTGPFVAAVRVLTWPGVVGALVLGSIGVLVQAQ
+RWRLIARRHGIELGWRAAAERCWQAAFINSVLPGGLAGDVVRAAEQRPVGAGRRRDMVKR
+SLGVVAAERLAGTSVVFLAAGFALLAVRPGLGGLGLLVAAVAATAAWPWLRRLGVRDIGL
+VWGLSAVGWCSFAGLFLLACLAVSPDLPPAQIPYLAAVTLAGMSIPLNVAGWGPREGAAA
+LGFMAWGHAAQQGVEVSVAYGILALVSVLPGGLVLLVRTVQGSRRRRLGGGEIELGAHVI
+AQDEAAHGGGEGSGKSVGPVETNPGDPVSHQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002400.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002400.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6082184c7780370600f77a81e2982479a265e5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002400.fa
@@ -0,0 +1,6 @@
+>NZ_CP042169.1_817
+MRHPTTPFRRQAMVDVLCTVVGSVGLGVTLVHFGKTSAWGSVAAIASGLTLVSVAVVTMV
+RRNPLFSTLADRVTLSRAVLGGGCATIVMLAALDTAPHRSWWLVLLAAPAVLLDAVDGRV
+ARHTGTASAQGSRLDMETDAALLLVLTVPLAFTIGPWVLAIGLMRYAFVVLSWFRPAWRE
+PLDFSQFRRVVAAIQAVVLVVALVPVVPLTGACIILALSLALLLTSFLRDIITLERGTSS
+RGDREPTRVGRTCSSHADLSDG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002403.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002403.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f0b164e5318d29fd81427971570b884a63c7eba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002403.fa
@@ -0,0 +1,13 @@
+>NZ_CP042169.1_871
+MSRPRGFRVLPRARARSAALAVTLGAGLVLTGCTAPDGVEEPREPPTVTASPAPPSAAPT
+ASGAAAPADPASASASTAELARAELYPCQGYGRVPRHNTVESNARDVYAWHVFEPVAVGD
+GHGDVDWDADPYEDEGWRLWLASLRWIGPSIEAAREGDEEAFAVAERLIADWAADHEQGW
+AEDHDDLEANTHRLNVLLCFRSVVLQREGGTVPEEYAWVDELIGRHADQNMARYSARHNH
+GSMENRGLLGAGCVLDRPKWMRHAMQRVEADLPYQIDEEGLSNEAAPHYAQFNYTLFHAI
+DTTSTACGVPSEAFEGRVEAMGEALPHMVDSTGSYWQYGDSAEYPVKPFTGISEGLRYAA
+TQGAEGVAPADRVRAFENGPVFGRSSWGTPEEGFRQAASWMLRSGTGTEKKAHRGDLLQF
+LYTARGRQVIEDGGHPGIVTDDWRPWGLGPTAHNVIHLPTLEEFPGDGAAERTSLTVSPD
+GSADGASARQALTAGGERGRSVLVLTEPDAAVVVDRTRIEDGRAGHVVESLWNLPTEFTA
+ERIAPDTVRAVESASGEATTLVQVRLDGASVGEDDLAIHRGRMDPEGHLHRGWHYPAEQV
+REEATQVAFRSAGPEAGLVSVLIPAGSEDEVGVEVEQHDDGTLTLVVRGAEGTARVGIDA
+DGTPTRLP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002411.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002411.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b3a796bbc0c6028726ef1a3bd0dd24b89189716
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002411.fa
@@ -0,0 +1,9 @@
+>NZ_CP042169.1_1452
+MPAEFWKAAGCRLTKSAGESSWMLEAGDLVGVSRVSTALGDVTLQVLPKLATADVFFLAD
+YAYDQRHEPLRLLPFEQVELDALRRDPAACLLVWHARAIHRFATRWLRRDYRRVDQVLNG
+KIKGKPLISRYVSQHLAVGDPARIPCRVKERTQDTPNNRLLKAGLHYILSRSHELELPAA
+RRVAVREAKAALPLFSQVSDIRTEPVSQRDLTATTHRGAMSHYRSILLSTEALLRGEIMG
+PEVGAGVSTASFMWDMPTLFQEALRGVIDSAPGLALSVEGIGRARVHAHDGKQVRSSKVD
+PDLVLETAAGGQLVIDTKYKDVLPSDHGVDDEDVTLVADRRRIKVTRADIYQVVAYTAHD
+KWRGATGALLYPVVLAEGDTLPRPMQIRGFGPPVWMLFVDVGQQAKGNLPAFLDSVRELA
+DRSAAGAVVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002415.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9aea07da677f36615ce1353096c9bed00ac5a44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002415.fa
@@ -0,0 +1,6 @@
+>NZ_CP042169.1_1462
+MGTLGNPHGTFRLDDPDHWIGSYLRRQDLPEILGVGDDALADLPFVKTEEGEVVDENKVH
+RALGEGRIPGALPPGSRKISLNELVLTAVLRRTFPDCEIQRQVKVKNPRTGRANTVDLRL
+DVPGQEPILIEYDGPSHFIRQYRAEIPHPLARKTELEPSAGMEIVIWPYWMHICSASAQA
+LFDPTVHGVPALWSSNKFFGDFATPDAACVIEEITGRFNAVGEEGYGTVYEAGVDGMHKP
+AHPIIESILDGRAAKETLVPNGAENPNRWLPISVRDS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002416.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002416.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9a97e3b3c0d6e90d30f26599d33c290986f0cef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002416.fa
@@ -0,0 +1,3 @@
+>NZ_CP042169.1_1560
+MTFACGVAIAGLHVVNRRFITPMYDVVLNLAAFLAAVASSVLLGHVLPAVFAALAVLAWL
+ILAVRTVRARRAGHKSAGQRPAGAGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002419.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002419.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55869c130bf37b1f08fd86be6a684623c94370c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002419.fa
@@ -0,0 +1,22 @@
+>NZ_CP042169.1_1900
+MTDLLKDLLDIPATTGAEDYVLRLTDSVGERSRSALKDYVVTEDIAAAFDQALGLVSDAL
+AENTSRAAFLVGTFGSGKSHFMAVMHALLRQDPQARSIPELGPVLHRHDPALRERKILPL
+VFHMLGRTSFEEAIYGGYLTQVRALHPDAPLPALHATDQVLQDADTYRQDLGDAKFFARL
+NGRATDVDEDPDDPWGSVVEGEQWNAVRYAQARAAAPENPLRQELVTALTRTLFTSYTKQ
+ADHVPLDTGLRVISEHAKSLGYDAVTLFLDELVLWLAFAATDVGFFRRETQKLTQLVEAN
+DARRAVPIISFVARQMDLKQWFADAGASGNEQAALDQAFAHQSGRFAEIPLGDDNLPYVA
+HRRLLAPKDDDAAARLEDAFRAIKDESGAGWNVLLDGVNTDERHRGADEAAFRLTYPFSP
+ALISTLRSLASSMQRERTALKVMKQMLVDRRDRLTVDELIPVGDAYPYLVEGQKPLDATA
+QALFSSAQNLWAQKWEPLLRSKHGLTPEQASAPDENVPVGYRTDRRLARTLLLSAIAPKV
+PALRDLTPARLAALNHGSIVAPLPGKEAQIVLGKVKEWAQQIPEIHVDGDGRSPIIRLRL
+AEVDYEKVVERARAEDNPGRRRELIQQTLLELLGVDATARENLFNTKSVPVTWRGSAREV
+DLVFGNVREASWLPDDVFEERPGTWRLVIDHPFDEVGHTTAEDLARVEQLRSSSRERQTV
+VWVPAFLSEERLRDLSRLVILDWLFEGVGDRWDQHSDHLNENDRRIARAMLEGQRDALRD
+SLRLTLEQAYGIAQPSTGALEAGTAEHKMLTSLHRGFADTELTEPSFSTAFSALVDRMFS
+FSHPDHPRFEPGDQPVTVRQLTHVYQHMERAMADPDRRVTLGDGAADVRRIAEPLRVGKT
+AETVFLFGSNQFAFWNGVISRASGDRAQDAEERLTVATLRSWIGTADPDWGLSRELENLI
+ILGWALQHQRSWYMGGAAMAAPDVHKVHDAMELRQQPMPTPEEWARTVETAGILFGTRVN
+PYLTGPAMTEMTGLVNDAAADALPATQALATALTAARAQAPAELGLREDADRERLAHLAV
+DLLGRWSRLGGKALVESLAAVRDSVDPVHLSTSIGTQAADVARAVKAVRWKPMSDAVGKG
+TDEARQLAQDVRRVWHASQHEVHLPQVLPGLEERAYDLAVSGDGPAPGPTPPAVVPEPLT
+NPEQISLPSVRQGAATGRGRLGLTDALQRARTAAEAVLDEHPDANVEITWRVVE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002430.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002430.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa443196b3105c6f4f2754c7379cc5e763df0936
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002430.fa
@@ -0,0 +1,3 @@
+>NZ_CP042169.1_2225
+MSRFQMLSRAQWELITPRLPTRTGRAGRPFTDARTMVEAIIYRYRYRCFDSLEGPARGLR
+ALADRVDLAPPDGGRGHLGHGADKANRRH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002432.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002432.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5f04835a35733438d2f8f852425f2c6ebadeca8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002432.fa
@@ -0,0 +1,8 @@
+>NZ_CP033200.1_13
+MIPSEEEVDWSEVTGSAHSSGPSGSTRETGPIGPTLDAVDGWLSRFIRTTTPEDIHLLTL
+WAAHTYVVEQTYTSPRLQIDSVMPGSGKTTCLEHLAHLARRPLSASTISSEALLPRVLES
+GIRTILIDEADRSLDMKNPIMAGVLATINTGYKRGGSRPVLVKDAEGNWTDREMSTFAPV
+ALAGNNPNLPDDTRSRCIRVLLMPDLDGTAEPSDWEDLEDDADRLQVQLSEAMDAARDAV
+AEARPELPPGCVARHREKWRPLARVAAVAGGRWPSIVERLILRDLQEHETEKEEGLMNRP
+LRVHLLFDLAEVWREGEAFVPTPELIARLAHVAPHRWGAESLKGLTPQGLGRMLMTGYKI
+ASDREPTGARRRGYTRQALEPAWRLFHIDLSDSDRTSPV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002433.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002433.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a37d1359ee38c9d2055596676603779dc950dde2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002433.fa
@@ -0,0 +1,4 @@
+>NZ_CP033200.1_14
+MTLPQTRERRPHAVGAAPWKSYDGDETRIPTASAPEGLATPLFVADLLGRLAEAEHAPSC
+TCGDWGRALALVLALASEHECTAHPAIVESVARTFAGWDGADAAEDRSVTRFRVWHAAAR
+ADINEGMAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002435.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002435.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbf7e754b0fd634e7b8144e4cf8fdb6715ba213a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002435.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_78
+MRTRGHGTQHPRHDHVDEFMRPVRFSLMAALAGVTSLDFPTVKEQLDVSDSVLSRQASAL
+ESAGHLVVKKGYVGKRPRTWYSLSAEGAQAWKGHLAALRAIASD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002436.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002436.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a125147ba2098388b5560cb02bb5a2637fb7406
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002436.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_79
+MAGGPLGVFLAAHLRRAKRRFGLRWILTLALWCLFWVLGLLMGEARPWAGAVTAVGIMTV
+TVGGAVWELRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002437.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002437.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf2ca5f12bbbe5a24773a55f7f5f9157b6275a69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002437.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_86
+MSSSPQTMLSGSFFPISRFRLISATVLLIMSIVALTPWSFETRIGGMALINILLTAVMLY
+GLVVLIIDLMVTRETAAARTVSTEERHD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002439.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a41e897ef085913be453d8f8d94240abb804e16d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002439.fa
@@ -0,0 +1,2 @@
+>NZ_CP033200.1_197
+MLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002440.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002440.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88d302ac4401b4ce028c65dfbef6ae6affe608d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002440.fa
@@ -0,0 +1,4 @@
+>NZ_CP033200.1_221
+MDILHSARRLKHRLWLAQKHGAHVVTEGRDLIYRMSSAVSPARYDAARYELDFTALTGRN
+TSWKPDRPIPRVVWCVWSGTNAMSANRAACLQSIREVQHDLDVRLVTPDTLHEVVVNGHP
+LHPSYEHLSDVHR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002441.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002441.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3922ea7ec5aff4ee79e86a060b81922c55b4201
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002441.fa
@@ -0,0 +1,4 @@
+>NZ_CP033200.1_253
+MTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGKRGAPVAAAVSTDALTAPMQ
+GTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVEPGQTVTAGTVIATI
+ADAE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002443.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002443.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4673f0e172c1ee4e036094a4632482234bffb83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002443.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_341
+MRTGSVSSTSNGGTSRIALNNGKTYNATNGLAVPANGSVGRTDGTCRLGLDRTEACGTTG
+QSPYSVAGSTGASSTAVTAISLYRSITVSGYGTTVVYLNATGVGTNLSVSAAPLI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002446.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002446.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08d74867aba821aa01ad5bf4e59e66f1c5411cd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002446.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_350
+MARFSAVLDACVLVPIAQADTLLYMAEAGLYRPLWSERILEETIRALETIHPDMRETGAA
+RRRAAVMNQAFDDACV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002449.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002449.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b24274abc64a36d736e7b6882ea85faf6af29c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002449.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_362
+MVARCLVDADQGSQFRSGLLQDALTRHGLIGTMGQVGPAGDNAAMESFFALLQKSVIDRG
+RWATRDESIMDPTPAHAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002450.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002450.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d77e100c6ccbd3ad5a133e00a1bc2d91d9bac074
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002450.fa
@@ -0,0 +1,5 @@
+>NZ_CP033200.1_485
+MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVKR
+ISELLAERSKDIAALITTEMGKSLGAAVGEVRYSAQIFGYYADEAEELLADQPIKQFSGQ
+EAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFTE
+AGLPEGVYQNVFATHD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002454.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002454.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cfe2a90c8f0e3a3bf369453d7a484a50d2c1e777
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002454.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_1075
+MTTPTQFLRSKYRAIEGGCVTCAGDLAVVESLPGVKEVDALASGLVLVTHDGTVSDDAVV
+AAAKKSGLPLVAAGPARPVRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002455.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002455.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf03ab90ee5ce9d52b31f76294072e9ecc7160de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002455.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_1108
+MLAGDGALDGQEQVDAVFRVSRERRAEALPKGLTESTLREVVELLGADPETALSAAEVGE
+RLGISRVTARRYLEHLERIRRVRRSARHGGRGRPEQEYRWAGRT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002457.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002457.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97de2a349214c21fbb226eb7988a4bbced58391e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002457.fa
@@ -0,0 +1,10 @@
+>NZ_CP033200.1_1291
+MGQKQKTKSFQLGEIPSSSDAWWNLFNFAAEAQWEIPGVSLESFANPESIFLRSAAEISL
+NQPTRLRLEHGGFHFAVRLADNSSVPIDIDADIIPNEYILSSYEYEYSTKNFTYRGYKAQ
+RTSPADLTVILGHELTIDLKEVGSDNGKCDIKYPLSRYLAHRVRDLELYIDILEYGFLTI
+GSYGIQVDTTAVSDVHIQEDKEYLETLRNLLQNIEYFGGNAEKVLVDSINDDQVRAIQAA
+VESSRSHQRPPGYRGSTGRVRFGVGDKSLELFVYARDDEGQIDVTNLFGDDNGFWLASTE
+TVDGGESSRLVTPYEFIDDEDLVGLININLSSISRHYERIKGYDGVEQIADSMIIRLWRV
+AVKQEDRREEFRSAALSLALWVSCAYVNSTQRLRYLTNIHLLRFWANGFAWSDDSQRLAC
+RRLQQDVMRANLSDISLYHVCLTFLLGSEVDLGDTIQGLNENEMKQLQSWPVWDLIGEAY
+PKLTAT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002458.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..152905e7ea100cdae52abaffab355817b5a18b70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002458.fa
@@ -0,0 +1,4 @@
+>NZ_CP033200.1_1357
+MAENTSPTPDPRTRGEHGTEHAAQAPFAVTRDYAAEVDEIRELGRKLGGEKKTPTPDPQA
+WREGYPYKTKLSRKSYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGGAICQG
+PLSSAHRRPVFLPAGGHQNCPLVASWFARLGGGAGHRDGISSVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002461.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b52e46c6c7808838c3741d074fc548a4f7b79ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002461.fa
@@ -0,0 +1,6 @@
+>NZ_CP033200.1_1610
+MTFRPTHYRLTTAALGVALALTLTSCGTAQDAGSSSEPATATVVDSALTRIKEAGTLRVC
+STGDYPPFTEQTESGDWKGIDVDMARDLAETMGVEPEFVKTSWKTLMDDYTSGACDVAVG
+GISLNPERAEQVYFTVPTQEDGKTPITRCEDVEKYDTVAEINQPGVRSIFPEGGTNEKFA
+REHYPQGELLTHDNLTVFDALAAGEADVMTTDRSEVLYIDHEYPELCAANPDEPFDYFQK
+GYMLPQGDEVFKHYVDQWLAIALKDGTYEGFAEPWVGDVELSLED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002464.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002464.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c8fdd090e5e608edaf006b678b8a9440381e3a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002464.fa
@@ -0,0 +1,2 @@
+>NZ_CP033200.1_1890
+MTLAELEEGQVLVTSTVMSVGPCMGGHMNDVASDVAPFEVDAPSTAAGSAP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002465.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002465.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f63d0691960b278324923086c648d95f0fbc1951
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002465.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_1891
+MKYSFQANEANGAPQQAVLNGWHTNDLLGIQAKIAGDQRDQSHRLTALVFFLGLGLLGDL
+VLRNAEAFRESKGS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002468.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002468.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67cfd407833b4a68b30bf9449eef7a4a5496b63a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002468.fa
@@ -0,0 +1,11 @@
+>NZ_CP033200.1_1928
+MSKFHVDQIATRIRELYSTDYWDANLSDVNNLSRLLARYAVDLTIPESSDSGNQRIVEVI
+DGGEDRGIDAIGIDFVSQLVVLVQSKWRQDGSGTMDLAGLLKFRRGVETLLGIRTDNVPV
+SASPEMRMAVSDILKKPGTRMRFIAVTTAQEELPTQQQESMNELLSSVNEGGASEPIASF
+VHLGQGALFDSIVEREPMDLDLNMQIFNWGKIDEPRRMVYGRVDAAQIAQWYRDHEHKLF
+AENIRLVIPRSDINDGIRKTLTSEPENFAYFNNGITMVVRDMQVAPAGSATREAGYFTAK
+GVSIVNGAQTVSTIGRISKSEGSLDFLEAASVMIRCIVVSDEEAEFGRLVTRYANTQNDV
+STQDFAFLDAEQHRLKSEIKVMGFEYLLRSGEDVLTESSDKRIDVRSAAIALACAHRDVE
+LSVLVKREISQLFSDRYRTIFNPSTDPRLLVSSVLVNQVVENKLGELEPLTEGVKNGVII
+HGKRVISHLILRGIGTTNLSSSEFAIENYDSWIEDECERIVAALVENFPDNSYPGNVFKN
+TIRVRALLNESSLL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002470.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002470.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9827dd60af8534dabcfc75d4176d3e76211e38d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002470.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_1981
+MKDRGRLLGIAAISVTSLLWGTTGTAATFAPDAGPLAIGAAALGIGGLLQAAIAIPALRR
+A*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002473.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002473.fa
new file mode 100644
index 0000000000000000000000000000000000000000..241a7580ca5f24b3e35c25c455fcdfb478975548
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002473.fa
@@ -0,0 +1,4 @@
+>NZ_CP033200.1_2134
+MFGAYADRVGRKRSLFAAMMITALGSLIIAFTPTYGTVGVLASVILVIARLLQGLAHGGE
+MGTSVTYLVERAPQGRRGLFGATSWVSVVVGTILATLVGLAVNTLLSHEQVASWGWRVAF
+GIGGVLGLYALYLRRSLTESEHFTAAQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002474.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002474.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8181f35ff30cb5f881ffda87157f5a2fe1e6889
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002474.fa
@@ -0,0 +1,4 @@
+>NZ_CP033200.1_2163
+MPPDGCRRRGGFICGERRHSDLYKWAYKLVPVVDSDLLADCFDLAWDIRRLDMEASPYDL
+TGVDDLSDGCGGYAAVRIEEPTGRAEYARRQREFAARGQALRVRLLAVLDEAVGAAPGTG
+PDAEWTSSARP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002475.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002475.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fdf040fe661e56726cae3564f1bed4daa3a4fc25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002475.fa
@@ -0,0 +1,4 @@
+>NZ_CP033200.1_2165
+MYGDGFAEERSWGINDGPRVGNVGSSWAPDRGFFLEVGPCGIDNLIVGDLTPRQARTLGS
+RLLEVADRIEELQAEDVRDAVRAIASKKGGGTITDLARAADRLGVQVVTMGAAWEAAWAE
+LGGEQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002477.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002477.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07f7ea7cce511cd779b95fcc1a506e5c4c78a693
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002477.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_2167
+MTGVESPEAGRVEVSTDLTDPRTENSTEADQAKAICEAAADVEGVDYVNVTESDGTSWVL
+FGHPRYPAGECTEV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002482.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002482.fa
new file mode 100644
index 0000000000000000000000000000000000000000..435d8cda14fea6d85527c394eea84da37a113f72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002482.fa
@@ -0,0 +1,4 @@
+>NZ_CP033200.1_2172
+MKHPHITHAEAEAQAHPLPLEDQITYWKARGRALERAAQRAQTHPRPEDAAPETAPTPTG
+PDPVQLEMLEARMEAAAARRGIDPDPLLPYLRAEPFMNEDGRVERAAVETFFQQLADARD
+ARMVRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002484.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002484.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b75c5e39209dbd1147fdc34287964fb842e490e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002484.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_2175
+MSTRRAYTEDDVARFMDLARGGRDRHRPTTGTRELTDRRPIPRDWPAMTNADGSPSAPLP
+TADPEKE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002486.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002486.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b5c4cc666966a87d9b7b180507abc49f83626c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002486.fa
@@ -0,0 +1,2 @@
+>NZ_CP033200.1_2180
+MAPTLYSPREIAEMFGVSTRRINSLIREGALPVYVLGPRTRRIDVQAAREALALERP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002490.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002490.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54b251e8a3c1f0f3739cf97ded58370f6bf2622f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002490.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_35
+MSTTSRPTPKHAATTAPERIAAELAYLRNECDSIRHALNRSRERA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002495.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002495.fa
new file mode 100644
index 0000000000000000000000000000000000000000..860c4163484641127c1b0f664f037164ef0d0406
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002495.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_43
+MNHLTDAECRAELERALDEVDALVRVTEPANAFMDALGRSETWTRFLTLPHAVPTTGAC*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002498.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002498.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0727f13e7190b51eaab03f8fd77a93ed1df06a27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002498.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_77
+MTSTGSAGLDPADVAAFRALLARPETPAEELDDDAVARLAELGLVRRGGDGSLAVMPPHR
+PLLAEAHRAQARADALREAAEVLRGEFRRRPGAGREAIEVVVGGTEIVGAAVQLTRQARR
+IVRGFDRGPYFHAEALPEAAQSRSWERGVHWHVIFEGRSLQSEPPERWELLGSTPGETGR
+ILPRLPFKLLIADDAVALIGLAGVAGQGEGLVVRGSLLVDALVRLFELQWEMAVPIADVA
+GPDDDAAALTEQERRLLAMLSSGMTDEAMARAVGLSHRTVQRRLAELARRVGAEGRFQLG
+VQAARRGWV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002499.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002499.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1374dcfff0832714076c3e306eb32e5719723d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002499.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_93
+MTTTALTGLDLRIATALQVDPRAPWRRIARVLDEPERSVARRGAALIETGAVVVAGMRVR
+AETALLRVEAAPGIARVTTEALAQRADTTFAYAVTGGADCVAELIFDPGRMRPVLVNELP
+ATVGVVRANTYPVLRYFRTIRKWTTGALSAEQVAALSGEDGPELSAMHPTLDPLTGTDLR
+LAEALEADGRATMDVLARAADVSESTAARRVAALLGSARLQVRALVEPAAVGLPVEALLW
+MRAAPGSVEELGRRLARDPRVRYAVAVAGEHQVVADVTCRTNQELYALMTSSDWAPLADS
+VDTTLVLHARKRGGRHRAWEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002505.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002505.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2ab02e77c5ef0897056f2ffe79e26935f41d9aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002505.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_132
+MLFLARMDVTFPETMTDETKAGFQAREKEYSGDLQRRGVMKGIWRIVGEYANHSVFDVDS
+HDELHAILSGFPMFPYMNVRVTPLATHPNAIAEDFFTTAEDRAAL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002506.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002506.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e804f0b69557f9d032366d18db2a942269f79c89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002506.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_133
+MKITRIEAIPYAIPYTRPLKFASGEVQTADHVLVRVHTEDGIVGEADAPPRPYTYGETQV
+SIKNVLEEVFAPHVVGLSVFDRSQIHAVMRRTIHNQVAKGALDIALWDAMGKALKTPVTT
+LLGGWTDSMRVSHMLGFKPAQELLDEARRFGEEHGITTFKLKTGRRPLSLDIEACHVLRE
+GLGDDVDLYLDANRGWTANEAMEVLRRTEGLGLSLLEEPCDAKEAMSRRRLVEKSPIPVV
+GDESVPTAGDASRELLSGGCNAICIKTARSGFTEAQEILGLCTGLGVDVTMGNQIDTQVG
+SLATVTFGAAFEATSRRAGELSNFLDMADDLLAEPLQIRDGRIAVRHVPGVGAAIDEDKL
+TRYRTDR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002509.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002509.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd0dccf138adb773386748b106a035c9ef331f3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002509.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_156
+MPRRQPAADRSALLDHALAAAAGFAEATFFVVVPDVWTSRVAFERPRRGLATAASALAGA
+LAGGAVTHAVSRRAGAARTRSWLTALPGISDGMVDTVEARVGAGGHLALITGPSRGIPYK
+VFARCYGVDAARPGRGLGALLLASVPARLPRFLLVTGGVGLLGARLRRRAPGLGRRGRGV
+LFWTGWGAFYAWYLPAVTRAYRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002510.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002510.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03ecb8016057247e300788e7d8ac1a961ea32020
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002510.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_167
+MRKALPTAVTAAIGLALVAPLAAAAQEGDTAALSVLHGVPDLTVDVYVDGELTLDDFTPG
+SLAGPLELPAGDYEVAITAGDAEDDSAPVLGPVDLTLAGGGDYTAAAHLDAQGNPTVTAF
+ETDTTPVAAGEGRLTVRHIAAAPAVDVWADGAVAVPGLANPDEAALELPAATLEAAVSVA
+GTTDPVIGPADVEVAEGVNTVVYAWGSATDETLALATQTVEGLQSAPENVNAGMAPAAQD
+DTALYAGAGVAALALLAGGAMAVRRKAAVRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002511.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002511.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c258db701b4fe9b1225ec46d2e1e57d9d55f8105
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002511.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_168
+MPDRLSAATRRTTARATAAVALAVGLAAVTTGCTAPGAAISAESAGPSATSRPSDAATAV
+SDEGEVGARDVSGRRPVPVRQATPRPVQAPIPPTRLNYPALGVDMAVESVGMADGGEMQI
+PDDADVAGWYRFGSVPDRGVGSTLLAAHVNTVHQDRGALYHLDEARIGDELQVVDAAGTA
+HPYRVARVEHLQKATLDWLPYVTRQGPEQLVLVTCGGEWIEELGAYDENVVVVARPAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002513.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002513.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f40539056a2e9336b266fc484a6f0bde3d146b96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002513.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_170
+MDRIVVHDALDRLGPPQDEILRLAFHKDLPQKEIAERLQMPLGTVKSHIHRGLAALRATM
+TRTEEVHDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002516.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002516.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e27403478e797111542b54f9a7434fd7f5292285
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002516.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_217
+MKDTTGLSIGYRLIWRLQYIALFFLGPAQRPAHQDPRRLLRRERAQKVLDAHAARGTEAD
+QTVHDEAAGRF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002529.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002529.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3fbc451e7c002576e08165bfef4f5755a67f843
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002529.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_354
+MVSRYGLIGEDDDGAPDTVLNPGDAWFEWGARPASLAEAQAAVEESLAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002532.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002532.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd84e2547d195f3e81eb20ac55ebb99c4df5cad2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002532.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_379
+MPAAYHREFRQDVIAIARKGQMPIAQVAKDFGIAESRLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002533.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002533.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07e6fb0b5abb346c991762cb706bc5f51b203bda
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002533.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_395
+MLETPTALIVDYIDEHKHEFGVEPICATLSAAGTQIAPSTYYAAKTRPPSVRSLRDEQVL
+GLP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002540.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002540.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2026362032ed31b7996849a61e63a7920f86cfba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002540.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_451
+MITGSETPRETIAFFALIIGCYALPALCFAAAKRVLLALLSGALAVVSFPLALSIGYVVE
+MLQSQQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002543.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002543.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d246d1d50e2e0e4d2f80217f504336b37a4a111e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002543.fa
@@ -0,0 +1,20 @@
+>NZ_CP040019.1_463
+MTAPHPAQEQDTFDLGIEFPGRDTADIRQWRLEEVQIANWGTMDGRIHRFPVSRRGHLIT
+GPSGSGKSSILDAIAAVLTPDKWLRFNQAAQGGAERTATRGLVSYVRGAWTRRQDEDEDR
+VVSAYLRPGATWAGVVLTYRDGAGGVVSLCRQFFLRGTAMSRADMKDLCLLERSAVDLAE
+LQTLIDDGIRTRRVQARWPQAVVTTNGGHGPFYARLRSVFGIRDDAALHLLHRTQSAKGL
+DSLDQLFRNHMLERPPTFAMADRAVEEFGALRTAYERVVDLRRQRDHLLEVRTAAQEYET
+AVAEESRLRRLEAAIHPYHQARFLAEIRRALEEVQASLAGLHAARTEADAEQERAEQRRQ
+HALIALASVGGDRVAELGRQIDAAQEQHRERLARRAVLANRLRAADVDAEPSTAVEFGEL
+QAAIAADLEAPPEHPGPSHAQLTELSRLREAVRELEADITALRRRGSTVPRHLASVREDL
+AEHLGVRTDAVPFVAELLDVDARHQEWTGAIERVLAPLSLTLLIPTRLLSAARTWIDRRH
+LGVRLRFEEVRPTRAAIRPASSQDSLVHKVTVKQGVFHDWLQARLSERFDLACVSTAAEL
+ARHERAVTAAGQVKLSATRYEKDDRFRLDDRSRWVLGDPAAKLEVLVEERAARQAAFAVV
+EGEVQRAQERADAERRRRATLRSVLETPWTDVDHAALERRIADLRAQADELSAASGDLQA
+ARRRDEAAQQDLRTARQAADEARLAAAQAERRRAELTQEARELEAESTGREPLPAELTAE
+LDARFRAVRRSATRSALTESADLVRRDVSALAERARSAGAQAGERCTVLTTQFSRQWAVA
+AADASPGVEDRGTYLAILERIVGQGLPEHEDRFHQILHERSSVLFGELHRAISTAPGEIE
+DRVDPINSALRRSPFDEGRFLHLRVRVRRPEAAQQFLRDLSAVAENAWADDSLDDAERRY
+TALAGIMDRLASSDHVDRVWRQQCLDTREHVTFLAQEVDDAGAVHATYDSGAAMSGGQQQ
+KLVVFCLAAALRYQLAAPEDPRPRYGTVILDEAFDKADARYTRMAMDVFVEFGFQMVLAT
+PQKLLQTIAPYVGGITTVENPTRRLTQIAEVMWEDEEK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002552.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002552.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e4b5a6fe249f60f3e7264387992d1ed53ba7c7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002552.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_476
+MTTLTHRYIDQVVGRVAADQRHDVAAELEGLLADMVEERTAAGVPEAEAERSALTELGDP
+ARLARRYRGAEEVLIGPELYPGFVLALRWLLPFVAVVALVTSAVDYAASTPVPHLGQAIG
+AVAGPLIQALFGSVGALVLLFWVLDRVLPVESREAVRRDVAPEWTVDALDDDPGSDRGAC
+SEAWASLVFLAVAAVLPVLPTSFLYVGHLNDGAPFVNQALWDFWIPAYYVLLAVGVVQAV
+WVLIRRRQTPGSLVLQAALTLVTAVFFTALVLTQQVIDPAIAAGPVQTGVHPLDWVDGLY
+VAVIWLVALWELWTLSRQWRTRRRSGRRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002554.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002554.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cdcfd94119a696fd35b52996fe8c2a7d515be2e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002554.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_479
+MPFDQVTAEHAAAEGDRTLASWRAEHERFWRAHAASGFAPDMPVVCEAFRVVHRRS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002555.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002555.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1011698b1c6c5b7183ec6d67df25aa2bc7d48a86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002555.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_482
+MKFVILIHSHPQPWAHPTSEHTAEYQALPPATQERAEEIAAAFSCPGDTVELRPVWEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002558.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002558.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3af79eb8d6819d7d1bfd8936c7309312c7201703
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002558.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_488
+MGVYVAGGGLGIVVSGLALPWALNSFPDDVGWRVGWGLLGAVGLVAWAVAARAARRVPAP
+APRAAGSRAPVRGMVPLLVGYTLFGMGYIAYMTFIVALLRGDGATDQQVAVFWVVLGLAA
+VAGGFAWAPVVERLQGGRAPALLMVVVALGAGLPLLWAGPVPALASAVLFGGTFLALVGS
+VTHSAQRVLPAAQVADGIGLLTTVFALGQSVGPVLSGVLADSADGVRAGIALSVAIVVLG
+AVAFLPQRRVLPEAATTAGGAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002559.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002559.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3cce66e237134a0f59a7c860ce7e9e1dfb09701
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002559.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_495
+MPAATLDDLRRARRVLFHGVTGAGKSTAAVRLGAVLDLPVTLVDEELGWLPGWVIRTPEA
+QVALAEPILAGERWVLDSAYRFYREAAVARADVVVGLDYSRAATFARLLRRTVRRAATAE
+PVCNGNTETWGRALGPESILRWHAQTFEAKRAWIRAREADDAGTPVLRLTHPRQWERTLA
+ALAAGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002561.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002561.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb8597ae940a083f0a27bae967cc7b96bb1ff2ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002561.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_504
+MTASAPDPATTASPLTVLPVLRDAPAADPDGERGVVRRHHTGDGASLITFTFAPGQGWPE
+HQAAHPITVQCLAGRLDFTVGDRTERLVPGVVAHLPARVRHDVAAPADSPDAANVLLLTM
+LT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002562.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002562.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b645659a3be0194c3ec04286e868b98e7dcbe7ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002562.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_506
+MSENAPDPRRRLSTAEIDAAGLTDWRLLAGRLQARFAPADYAAGLDLVARIGAAAEDADH
+HPETTLTYGHVVLTLSSHDVGGVTSRDVRMARRISALAAELGAGADVAGLTRAEFGLDTD
+RGDEHARYYAALLGAEVTAGGEVTDPALQAPTLWWQGSAGEGSASETPLPAPEVEQRWHL
+DVWVAPEEAPARLRAVLDAGGRLVSDAAAPSFWVVEDVEGNRSCICTSQDRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002567.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002567.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a11d87ce5957e67e42986438fc1ffc56e525265
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002567.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_571
+MSTASTHPTTAGRRPGGAAVAPGTAGPGRPEPRRTEPRRTPFWTAVGTVAAREMKVKGTS
+KPFIITTLLLVAAALAATLLVPRLGDLFAGDGTSVGVVEQTAPAVAALGEDYDARTLGSA
+EEARAAVERGDVEAAVLPSADAPGGLEVLAMTDVPTSLVQALSVSPAVELLDPSAPNPML
+RYFIAFGFGLVFFMAALTFGQQIAVSVIEEKQSRIVEILLAAVPARAMMAGKVLGNAAMA
+ILQVALIAGALLLGLQINGDVLPLDGLGVPILWFVLLFSIGFVMIAALYAAAASMVSRQE
+DIGSTSMPVMMMIMLPYFGVIFFNDNPDALRIMSFIPFSAPVAVPLRIYLQQGQMWEHVL
+ALGILVVSTALAIWLAAAIYERSILRTGKALTWRQALQRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002576.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002576.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c86c1f5c6fcd023fe09751af43ecd94c6d1f92f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002576.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_608
+MIAFIDEHLDQFGVEAICRTLRATECGFITST*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002577.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002577.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5b2d6a4c92fb6eafe27c189fe8e2b9b3c252aa7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002577.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_609
+MGTVGDSYDNALAESVNGLYKAELIHAKRIWESVEAVELATMGWVHWWNTTRLHEALDYL
+TPAEVEAAYTHDQDSAPVAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002578.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002578.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41719953ace795cc89bd6a21e6a325ba376bc7b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002578.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_614
+MRPSSSRALAMLAAASLTALTAAPAQAAPAASTGAPSSSSKHAFEFGVIGDVPYGQAQVE
+RFPDMIDELSAQAGELEFLAHVGDIKAGSAECSDAYFWMIRGEFDRLALPLVLTPGDNDW
+TDCHRKNNGSYDPLERLDTFRDVFYPRADRTLGDTSMRLDAQDEIGLPENAHWREQRVEF
+GVVNVQGSQNSTLPWSGLGLTEQTPEQRAEVAARDAANHALIRDLFTDAERTNARGVVLM
+LQADMFEPRLAEGGVISPEDAAASQAFTKTVRLIADLSREFGKPVYLINGDSHRYTADAP
+LAAGSPWLDVYGVAPVANLQRVTVEGDATSNEWTRFTVAPNSAGKGKNAQQPLLTWERVP
+YTF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002582.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002582.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb44931e407e88ce1a62f027ef379115de27a444
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002582.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_691
+MPAPYPREFRDDVVRVAQNREPGTRLRRIAQDFGI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002583.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002583.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d9994ee2081cab06bdb4bca07542696c941ac0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002583.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_692
+MVSRSSHPDTETAPGRVRIRTDDGVVLLRCARGAQGEPPRLGLEDSGSTFGLALHAERCA
+APVPGVRVEVTRSGLFAERSPAGTVLLPDDGGEPLWLSAPERSAAGQILLGVVEALRAEV
+LPGHVSVPPVPAPRARVERIARWDEVLAPNGLAGGLAPGERPSQAQQALGGAWRLVLDAA
+PDLPVEARLWLAHREQVAGEKVVRLTATWHGPGADVPWHVELHVSHRLGEGQTEFLVIDG
+STQEEWTIADAVHVPGVPLTWRVHPAPRPDTAGRTGEGLYALIDALAHACPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002586.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002586.fa
new file mode 100644
index 0000000000000000000000000000000000000000..095eec465a01c2e5236f6a8821f08e5517fc61f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002586.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_701
+MVADSEAAMPGHAMKIGEVAGRTGLSLRSIRHYDDVGLVPPSARSEGGFRLYTEDDVTRL
+LRVMRITPLGFSLEETALLLEVLEGPAAEAPREDIAAYLERARKGRATLARKLRQADELL
+AELEALGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002590.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002590.fa
new file mode 100644
index 0000000000000000000000000000000000000000..661ba422dab4af699312fd7616579fc76c5e7159
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002590.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_731
+MKVREGGRVVNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLV
+TSDAHTRDCARRLPRTCPARPGSAAAPTTQRI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002591.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7850022552f4ed0b981d0dcc7ca6047478d0e974
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002591.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_732
+MGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLDYVSEKLPAVAEHLDAARADILAF
+TTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRR
+YLGLEVLHRCRLTPVSNTGDEVDTDTALELSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002592.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002592.fa
new file mode 100644
index 0000000000000000000000000000000000000000..afb726312e3acca740e349658cea611a3e8f3492
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002592.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_735
+MPKKYTPELRERAVRMVLERQAAEGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEVAPV
+PAGESPAEEIRRLKRELAEARRANEILKAASAFFARELDRPTTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002598.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002598.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62a6b1319a66c3ee5ea6330b1d2d48cc8f5e631d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002598.fa
@@ -0,0 +1,12 @@
+>NZ_CP040019.1_774
+MPRRPPSSSASGAPRPARLAPLDARQRLQRGGEGRVLLLERRRGLDQRFVPGRGVVDGTV
+RDGGLLGLDLRQQPVPQPRRGDAVVPVVVLDVGADRPRDLGVPGLHRGDVPVVLGDAVRR
+RRDAVLRPVLRPHVERLQLLDGVARHTGPQGGADRGVEVHEQARAEPVVQLALAHPVAHR
+EPLERRDLVRGVVVDPHPRVGRAPRLHERHELLERRPLLAAGVRPQPREPEVPEGRAGGV
+PARGLHPAPQVLQPLHLTGGGGPQRVALEVEEHVPLAGLGQPEDRHRVHDGERRGPVRPP
+GRQLGRGLVPQRPPRALRHPRGGRGGVRQLLDGLDPGLPQPRALQAGGPGGEQHVPVRLH
+RLRTGLARPADRQGVVAPAGGLPGGHVCPQQALQPGPLVPIHRDDLGEVRPVPGAVAQPE
+AAVPGARHAHPVQQVRVGGDLQQRRHAGVPGQLGVHHLVGALGVLLVPAQHQEVGEAAER
+AVVQHRLEDDGGPPRQRLRGPLARGRHGGRGVRARPLQPHHLLLAMLGHQAPEGALLVGV
+AEPGHALQHGVLDGEPRRPPQRRIHLHAQPPVGARGGGRDVRGAEGDERAVGRDADHGHT
+LGVTPDTARPHRSAPAVVIRCHEVGGAPVRLDAGHIDGVT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002602.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002602.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f1b22b7b68bb60145c00d9b458ee16fc817a477
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002602.fa
@@ -0,0 +1,9 @@
+>NZ_CP040019.1_798
+MLVAAPIAALVAVVFAGGPLLASYTQVFMPALGKFIVGFFPLFLAGAVFGKLMASTGYAM
+AIARWITGLIGARRAILATVLTGTVLTYGGISVFVVAFGLFPIAYELFRQADIPRRLIPA
+AIAMGAFTYAMSALPGSPQVQNTIPTRYFGTDAFAAPLLGVFAAVVMFAVGMAWLSFRAR
+QAARRGEGFETTWTGGGMAGELRGEEDHLTEDTAHLEQESARAARTRHGRPDPPVALAAV
+PLLIVILVNLALSRWILPTLDFGYLAEEQWGATTLTSVIGLWSVFVALVTAVAFVLLVNL
+RRVRVLVEDLHQGAKDAVLPVFSTASEVGFGAVIASLPAYALVRDALLGVSSNPLVTASL
+ATTSLAGITASASGGLSIALETLGADMLASAQAAGISPEALHRVASIASGGLDTLPHSGA
+VITLLLITGMSHRESYKDVAMVTVVGPLLATALVVVAAAAL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002604.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002604.fa
new file mode 100644
index 0000000000000000000000000000000000000000..990d882ec9d4e8cae6308b86fdfd008656cccea2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002604.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_800
+MTTHDLTASNPEQTERERFDRGMARMMELVGDGAGTFDHAKLVESYRDVDPELSDYIVSF
+AFGDIYSRTSLSKQQQTLVTISTLVGRGAEPQLKLHINVGFTVGLTREEIVGALIHCIPY
+VGFPHVLNALSLLKEVEAERAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002606.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002606.fa
new file mode 100644
index 0000000000000000000000000000000000000000..876deb4d98ae04fe7bb6cfb21e6a5a1a497d3eb9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002606.fa
@@ -0,0 +1,12 @@
+>NZ_CP040019.1_803
+MTTETAGDFRLQTPEEIEAVVAVLGDAGMLGENARIAYLGLLDPPRGAERAAVSRDRRFR
+VFVLDVAGGLPVEAVVSATRRELLSSRELDSTVDGEFPVMEEEFAVVEEVLAQDPRWQEA
+MRARGIPVEEVRVAPLSAGVFEYEEERGHRILRGLAFHQQHEADSPWAHPIDGIVGYVDV
+TAKEVTQVIDLGAMPVPQEHGNYTDPELTGDLRTTQKPIEITQPEGPSFTVDGGNHVEWE
+RWSLDIGFDMREGLVLQNIAFDDPHTSRRRTILDRASIAEMVVHYGDPSPIRSWQNYFDT
+GEYLVGQWANSLELGCDCLGDITYLSPWVVNNAGEPRQIKNGICMHEEDWSILSKHTEMW
+TGISYTRRNRRLVISFFTTIGNYDYGFYWYLYLDGTIGFEAKATGIVFTSAVPEGSTDFA
+SEIAPGLGAPFHQHLFSARLDFALDDGTCRVLEEDGVRLPFSEENPRGNAFTRRRTVLAT
+EQQAQRDADMAVGRTWVVESSEHTNRLGAPVGYKLHPEGLPTLMAAEGSSIHRRATFASK
+ALWVSQYHEDERYPTGDFPNQHGGGAGLPEWTAADRNVDGEDLVVWHTFGLTHFPRVEDW
+PIMPVDQVGFRLRPEGFFDRSPVLDVPGPRKGACHSGGAPGAGDGGSDDACGCGH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002607.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002607.fa
new file mode 100644
index 0000000000000000000000000000000000000000..13e13dc4e918a90f76f047f07bf0a4655daa85fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002607.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_804
+MPKVVDHDSRRSELVEAAWRVIARRGLTGATMRQIAEQAGYAHGALKPYFPAKTDLLDAT
+YAHVFGRTQARIDDALVGVRGLEALRRLCLEVLPVDEDLLVEARLVISFWDQAARHEAEA
+RVSAATLEAWRTRLDAALGEADDDGTLRPDLDRRALVDLILTWLFGAQVTAVVDADRHDR
+AALEAQLALLTAAIRRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002611.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002611.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eecd6175a218c2712f7ca07e45ba5a2361ad3d88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002611.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_858
+MNLLHGLDGMDRRLLELLRQDARRTNASLAEELGIAASTCLARLKALRASGAVRGFTVDV
+DPAALGHGLVALISVRIRPGARHRMEELFDRLRGLSGVQQVFFLGGEDDFLLHVAVADSE
+EVSRFVLKNLSADPAVAATRTSLVFRHEGGERPW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002613.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002613.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4eb8cf22998a46015315c12a6aedb1cf24e2a0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002613.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_898
+MRADHRFEATLDEDLEAASASALHHRLVTEIPPLTDTQLRAFRRARIEIRADHVPSFDTG
+LTGLRLVVAAVALGLSAAALYNVAPNGIVLVWAVVALAVVLLLAMLGMTLLHGRNRRRSQ
+TLEMAVALAEIVEPLGARPRVRH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002614.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002614.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70ee302ca8593844e468f55e781cdfd253eb8f8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002614.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_900
+MTATMHAHVEDPTDGLATRRINVQVAAEPVVPGIGVVELA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002615.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002615.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb8fbb1f4d402ae8441cea770377197cf5fc093e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002615.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_915
+MGGRGSRGRGPEGDRASLAWLWALVAGAALTQTALNLARPVTSYRLLALDAPEAAVGWAT
+AAYALLPLLGALWMGRATDRLPSAVPLVAAGALTMGAGGAGLALATSAPAVYAASAVLGV
+GHLAFTIAGQAAIARRAGPGLLDAGFGWFTAAFSAGQMAGPLIAGPLLADGATAEATALA
+LWASAGIAAAGMLPVLLVPGARPRPGERDGTVEPDARSGDAAETAHASAPRGGETADAAA
+SPGEATTPEPAAGRHGGGRASRASCGCRAWPRSCSPGWRCWPWWTSSPRSCRWWGNTTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002619.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002619.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba884ffb41e07cb460ad823916e5b1fa49ceecaf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002619.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_995
+MRRFTAFTSALLMASGMLAAAPVAMAASIYEHRDYSGAAQGGENVNKLGTMNDKTSSIRV
+YGKTVTFYEHAYLSGNALRLWSDASNLREYQYPFAPTLSWNDRISSWYTP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002621.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002621.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ed827e2bf5bd2b4a6071f14902d4a28a75214ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002621.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1037
+MNRYQQSRYFQDQEKTRANTASNIEFTGIGGAYSANVKAQNRQSGDQYAEQKGLGRNKIY
+NIPNATPTGQMTRLIVTNDTWTTVTVSINGWYRTN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002624.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002624.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf0ad37e7872e7cb65c36a5ea0994ff67dec14b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002624.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1057
+MLLVAEAEGRPLGVAAWAAPGQAVAQRRRSLLAAPALLRAAWPHRAALRVLGERGPRVDQ
+ALEARHAAEPHWYLGLLTVAPDAQVGGVGSALVRAGLARADADGLPACLECDRHLEAYYA
+RFGFARTHTVEIDDGAPAHLGMGRPAGG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002627.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002627.fa
new file mode 100644
index 0000000000000000000000000000000000000000..849845ae2fd7789fa9e5694945032213c4c09521
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002627.fa
@@ -0,0 +1,9 @@
+>NZ_CP040019.1_1195
+MTFLQRVRRKAVGDGRLLRQVLTVLSGTTMAQLITIVGMIPLARLYSPTDFGLFAIAQSI
+VLAGTMVAALRYDIAIVLPESQSAARTVHRLASRIILLTCVVLAVILLLAHRVVSEHYGN
+PSFGIWLTVTALIVYAMAQIMNTQNWLIRMKQFGLISQNRVLAAALMLTAQLVCAPLVGG
+FEGLLIGMLVGQVLTLIVLNRRVPELRTSHPVDAPAIREMAVRYKKMPLLNAPNVLVDAV
+RDAGINILIGNIALGSLGQYSLANKATNAPVYLIRGAIAQVFLPLMARARPGELTPLVTR
+LLIRIGLVATPVFLVFYWLAPWLFPLLLGDQWGQAGLIAQALMPWLFMNTFTSPLANVYV
+TTERQGWLFGFAVVYAAAPLIFLTTSTLPLLPRVQVMAWIMAAALMCMLVMTLIITRQFD
+RRGQPAEVTPDMARPTKEPS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002630.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002630.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8df08632082f87800ac5b5e73564c231a5b471ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002630.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1248
+MPYYLRMHADTKISGTPEPFPDHVEMAAEVLRLLSDATRIRLVLALHRDEELPVNALAEA
+VDRKPAAVSQHLAKMRMARMVTTRHEGTRVLYRLTDEHAVTLVLEAIRQAEHSAGPGQPL
+RHTHAPRD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002631.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28370b84817bb614c5d0d7b118e284ea4c57d152
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002631.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_1252
+MEFSRVGLTDMPRTLVHYTNAPAFMSILEGHALWASSIGYMNDSQEYHYLYVQARHFLEI
+GYGALRHYGDAHPEDLETFINGVGWPYANSPSVYVIALSTDDDDLNLWRAYTAPGEGYCI
+SFDSQKIRELAEKSGWRLAQVEYGASCIPVLEDLWVRAFTKVEEGESSQEVLTWVNSRLA
+EIAPFYKHESFASEREWRLVKVQANFDQEDLRFRPGVSFIVPFVVFDFGAPDQHSIVQVR
+CGPGPNQKLAFDSMDWMVDKIGWNPSRGVSNAPFRPW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002633.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002633.fa
new file mode 100644
index 0000000000000000000000000000000000000000..569daa82db93af11af77f90fb5601dc6d40b62c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002633.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1261
+MTTPQLFHCLRYTDADRGIDFLQAIGFTTAMIVRDPDDATLVAHAQLAWRDNGGIMLGSV
+RDDDPHYGPGICNLVVASDEDVDSLFAAALAHGATTVTEPNDAPHGGRNACVADFDSHWW
+NLDSYPGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002634.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002634.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b2afa5907c33ceb6fa3a648cd3b2cbfe7db27ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002634.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_1262
+MGVTVVLSLGEPIDCGWLHGDARHLCDVLVSGLHTTPALIQSRGRQQGLELSLHPLSTRR
+LLGLPAGELAGSMVDVNDLSWPRHLLDQLRQSTWPRRFHLLAAFLTKRLEQHPHAPRADL
+VEALARIHRTRGTIPISGLAQDVGLSRRRLSSLFDLETGLSPKQVARIARFTHAKDLVQR
+GAQPSDVAAMAGYSDQPHLSREWKSMTGWTLRQSKDDFPLLQDTDMLPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002642.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002642.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b345ae80abd55b55ad80cc20a08a50ebf3e27e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002642.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1301
+MAYEQKTTVTDVPVEEYLATVEPARRQEQGFALLRMFREETGAEAVMWGPSMIGFGHVRF
+TYPTGHSGEMFQVGFSPRKSALSLYGLTTYGSHADLLARLGKHKVGKGCLYINKLEDVDE
+AVLREMIRVGWGDDESFVDSHDGTVIERLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002643.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002643.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0200e50ead906412f30ac8cea232f953739462c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002643.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_1303
+MLNWPLRARRLRGDVNAVRSGPRAMGRRAGSRLARRLVSRLFR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002645.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002645.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ba7be48f4c3b38e4c02ea6c6be19e44b88e8ffc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002645.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1306
+MTVTDALPPCPACAEEYAYEDGALLVCPMCGHEWSPESEAADRAEPAAAVVKDAVGNPLA
+DGDDVTIAKDLKVKGGAGIKAGTKVRGIRLLETPVDGHDIAAKVPGAGQMYLKSSVVKKA
+T*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002646.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002646.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a75e65d0f9bdccdda721962221f1fc9a953c18e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002646.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1307
+MDPDRSGQRGPKDFHRRIVRAEDPAHPATEVLRTITEPGSRGSRIRAVEGRAGEQAGPTL
+EH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002651.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002651.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7fecaf5c810c7559c8d9418395d5acd45b14be5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002651.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_1335
+MSTGRPLRASVWRHAVDVLRPAATPARPAVVRLGVGAFAAWNGHRRRDLVRGLHRQDPRR
+FEPVGVVKVLKRPLPPRVADGLFDAAQAVNALATLGVAHRVTGPLNAALQLWTLSYRNSW
+GMLYHNDNMLLMHQMVLGVSPSADALSVDAAVAGRGLAPAVLERRYGGVLPMVNAATCVV
+YLISGVAKVRSELGVKWAGGDVLRGQIAIDGLRKELLGSEMPAAGRALYRQEHLFTLMAT
+VALAVELGAPLSLVDRRLGRAFAVAAWGMHVGIRVIMGIKFTYNTSGVSYLGYFPVGPAL
+PR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002652.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002652.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2341f10f246546db20807d802479c5fb6540e66b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002652.fa
@@ -0,0 +1,12 @@
+>NZ_CP040019.1_1407
+MDPGPRLARAAPPLGPVPAAAHRRAGRAAHPPGRAGVLRTAHPADHAGPLRLPLRAGPGR
+GPPRPEPGAGHVRPDLRHGRPEHGRARHPDAARPRGRLRHHHPPPLPPGAAAGLGVRLRG
+HDLLDRPGPRRDPGGSAGGRRLRPRRLRRQRGPARRLRRHAARPRLRCPGGAPAGRRLRP
+LPRLRPLRRAGVPRLRAAGAARVRRRVPAGQRARVLVGLAARGAARAAGRPGRRVHLRRQ
+PGRAHAGARRGRDGPPGHLVQPDGGQHPGPDRPARAALPDAAAVRLGRLPRAAHPADHRA
+DGRGRALRLPRRLRPRQPPLHRAALPPGRPLPGHARRPARDHPVRRRRRHPGPRGDRHAR
+ARPRRRSHRPAAGGPDRRARLPGADGPGSPGRLRGVRGPAPHRAHPAQPGEQRDRARRGP
+ARGRARGRRRRGRQPGRGGPRHRHEPRGGAARVRPVLARRPLAQAHHGRLRARPGDRHRG
+HPPARRTARGLGRAGGGLHLHGDPAAAAARDRPGRRGARADRPVGAAHAPAVQHRGPSVR
+RGPHPARAAGPRRRRVRRRRPRRRGGDGRRRRARGGRGAASAARHAEQALLPPSRLLGTP
+AAQGDDGGRSGRDPGEDDR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002653.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002653.fa
new file mode 100644
index 0000000000000000000000000000000000000000..063e8a59dc4b75b26802212d61f09b8fe71de3f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002653.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_1443
+MSAPALAVPRSAVAGPRARRRPLAVGAALCLALAGCAAPGVPAGEDPDTLGGRWTELNES
+LDSARSVAVTARWARPAAVVTLAGSLEADGAYRGTSTGAEGAVEAVHADGVTYLRGEGAG
+DALDGVDPGRWLALPGPAQDLVSPAELIAQVRAELPDTLAPEDAAVEGREVTVDGERLEL
+FSGVRLDGAGPVDLYLDARGRLARVARSADATADATAAPSSRSGAAPTSNASPDPAGALL
+PRVESVDFDDWDAVPPVVAPPAADVWDRPGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002659.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002659.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0176effc6059a02158e37eff7800109dd1514d7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002659.fa
@@ -0,0 +1,10 @@
+>NZ_CP040019.1_1472
+MRLAPDLTPVGWFLFGAMVLLILTYLYFWWMVIKASAHKHVSREKVTNRKLTASLAHAKR
+KGNTHRFLIQITTKGGALSVVQRGIDNVLAGVARYPVLQKVVWVEIITEDANEVAALQTR
+YRNAVIPVTPYLLPTDYRTPKDTHLKAPALEYMVEQHRASPTESYVVHYDEESVFTPDNL
+ARLVHRLSRHPVGISEGMISYGLDWNETTLLNKTMESNRPFGCHECYSVMTSPPPMHLHG
+SNLVVRQDLENQIGWDIGNLDGSALIAEDLVFGLAAYLKFGKDVFGWHHTEMIEQPPFTL
+KAAYKQRERWVFGAMQALAHIRQQPDWMRLSRKDRWHINVIIRLRVLTYALGFPVSLLAL
+GSNVVILLILAAEAVREGTITVVAPELTVYGIVTSIGLVLWLAGTQLGLFYNLRYTGMTR
+LQRLRDHVLVLLVTPFAGVIDTAGPLVAVLKWLAGIREVAWKPTPKLAVPSRETTPKRVA
+AAEVAAGEKAV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002660.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f3594484d6bff20c830f4a2f7ec83b291875296
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002660.fa
@@ -0,0 +1,11 @@
+>NZ_CP040019.1_1477
+MRAVEVQIHNFRSIHDARIRLEPLSLIAGANNAGKSNIIDAIRLFYGDLKWDDARDKPKV
+ASGDAEAWVEVEFKPTENELAQLKDDYKSADGTFRVRNYVSPSTGADGKARSGYYAYEND
+NLSNNLFYGAKNVGSGKVGHIVYIPAVSKIDENTKLTGPSALRELVAEVLNKVVADSPAY
+KHLTEAFGTFEGSIKAQASADGQSLESLEKEVTDEITSWEASFSLAVQSIQPEEILKTLI
+KPQLIDETHGGEIDQARFGAGFQRHLIYTLIKLAAKHANPPKVLSSEKKEFTPQLTWILF
+EEPEAFLHPSQEEVLHDSLLKLVRDGTTQVLLTTHSSRFVSRSMDDLTRLIRLRRDAGVT
+TSYQLTQPELDQLFSDALVADDSILPHGTSSADVNKAAMMASLKTELWMQSTRTTAFFSQ
+RVVLVEGPSETAIYSYLTSRGIMEPPVRGLAIIDCMGKYNIHRFVAILSAFGIDHSVLYD
+GDNGGAYDAEVTQAISGAKTTFTKRITRFVNDLETELGIAPLPRNQSSRKPQYALYNLES
+GLVDQVKLEALKQEFVDLATAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002663.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002663.fa
new file mode 100644
index 0000000000000000000000000000000000000000..052ea927f1cc3a39a7cb4eb0cf85ab049b72774e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002663.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_1483
+MHLPIRAQGTTLADEQAKILDDEFFLSNPLSHFSSRVSMLLETARSSYEASPENEPEFFN
+ALGLDSADTALKFDTQHRSVQVAIDALSLRHQAAEALTRFIYARVAATPRKGDAKSTYLA
+IADCPNPMIKVIEANKAAHDADPHRFLQLLFPPGIVVEGPVVGAAETAVEWANHAVWLLT
+SDELSINAAHNKLKHGLATSARGDVRIELITTPPNEDGTIPTSAFGEGKSLPLFDRPMLT
+YLSRPPKDLRQGLEAVSLRVDLPVVLAQTWMMANVYAAMFHIAAREHYGKSLPEGVAPFP
+TRVVGRLPEHVIGGRPLGYRSAATLPPDGTTAPRPSGVAFFKQFWPMTVDFESKTQGVVV
+DA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002678.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002678.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d18e9021519b492a35fd1a7b93a57ead97e3f206
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002678.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_1824
+MRARLLPALLDLTLTSLVSVPSVTAPARVRAGVIVGEGWIDLSTLWKGDVT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002679.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002679.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40ef652488efcc374e8319dbd9c54bdfda4e7ebb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002679.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_1825
+MMMSFRSTGKGRRGACGAVAGFVLVVAAAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002681.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002681.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cfb394dd3ef50ea2c49b677513892e34fe5bba77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002681.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_1831
+MLRANDSGNADGTGVLVTSPDADCIPVSDPADPSALHWLDVATTTRETNSLMETGPLLSM
+EELPATLALMDGARGYTEYIWSSGITEPWMWHAYTGPDKEGTVRTRIALLDFMGPEQYEA
+TSGARYAAPGLDGDALRPTDWALLRAHGLGGDDEDGVRQGPRPSRPASRTRARRRPVTTT
+PRTTTPTRSPRPWRPATAPRGGSPPSARPRRACWSASARDSAWSDPGCSHLVARTTRRLQ
+IARTASREHNPAGERWEAASTSPDGGHRSPVAAVVACAGRALIPSGSTSSVRGEGDTPTR
+RGGARDFRHRKRGTRVLHRLWTSGGGLGVSRMAVRIARGARMWTVWGGTGDP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002682.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002682.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74ae1e9fb029f9b1cb0bb252347a6076d0c894a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002682.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1833
+MPSVLFVLSASGHWTLKDGTRYETGFWAEEFVVPHDVFADAGWDVAVATPGGVAPTVDQT
+SLGLTGGAPWKTARLKRDLERLAPVLDRPVDLASVDEAGHDVVFYPGGHGPLAERILADA
+EARR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002688.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002688.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3264281fa527a6b12fc2c8a08bd2886443dc8673
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002688.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_1903
+MTALTPFQYGATAVRTAVVDGEPHFVAADLCAVLEIGRQQDATRYLDADEKRGCLVDTPS
+GPQTMVVVTEAGMYSLVLRSRKPEAKAFKRWLTHEVLPAIRKTGAYSVQRELTEDEIIHR
+ALTLTVAKVEALEAKVAEDAPKVAAWESIVSSAGSWSYNDAAKVLCESGQIEIGEKRLVK
+ALVDWGYLYRDARGRPHVYQRYVEQGLFVVKARTYRDLVSGEVRESAAPQVRLTGKGLGV
+VRSRLTNQPAFELLGIRVVKA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002689.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002689.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20a9302a7e6f69d15663104bd1ef72a5250dd725
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002689.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1904
+MSTPLIEDLLPSAPGSGVYDVEVRGGVVHESVWLDEAGFWRSADDVLVMPAQIERFAVVD
+GPDVIRWVRDTDHRWSSIVERDLEAGPAVAGGVVTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002694.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002694.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b07eecda9b8cb807cbe5878efb5cdda45c4ccb9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002694.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1909
+MSARIAEWPPIEAWITAPDPNGRGRIVESVVLRDGRVVPAETDPADLYPWWAPAAGTRAH
+AVQRVARAVTAALVPVLAGLVFAAVVLLAPAGEWAAEQLIRGWGW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002703.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002703.fa
new file mode 100644
index 0000000000000000000000000000000000000000..365a85f2b8b0b8b754396b01a2ab12a106694a42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002703.fa
@@ -0,0 +1,9 @@
+>NZ_CP040019.1_1919
+MPWLKVSDASAMHPIALAAMEAEDADERLVNELFGYVARCAVMSAQHEQDYVVTLATARV
+TAGGDARFKVLAAAAERAGYWTRTTVKDASGAERPAFRLVEEKDLFHMLLKKERAWETQR
+RADVANPELTVPVRLRDGDGCRWCGKSVAWRDRKSGRGATYDHVKPGQGAASPEDLVVAC
+RACNGARKDEENTSFSRTLMAPPFRPLYGPDTLAFLAEHDVVPEQQDTATAAERQSQRET
+APTPTTAAPATAAGSTARTATAAPRQGVRETADGQERRRGAQVRDVDGQAADAAAAHAQR
+EADARRAEAERERRLDAWLADHGISVAPAPATALSPLDVEEADWAPSEGDAGPPGGPDLQ
+IPADRQAEGSGFPGTGRDGSGREGPGLDVSGTGGARDGSGLDGGSAGSGRRRRRRGRRGG
+RGRGGEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002704.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002704.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1863aaac51f31d26e02a445bec9414833977f90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002704.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1920
+MRQDEYVRMMAAGMSEDQLQRGVERLARSLGWLAYHTHDSRRSSPGFPDLVLVRGDRVLF
+RELKTEKGRATPAQKTWLAALTAAGMDAGLWRPVQWFDRTIERELA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002711.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002711.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48e88cc87b825da22900b3fddc8c2e3f8bcb3d77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002711.fa
@@ -0,0 +1,10 @@
+>NZ_CP040019.1_1927
+MSVNPRYLLTPPADDVDETHADGAIALAAGYGLVLDDWQQQAVRAWLRCGPDGRFLASTW
+GLSAARQNGKNAALEAVELYLMTVLGWKIIHTSHKLGSARKAFKRLTKFFGRFKGDPSAP
+YPELSALIQEFRRTNSQEAIELTNGGLIELSARTSGGARGTSYDLLVVDEAQEYEELEQE
+ALEPTISASAHGQPIVIYLGTPPKTIGERGEPFIRVRSKAVSGQMERTAWVEYGASLEID
+RMTDVELQAAVRDDHHVRDANPAVGARVTWETVNGERGRWSARTFARERLNCFPLPRTSS
+EKAIEEDVWAARHDPDPDPHARLAAVGLDMDPARTKVTITMAYWAEAGVHVEVAAAAPYA
+DAGVASLVAWLWERCKARVPVVIDSFSPARAIEVHLLQKRMKVRVLSAREWADACMGLYD
+AVSAGAVTHFDQTQLSLAVLAATKAPVGTQGAWRMQWPKDDVDRAPAVAGVCAHFGAMKF
+GRRPREGAASQKQTGHSFV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002714.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002714.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b400ddb8519564bf81cfeca2a600c4b04f52ab0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002714.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_1930
+MRRSFNPLLAGVLRFIEAGAQHGAAATPPPSPATVAAQTTPKSEPATGDADGDQGESPTE
+AGLSEAGKKAIKAERTARRTAEERVRELEAELAAQKNQEPATGSTQRNQEPATGAAPEAA
+TAAGADEDLRAKLRTAEQENWRHRALADHAIPRELVELLAGESEEEVRARAALLSRHVTA
+APLDPVPKSGVQTDASLPGSIAEYRRRIVKPNS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002715.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002715.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0023972284d9867953e28ce54c1350dc3ebc8a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002715.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1931
+MPMLHRQNIGSGRKNWLGSAHGVNHAQTATLDVSTFTAAADHPEGRIPSGTPVNAADRTA
+VVKWDPAAGGGALGFLIDDVDVVDGEAVPCAVLLHGAVVVEELPVEFTVPTAPTAFIFE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002717.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002717.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e0decfe75ea92e5c1bc4eafb83e0990b1e0b3442
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002717.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1933
+MIVTHTTTVLRDGEPVVLLAGQHVPAWAEDLVGAHLLAESAAPAEPVEGAEPAEPVEGAE
+PAEPVEGAEPGPADAGEPKPPVAVAVVDAEAEKPAPRRRAPRKKPAEDLEPDFTRPPTEG
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002718.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002718.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81ba11d70d11f437f5ef8a4304e1b7ee3bf61306
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002718.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1934
+MSGFATVQDLEERWPGITTGAVTRAETLIEDAELLIEGDYPAVGEWVASGLLRADVVTFV
+VCRMVKRALGPDADDAPGGQFESMSRTTGPFLTTLNFREPAGDGEELFLRRAERNLLTAH
+LRARARAGRAFTIQPGAGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002720.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002720.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00e5e143d6dcd164aac25e76a50417c309dc31d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002720.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1936
+MTTAGLRRVPGVRRYRALADGVRGLGTSSVVAEASLSAAERIAARARSTGEGEYQAYPTS
+VRAGWANEERAGARVVETRRVPSDARQRVLVTALRGSTTGGGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002721.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002721.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d1bde1454d6a32afc9881ee650011a1df9d88fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002721.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1937
+MQGQRFPQPREVLRELTDGREFAGHVVTTVFQEQADAYGAHDPVPQLLVFETSVVEGFLD
+RVTQVQLALYAEGPSAALQVLEAILAEVCGVGITTSAGYIDSISVVQGATEAPYTERLNR
+GSALLQVVSRPI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002722.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002722.fa
new file mode 100644
index 0000000000000000000000000000000000000000..434c81c766cbf49950d89184e1e02dc9c9bde0e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002722.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_1938
+MVTFHELQTQSDERKLVRKIQKAVALIAPRNVDLPESLFAGAGQLVNLKEEGWLPLGIVT
+PDGYEFTRDVETEDIDGLGYASPVRTDVTRVPRAITTTLIESGRKHVQEMLYGTDLSTVT
+QDPVTGEVVFDEPDMPANREYRLLLLGKDGPADEEWVLGKGYGTVSLTAGGGATWGQEGA
+VSTEVTLSVYADDELGTPVRHYMGGTGALKYKDVLGYTAGTP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002723.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002723.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7fb4e499ff6873ec9d6c810c54cf5bce7cea8b02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002723.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_1939
+MSEKTTFTKGDLSITTTDPAEKVRLRSQGFAAADTTAPAKATPKRADAPATDQKN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002724.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9df74a970469e941670a5898036a9ef8cf6787c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002724.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1940
+MATQKKTDSPKVHASLAKLRKESPAAAEPFQIALEDSHVITFPDPFAMDVDAAERMFALP
+DTQVKAALREWLSEEDFTALFRVKRSLRDLMLISQAAQAHFEATYGPVGEDSASRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002729.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002729.fa
new file mode 100644
index 0000000000000000000000000000000000000000..814cfc6f02541188312bd01e7020ef873a96f164
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002729.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1945
+MAGLVQALAGPQEAAKTPGLRVSDGVVVSTNPVRVRQAGADPSTDPLAPLSLVPAADLSV
+GARVLLLHRGTQKILLGRTYPL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002732.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49911db6050d6ada6769a08ba3128cc952154fdb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002732.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1948
+MPDRILRTSAGVLGGLIIILGLTYAWLGITWLISPTPTRLAGIEWAPIGAHTVGIWWIAG
+GLVALIGGAWSARPVAAGVGAFAAILTPAVVAGLFLVSVWHGNDRGLITAGSYLPYALLA
+AWVTWRSGRGSEDTARDMAATRHDSQEGRV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002735.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002735.fa
new file mode 100644
index 0000000000000000000000000000000000000000..042d010471dfc2e6584d69e05c35e81ee689f54f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002735.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1951
+MTKNAILRYFTYDHLTRSPLRDVSKLFHDLAGTLDAQLPDGPEKSTALRKLLESKDAAVR
+SALDIEGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002737.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..416212aecacd4feb488dbd0326fcbd80e651817f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002737.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_1961
+MITTMNVFGVVFPFVLAVIVVAMIVGIRSSGREHTQASEVELRLRERTFTG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002742.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002742.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ade2cfcd6100307ac3021c5052cda7e3a000001
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002742.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_2011
+MNPYQQLLYRGMAAQDIVTTPVLSVDGFNPLLAVRAETSGVGVHLHWLNPVLAGARNGAD
+ARARVDRFLERVDEFIDADGRVVWTVHNVLPHDAVHLEQERRLQQGVADRAHLVHVMHPD
+TADVLGESLRWDSARTVVAPHPSYAGAYPDTVRRDEARGVLGIHEDEVVYVALGAIKAYK
+GIDTLLDAFDQLCREDATPRRLVVAGPVDTSPHTRALVKRLRTNPRVLVQAGPVPGDRVQ
+YLLRSADMAVLPHLRALNSGGALLGPTYGLPVLAARVGVLPAVLQPEFTEFFQDHTVPGM
+TAGLRAADRLLGAEARDAASDFARQHDPDLIGERFAQVLRARLWAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002754.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002754.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea008f009aac4b20478cc9a35dad97585b07eb66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002754.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_2164
+MTTDTRLVHIITLTGQDYDDAVRVAETEGGSVDAVARHLAQWDHGAEADDAALLWPEDMP
+TRADLGCQPHQLHAARVGGLGYLVQIDHGLRMYALYRPTLTQEAAE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002757.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002757.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f5f07ee6161541206c25c07a8b6763a21bf0698
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002757.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_2171
+MTRRSGVDRNAIRRIARQIERDFNKEFERRPLRIPVEHEIAPGSPQPHPHVVNHYAGPVV
+TINGDHAQVAWNGGTNIGHREESQTVTPGFEQVAKVVSDVLAQADALELEEDERLELQQT
+GEEILTEVVKEEPDTGAIRRTLRTLKGFLAPALTAGASAAVSTEAQEAAQAAFDAIQALS
+F*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002761.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002761.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2094d07fd8af854fc3d9bd9c2c706b5f86c41cc9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002761.fa
@@ -0,0 +1,9 @@
+>NZ_CP040019.1_2181
+MPRRGWDSVTVPGAVSGWRALSDRFGALPFERLGAAAVAHAEDGWIVPPIVAQDWGRAAT
+VLGELPEFAATFLPGGAAPREGERVRMPDHAVTLREILATGGESFYTGPLAARIVAHAEA
+GGALSAQDLAAHEVDWADPRSVSWGGHELYEIPPNSQGLAACVAAAVLEVLGGQHRNPDS
+ADGVHLQVEAMKQALAVLHAEVADPDWMRLGPSELLEPERIAALAARVDPERAGAAVSAP
+PTAGGTIYLSVGDRSGMMVSLIQSNYDGFGSGLVVPGTGIALHDRGAGFSLVPGHPNEVG
+GGKRPLNTIIPGFLTAGGEPVAAFGVMGGPMQPQGHVRVMHRLLVGQDVQSALDAPRWFV
+EGSGELKLEAGWGGDVARRLGDLGHPVTRTGPGDRTYGGGQVVRRLPGGDYAGGSDPRKD
+GHAVAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002767.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002767.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e4fe789c0c58b36dee6a9d935ebfed609ec22220
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002767.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_2254
+MATGDTVAVGQELAVVEAMKMEHPVTAAVAGVVTVHVAEGDSVAAQALIAAVAPAGADES
+AEPAPHEASAQNA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002773.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002773.fa
new file mode 100644
index 0000000000000000000000000000000000000000..64fdd2dea42fb9b12fa4ec8baa0deee1a2541b9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002773.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_2317
+MKVELLHIADCPNTGIAEANARAALDALGLGAVPVELVTIGTEAEAANTGFGGSPTILVD
+GIDLFPTTLVHSLACRVYVAENGFAGAPAATQIDEALRDRMQGGESDR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002779.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002779.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c32a9b307807f6101b1f1aedfaa685372c2dba49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002779.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_2446
+MSLCQTKWICVRDTTTKMPAVLAIWSGGELNDLAAVEQANYLFPRACAEMVGLVDIQALT
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002781.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002781.fa
new file mode 100644
index 0000000000000000000000000000000000000000..375e68733221342a5ffc203de9ea0c45e72bda1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002781.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_2451
+MKTNIFAHGFSDNHAVSFGASRKGRVWSNEQARDIHDWVRWASQVGPTITDTSISLDSVM
+SGFLLPEPARERPPLVPLSIEWPYQLVSTFSDRRKVSHEDQAFSLLDTELSLTDHTADQP
+LRFEVKTPSWSLEFEFEFHEDGPPTIRPVSDDGQVVTPSGVGSLAAFLTGHGLLVTFEDE
+VVLVEQGFLLKPERERRLFPIDAVETIDWSGVNIRRESQGAERDPATIQHRAIQALSAED
+EWEVVLDDDGTGELADIALLRRTDDVLEVLLVHCKYSSSDTPAARINDLYDVCGQSMKMN
+RAKSMSELLTKRLFRREQERQNAGKSGLIVGDIETLAAIVFEARYRLLKVTVAIVQPGMS
+KSAASEDMRSLLGATDRFLAETYGMKLRVIASA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002782.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002782.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06dfa4d55d4f3543858b56cf4c79c927852f8cf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002782.fa
@@ -0,0 +1,22 @@
+>NZ_CP040019.1_2452
+MPVLRSLGPAYQEDLHGRNAAVLLDVLTDKSATAAKNIALAGHYGSGKSSVILGVQDGLD
+ERKIKWVNLSLSTLGIDDTKRARIQQDGSLAPLTNLIQKEIVKQLLYRKPPSDMPGSRYF
+RIDSFKPWPALMWGGVVAVGFFVIAVLLGLVSRIQDVAPASVINSHSWVAWATVGALGAF
+VGGVWFLGLRVLQNRIRVESVSAGGAAVKLSAKENSYFDEYLDEIVYFFQRTKTKVAIFE
+DLDRFKDPHIFETLRELNTVLNNSEQIKSRPIQFVYAVRDSIFEELQVDAESDGEGTKTS
+ALHASALESAPSANRTKFFDLVVPMVPFITHRSARDLLAAEFAKADHQPSTALVNLVGAH
+LTDMRVIRNIRNEYEIYRASVLGENGLKGLTADRLFAMMVYKNLHLEDFEAIRLGTSKID
+EAHRAFHKMVEYQTRHQAMRSKTTQNRVRTKALWDKHAQAAGERLQEVLPIVYRATGRGG
+KPVLRYQSQDYQLSDLTSGDFWKSLYENRDSVHLLRPGYGGIELSFDELISLTGNGTDGL
+DDAVDADVAHLQRDSRVALETKDFVMKATMAELIARTDLVMPTTDGDERNLDSIVSELLS
+PLGRDLLTKGHIDENFTLYCSDYHDIAISVSAMNFILHCVQSDRAAPHFHFDEASSIEAV
+EREMGSRFLDGESVFNVEVFDYYLPARPERLDKAMDKLAVRSGDDSSFLDAYLIDGKSRD
+VLISRLAPRWDGVFIHLAEKAPLELDVVATLVDAAITCAAKDTEYEASDQVAEFVSEHYA
+QMQAFVGETDAAKATDVMALLRRLGAQIGDLGVLGQTQRQAAVAAGLYPVTRMNLSVALD
+ESTGLALDVMNAADDSVYRHVLSNLDDYLDVLQDHEVTVDSPDAFVAVLGDVADAAEFAV
+RTVAARAADSCEVVDLTDLDDGAWGHVVSAGRFAPTVWNVSQFVSKFGVNEELIENLGTL
+NLTKAEEVDEEPRLGLAYALANSGALDSAATVRLLGQLNLPDGLDPERLSDVGLALLPTL
+LEKDLVPDTADTYALVSDRPFAFREEYFAASKQLASYVCELELSSDDLARVMRSRRLAPP
+VKRAIAHDVEFITDRLSRQSVIAFCEWASKGNDVSVELLVKLAEAGAPAEHVLGLLEPYL
+PNIELGLLDQILLGLGDDYEPLTRTGHHRPRLKDRAGTEELLKALQSRGRVSSFGREKLI
+GGIRVNMRH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002787.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002787.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fe4ff253f882b34fc26b827ceb5292689d05003
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002787.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_2534
+MIVTTEIRRRPARRGPDLGDVLMAAPFALWGAATLALQFNRGHRFIRALDPTGLIVPDWR
+FFAPRPASHEYHLLYRDARPDGTMSGWNEIDLGADRRLRHIVWAPHRRLEKGLFDATTEL
+MRVITDVRDPAVVRMSAAYLALLTVVTHSASHQDGAVRTQFMLVRAAAHEPDVIPSIDYI
+SDWHRLEGEH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002791.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002791.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea4afe9dd00330c26161ea1e39b1d214129c64bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002791.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_2568
+MTEKLLASAQARTRECTRAVLATVKELEASQSAITLKGVAARAGVSRNFIYTTPDVLAAV
+QKAAERQRPKLPSEPAPTAPSSDASLRTRLAAALAHNECLQQEIDRLTATNQALVEEVIE
+LQNPAPKNVTSIRKRRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002795.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002795.fa
new file mode 100644
index 0000000000000000000000000000000000000000..655d751c956453087b06c3047db432fd93a46b14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002795.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_2584
+MMYPLVSELAADGVPVAVSLRVLKLARQPYYRCPSPFLRWSRPTGPTPCTPLT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002799.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002799.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ffd0daf3b4e62fc46430381e8c98315f6c3bec10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002799.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_2603
+MHDPHDRTRPLRVGSLFSGYGGLDLAVEHALDGETIWFSENNEHVSRIFAHH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002802.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002802.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2d6c0809368e1dc3a97d190579833699a97c184
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002802.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_2606
+MTTIDLTEDAFSAAITDHPIVLVDFWAAWCGPCRSFAPVFEAASTEHPDILFAKVDTEAQ
+ASLAAAAQITSIPTLMGFKDGVLVYSQPGALPAKALHDLIGKIRDLDMDHVRAQMQASDP
+R*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002818.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002818.fa
new file mode 100644
index 0000000000000000000000000000000000000000..841967998397fcab7f700e9710591b1712b5a425
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002818.fa
@@ -0,0 +1,7 @@
+>NZ_CP083691.1_47
+MDFHRPSLEELRAAAALPSHTAAGLTHEVILTEIAAGRMKPEWSCIATNDDGDVIGRAMW
+WGRDSQEPIALDLWDVAPGTSEPGEVLTGLLTHGGVLVEAPDRRALLPHTLRVPVGWGDQ
+PEVAENVRLKMQVASANGLGRVNERLQFQWDWGETVPPNPARLRFTPASDEVFMRLFADA
+AAGSLDVMTARELEQTTAADLARDEIAYYLSCPGDRSWWRVAQTHDGEIIGLAIPSATPT
+NRNVGYLAVLPQHRGHGYVDEILAYITRFQIEDRARRITATTDAVNTPMVAAFTRAGYTL
+VEVRIDLEQS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002819.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002819.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad77f7622359b01668888c1d082e6a26dd9af326
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002819.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_65
+MMFSLRPAWKVPTVTTARPVGAASRETMHCRRVTAEEAMRIGSMERSGMEPWAPLPWNVT
+LKESARDMASPLT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002821.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002821.fa
new file mode 100644
index 0000000000000000000000000000000000000000..596f5f7a62438444afc0bb2f49ed5c75ce7f92e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002821.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_76
+MVNRTAKRAGWDYDALAFLMGFLGAAAGGFAVAFLQLLGAEGLDAFLGLTVLFGIGPVHA
+LVAALVSPPLLAGLRRVHPRWLHVLIAGGVQAGIAAGVASLWLQNADARHLPGYVLTSGV
+LLAVAWAWALRRSAWRPAGGPADGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002822.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002822.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7d24803f8f9810a4ddb634d435eecc1be00f91d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002822.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_78
+MSALITLLALSLTTGLCCGVPYATMTEPMPAHVHSTGIAIGYDVSVAVFGGSAPPASPVP
+TSSCERASALSGAAAARRSGRTG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002824.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002824.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ed10cdbc4e8a3b7c43a4e0617b0900fbacce88b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002824.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_158
+MDIPTRRSAVALAAAGAALLAGCAAPTPEITVVDDAGTRLFLAASPWEQREGESRGLLTG
+TLEVSEGGCLVVDDGAVGVPDHTSLPLAFPSGSTLVRESDRVTGVRAPDGATVLLGDSRG
+WTGGRVLVDDLERDARDALTQCTTEQAVFVPLAEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002828.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002828.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d204ab59514605f985de2a2a4171d6e5d7a8c15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002828.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_194
+MTTAQTITANLTAARHAYYAAVQTARTYQDPDLTPEALTRQRQDREAAARTAYAQELRPI
+REDYERAARLNAKALAKVPAPTGSTADVWRRVEMRLGAGATLDQIVATADVPTLQAVREW
+APTYLAVNGGDPAAAPALGDRLERATLARYATVTKDADMAAALAEAPTLAGLAVTLDDAE
+AEAQGIPGAGGLNGAVAAALAVQAAGSTTVDPDTTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002830.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002830.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35f03607b998b951edd54ee934e7f3a9600a30c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002830.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_197
+MTRTHPAENQHASGRYLDTTARDAEDLAAVADAAAKDADAMARIAADIVAQHAEDLAGIT
+ATTADDSQAHT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002832.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002832.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b435f57c2d85dd80150570efcb9448da4e2e6e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002832.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_199
+MGASNVIAAYTYWRDRLSHRDLHALVFMAVTALDSDRPPVYYGGWEAVARALGLDLEGNP
+ASAKRTTVKALTALTEAGAITSSGTARAGIRAEYALNLAPGTTYVPSGRGRNVTWTARPT
+TARGTAMDPQVGTVVDPQRGTVVDPLQGDRGGPRRGTAMDPPKRTQEPHGGTREEPPEEP
+PITSQPNPGTRVRESDAMNDDRTPSKAEQEARLLAWAAEHYTEDPNALTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002833.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002833.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e6443eccb3c592f4f85117f22ec735e66e77dcc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002833.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_200
+MSAPDRYRLDPAVLDVEARTPAAGARLPSGWVRAATAAARAMGEPFTPARLRAALPEPVH
+PAHFGAVVRHLHAARVIRPAGLALERSPDGSARPVRVWEAVPEDAQDPAEDTATPAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002835.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002835.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0709c1c2f7983807076e47c97ab00d935759e690
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002835.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_202
+MSATPTPAAALSLTHLTPQDLAARVGVPVATVYNWRTTGYGPRGFRVGKYLRYRLADVEA
+WEAEQIAAEDAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002837.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002837.fa
new file mode 100644
index 0000000000000000000000000000000000000000..461eb75f5759b367168be19d7acbe6a18ae81baf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002837.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_215
+MRLPESLDDIEAYADALSSEVADLGDYVLVGDSFGANIALALGARQPEGLSGLVLSGGFA
+ANPITSPAWKAAMRLMGRLRGPAYRQMVLRAHAHRLASPHDTEGQVPWSESQSRQLFLDH
+TPATSFGARVTAVLNADYTDELDRIQVPTLILTPSHDTLIGDDAARVLRDGIPHARERVL
+ERTGHMFRFTHPETYSQAVAEFLADESL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002845.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002845.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30a5e3a51151dd3dd53b668b401153ff7fd8ab65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002845.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_292
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+KPGPVTEEPGPGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002847.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002847.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ada0937ae63222b6c706d37c3b986937ce9de136
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002847.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_300
+MHASGQSPYWQNGVEMLIRHSNGQCTHYAHLDRALYRAGASVPQGRVVAWSGNTGASSGP
+HLHYQAIDCNTRVGIASTLQGTKPGTGSLPVSTNVRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002852.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002852.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9242923f0a019b3689e41c8ef59a7cecdf82083b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002852.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_318
+MPRPYPPEFRARAIALVREGRQVKQTAQALGIHEVTLHTWLRQDDIDHGRRSGLSSRESA
+ELRAARGRVRQLEQEIAILRRAATWLDEEGGVDPKGRTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002858.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002858.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1dbbc78d131cf0674867670d21541294c8a36c1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002858.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_335
+MAEKFGWRPNDYLENPRAFGKEDTSPAWRETWFDGTVIQDDPRHHDRQIAAKIQHLVAIE
+VTRAARLRDETLADVSKHTRMGADQFRRLMRGEGPMQVVDFATFRRVYHVDFGINPDPGL
+ANIRETKF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002861.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002861.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c49fc4e98ec50df0691553b01c288d84938217a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002861.fa
@@ -0,0 +1,12 @@
+>NZ_CP083691.1_338
+MARTFPNSAPTRDNQSLAGLYDMDFAPNEGAVRGEFTMLRNAQTAARIMEHAGLADLIAT
+WQAEDGQGNRPGPKPWLTEVNVLALLLLLALSRRAPLFQEVGEVLIEASDETLAALGIDP
+ARRTYSEKAAYHRAYHSYRRLLPLIDPEPAPLYRRLTVQECDEVKAAWVLEENAVKRERA
+HTMANALLYGTWMLLPRQVRRAYKGDIAMDATFVKSPAYNGNTKPKSSASEVVHYRSSDP
+FAGWYKRDGNHAGPNELPASRAKYQRTQDYVGWGREAHTAVSYGKDVPGIVLAVSLDTPS
+ARLPENALRMVEHLKRNNMPVGHVVTDRAYLPGTKPAELARPLRARGYRLVFDYRAEEHG
+MGQTASHGGAIQVEGRWYCPSMPAPLVNATKDHMLRKESDPEYIDEATYRTRIEQRKQYE
+LHLKERPDAEGVARYACPAVGPSATVSCPRRKEHPKAADKPKGRIMLPLLVKPAPQVCEQ
+QSMKISPLTGEKYAQEYPYKSEKWREHYTGGRQMVESLNASLKNGAHMPIDDTQMRPRRG
+FAAQIVSLAVMVAATNTRKIIAWLHEQVGVTSLSSAPVKRARRRERTAGFTRADEFGPAY
+SPPGGLPPERRETA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002864.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002864.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6272c19d416c74ef380f033b8e54c49f9394b7cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002864.fa
@@ -0,0 +1,10 @@
+>NZ_CP083691.1_391
+MLKVSDVFVPGKLPKYTYNPRENSKIEDQLKDYLDELGAILAISGPTKTGKTVLVSRLVQ
+NRIWIDGGLVGSIEDFYRLVVDRAGEFTTIEVAGADEYTATDETSGEANLLGAGKFAAKD
+ATGLSTTNSKSASVNRPASQVATDALRVSGHVLVIDDFHYIEPAVQTAIIRFLKPLVMND
+VPVVLMSTFHRVGDAVRAESDMNGRLATIKIDFWSTEELMQIASLGFEKLKIIDDPTVSS
+ILAENSFGSPQLMQTFCRELCKFNGIKTQQEHPVPLAPPEQWRTFFEAAIDVEESAAWFE
+TFLAGTKLRGKKRNIYDLVNGQRHDKYGVILSGFNSTLPPLTFTSARLMEEIQVLVAGQA
+PRSSDVSAGLSNISKMAFGDSEVVDETDLSEGVEEGLTTSTSLSSLDHAPASSPLSADSR
+SNLRFANAKKRPVLEYLEKGNTSSVYILDPFFAFYVKWHAPQALSEHAKLRNVAAMDSLE
+S*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002868.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002868.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f5c3c112b32e59ef0c18063a0d4f97033a65d86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002868.fa
@@ -0,0 +1,2 @@
+>NZ_CP083691.1_410
+MRVRIQEVTRTVVTVAPTVNGAVGEVAKSIDPAASITLSLPTERLCPAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002870.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002870.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c79d52c83adc80001a0e6cb960b8bb1ec5d892bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002870.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_429
+MFAGAAAVTLGAGGCAVPETVVWGPDGAAVKSATRDVIAAAQRGGDGLPACPGVSVVTGD
+PAAWRGAGAGEPERPGPDLPAELTRGGEPAWVINVEAGAEAAAPGARVPGSLAFSDLADG
+GLCLSGLDWANVGG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002872.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002872.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c96f575a2fd0b9fdacfefe786140a7f93fbf618
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002872.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_431
+MTSSDDDTVLLALSHPGRRALLDALHERDGQSVTDLGQALPELGRHAVLKHLGVLEDTGL
+VTSHKAGRTRLCYLNAAPLVALAQRWLDDYALGWGQALNRLKSTSERRPEAMTTAAPLHR
+QAIVIDATPERVWTALTQECSSWFFATTLNSSLEPGSDYTYTYPDGRRAAEGTIIAADPG
+QRLEMTFSPTWDDAVTPEAPFRLVWSLAAQGGATLLTVEHYELDPSTETARQVGPGSLFL
+ISNIKTWIETGKPMHD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002877.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002877.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2bf2878242be7cbc4742cc413593ed187dd8c6c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002877.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_497
+MDPRTRTRRPLLPLTTAALALALGLTGCTGGPQEAASSAAASETTSAAGDVVRGGAEIDA
+PESAEPLSNARAAAEGDDRAASARASHEAAASSEATAVPRHAVVTLPAALFETGGGGTTF
+DAWARTTDAWQADGSDPRMPDLGGWDPKTEPVVAEAVLPADQDSLRNPGVLTVPVSGPGV
+THRLVLLCEYTSPRRDEETAGVDVVAGETHAAIASSLGCTPIDVRHTVRPEHIVDGAVRY
+EFQVAPLEAGRLAVLQGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002881.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002881.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4cfcdf4d5c212ce5684816f955c63a81b7813506
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002881.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_514
+MSSSSPALPVTALRFPEHSAPRPGVPGADAPAGPRTRGAVSWGVYLAVCAVAGLRLPAIL
+EATRDRIAAEAGADAGGGFVDLALGVTGVLAVVAFVIVFALYVSTARLLERHTLAPAPGS
+VVGAHTLALGCTLLSVHGAALLTGTLAPVPVRLGIAVAASAAAVALLRGQLPTGSAPRRV
+AAAATVLLLSALSVAF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002885.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002885.fa
new file mode 100644
index 0000000000000000000000000000000000000000..730781eeea376064cdce3eaf4b315e5d49068e1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002885.fa
@@ -0,0 +1,7 @@
+>NZ_CP083691.1_546
+MITSAGGTWLALLLCGLQAVLTTGTVTLVTSGVQTFTASLVSAVPADQAQLAVLNIDDAG
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+LRQGGALRALQAPEGELSVVDPHAADPTRVSARLATFPVIVVEGAQGSLAQGGAVILAST
+AARLPAPVSREVAHVFPRLTPEQQALAARLPQELHVNPDWMDLPKPPDTMPIPPAVTCGA
+AVLSAVDSALGVLTVTALQGVPLDLHVPWTLVGIMAGGTVLAFVGALWLALRNLSVRERM
+E*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002886.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002886.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f563ab921a7946c0cc5fd2a8eee77400a9ba1a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002886.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_555
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDGARRPSHCPDRWRTRRAT
+GC*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002898.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002898.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e79560a84e6ff2a2b2b907557f254b4cccbe2616
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002898.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_641
+MPLTPDMWWPPAVLALALFSDAAMSLRPPRFIRDCLNGVGFPREWWWTLIVIKTLAVIGL
+IAGIWIPGIALAANTGVIVYFLSAAAAHIRTRFTGQAFWLNCLGMLALSIAVLILSFAL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002904.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002904.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a061433eda3aa5bd80145f6ac077d6ab1faa5bcc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002904.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_672
+MVESNTAGVVVVGVQSGQGHDVVGVAAAVAERFSARLVCVVVDPALLSAGVRADGSEIIE
+PIDPDTADSDPQQLPDEDMRVIRDLAAARSVDVDFVSRVGDPSHALAAVAEERDAVMIVV
+GSQAGRRRIAELLTGSVAAHLTHQQHRPILVVPHDPVGATVLLPSEAP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002911.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002911.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2666582653970c2a527463f1b27a6eabf789ab07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002911.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_691
+MTMKEVEHAHATYDTPHLNAAVGVFALLANLVSVKMILAIRDIEVSANHLADIVDLPVDQ
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+RPN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002914.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002914.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c180ef1c2a6e3750d3fc3e9b072a7f37997404de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002914.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_700
+MSSCCSTNETNPAVENGGRENLLGGGADDMTTCPVMVGTPVSKKTAEAAGLYRDFEDERY
+YFCCAGCGPAFDSDPAKYAANMA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002921.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002921.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80da8fe3f4bea0fa08e5068e7b24fbd8c8cf85df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002921.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_765
+MTGAERGGAVAAHPVPTHPEAVPGDRATLRWAVPAGLLGMVGPVGDGPAPLEALRADGTL
+RALVAEPAALRLTVGEGRTWRAEGARVRAALQEALALLAAGEATCAPEAPASVVGGPGGG
+GKARAVARAGASADSDAVLRAAVEQVLAGPAGEYLRSHGGTARILGVEDGEVELALGGTC
+HACPARGFTLQMRLEAEIRRLCPDVRAVRTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002931.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002931.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a91148bb30b5a079d2631b67d6d2606d795416da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002931.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_898
+MGVGKTTAVTALSDVSVAGTDVRRSTLAFTEPAQDGKTTTTVGIDYGEWTDPEGRRIALL
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+PGRAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002932.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002932.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5302262ee1f186fc3123747aea1e47da84190320
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002932.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_899
+MASQEELTRIIDNINADVNGFIGASIVDMETGMPLASRSTRADFDLEVASAYNSEMVKSK
+LKTIQVLNIRTTLEDMLLTLGDQLHLIKMLDERTFLYVAADRSATNLALLRSAVNRHTVN
+FR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002934.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002934.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f31836d159ddaa700d7c60cfe7bbd2f0e1de6d13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002934.fa
@@ -0,0 +1,8 @@
+>NZ_CP083691.1_915
+MAQDPAGWRRTAVLLSGAWREALRVSAPRVEPEHLFLGVLASGGPAARVSARQGLSLTAA
+RRGAAVRANRQLRAVGEDVARAGRIPRTPLAAVDRGGAATLPLSAASEGMLPARRLAMTE
+AAWALDLLQEPAGAVSALVAAAGVDVDALRHALRAADRDEPRLPGAALDVMPAPCPVPPD
+ALTPPDGIRPSGSRASRAGRLSAIGAEWFVAAPREHVMRLLRDPEPIRAITAQPADAEVD
+DAFGVVTTVRSRGARGGEHRSTSQLFPSETSTPDGAARIRWAEVLDEHRPPHQDSDGTLV
+PDGRDYSGDLAGAYVFTLVDDSGPDPDQPVDYPGHQPLSGAGTRVRLERTRRTVRRRDAL
+ASRATRWPQAWAVAQHLQSLASLAADRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002935.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002935.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30b7abc7bc8cc55710d85d85524e58403f346f5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002935.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_921
+MSVRQPRIYTIPCDRRGDFLDRWQSTAQPLMETLGFRFVRTWEGTPDPVHRPHCRGCWAP
+RSG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002936.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002936.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82f6d9694943f244fe5f6f7f85d17f812b52110f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002936.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_922
+MTSAQVASPTPLSPGHRFTWANGGTTIRSRVEVVRPGHDLTWTGIALWLVAVHRNVIETL
+PDGQARLTSTESMAGVAAALLMPEEKLQQQLQAFVEAIAAEAERRSR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002942.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002942.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c111a92ee012ca1de15101ec6010b661d0f30035
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002942.fa
@@ -0,0 +1,7 @@
+>NZ_CP083691.1_995
+MSIDQNTADTTTPLATTGVRGRSRRRRTAVGALGAAGALAAVGMASAPAQAATVDASVLQ
+SIQACESGGDYTAVNPASGASGAYQFLDSTWATLAAAQGYASAADAPASVQDAAAQELYA
+QEGTTPWEASQSCWSDAASVAAMSTSTSSTTVSDAAVAQADVATPVETVAQVEPAAGAAD
+EAEADTAAGADAAAEEAAGEETDAGGTAPTAAPDAAASGEQAPAPSEPAPEPAPQGDQTG
+RQPAERPAEQGRGTAEQAEQGRGTADQREQRGQDVEQREGRTGGERQGAAPETGGDAGHQ
+EADAAC*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002947.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002947.fa
new file mode 100644
index 0000000000000000000000000000000000000000..587d55d3331618075257c7fb94fa35b4d4c9a3ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002947.fa
@@ -0,0 +1,8 @@
+>NZ_CP083691.1_1058
+MGAVTEQTPDAPHPSPAPPSATGGPAPAAPPVGPLTVRPITEAEHVEVLRRHPGASFLQN
+PRWARVKTDWSGQSLGFEADGRLVGAALVLGRRLPVPGRTPLLGRSFLAYVAEGPVLDAG
+VDVVEALAALVAELHAQGAFLVRVAPPGVVRRWDADTVRKALPDPAHRMLTDLEPAEEHA
+DALELERRLREAGWRAPEVLPGFSAGQPMFQARIPLEGLDEEGVLARMSGSSRKRTRRSL
+RNDLDVVVGGPERLDEWEALQDETAERDGFTGRRKEYFARLMDELGGSELADVTYYLAEY
+QGDPVAAAFHFRQGHVCWRPYSASSQKERKRDAPRLLEFEQIRQGIADGCHWLDLGGVPG
+SVDSEDRITGLTEFKTTQGADIVQTHGEWDFPLHKTLAHAFGLYMSRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002951.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ed2d66612dbfa22a38e168414ff5cd6c7821370
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002951.fa
@@ -0,0 +1,8 @@
+>NZ_CP083691.1_1189
+MTGTDDVAPTRSPEVAVIGGGIVGLSTAYALREQGVPVRLYEAGLPGAGQSAGESRIFRH
+AHDDPRLVAFARESRGVWDEWAEHFDVELVSSDGVVALGDSALARLRVLDEVGGVEAHEI
+DAAELAQRMPLLAGYSGPAVLDESGGAIRTRAAITALAGALGDAVTTAEVISIDPRADGT
+VEVRSVTDRAVYSKVVVCAGRETARLARTVGLSLPVRLAAHVRLTFDVKDAAPARVACLQ
+DSSGVFGEVGVYATPLPGNSSYSVGLSDTVGVRDDGTFIDPAAIRSLDERAREYVTRALP
+GLHPEPRDFLHCWVTDLPWSEDGVAVWEAGSVLFVAGHNLFKQAPALGRALARAATGGGL
+AADLTPAARLGEALR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002952.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..adc144cd9ff7320f46f7e50f96860af31a646746
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002952.fa
@@ -0,0 +1,8 @@
+>NZ_CP083691.1_1190
+MTNPFLGRDDQAIDVSDTPRGELEVVHTFTDGPMPTGVSVSHTGRIFVNFPKWGDEVPAT
+VVELVDGAVKPYPSAEANQAKSKADQDAFVSVQSIVIDPADRLWVLDTGSPLFEETQRGG
+PKLVCIDLTTDEITQTILFEPDVALPTTYLNDVRFDLRQGEAGFAYITDSSDQGPNGIIV
+VDLASGAAWRRLHDHPTTKALPPGEMVPVAEGRVFAERSAGEAPQPVKMGADGIAISHDG
+ERLWYCPLISRRWYSVDTAALRDRALSDEDVAATVVDHGDKGGGADGLESDDQGRLYATN
+WEHNAVLRRLPDGEMQTLVHDERLLWPDTMSVARDGHLYVTANQLHRQAKYQDGQDLRVY
+PYHLFRFAIDAGPVLLR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002962.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002962.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ca76f5e445f27cf02a8aeda8e07fd65a414bda6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002962.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_1335
+MAVLAEGERTQAQVATAIAVDPRNVGATIRKLIEARWVQARPNPADARSRLLSLTPEGRQ
+WWNDLQPGLRQGRNAFFHALTPDELTALEALLGKLDASHAADSINVPGQYI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002963.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002963.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e73f1147b3919ff32ffcacb0580540c05bf04ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002963.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_1336
+MPSLTPPTGHNTINPFAIVPDAMGFIRFVESVFDGHEAAHVRTPDRDGSIIHGEVTIGDA
+TIMLCDRKPDWPFTPAFLQVYVPDAQDCLDKAVAAGGRIVTPVSDFYGGYRIARALDPWR
+NLWWIYEPTTQPLHQDERDSDTDWHDRKPSLVYTSLMDAMRSLDRPEPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002967.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002967.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e05ee3695fb22b83d703e746821b8d2ce0f2ed15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002967.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_1565
+MRAGRRSRSLTSETEAKAGSCTTKDGKSYKAFGRFADEGAWWDAERGGFVFDASFDKAFH
+DGQIWFFDVKAGTITIDAYYPLTAPNFSEERRSAPAADRAAPGGPQLTNKLT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002972.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002972.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a9c6bd199710a432e8c805f2c0e33043bcbde1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002972.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_1719
+MSGSWPERAGRPRRSPNEQDGRATLLAVLDYRDNGTAVSLTRAFTVPTFRGQGHAPTLTA
+GAVQDIAECGGAAGGTHVVPMCWYVAQWFDEHPERQAMLARV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002973.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002973.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e65926e16be5084763b5ff8764a7156dfa70cf6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002973.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_1732
+MNLTSLYTDLVFDHDRHPRHAGLREPFDAEVHHVNPTCGDEVTLRVRLTGEGPDVVVEDV
+SYEAAGCAMSRASASIMAELLHGRPEAEAQAVWDHFDHVMHQRGKEAGDEELIGDGVALV
+GAAKFPGRVKCVLLPWKAWQAAFAQARAARR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002975.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002975.fa
new file mode 100644
index 0000000000000000000000000000000000000000..460e56e773b1880aab16920d898357057fb4b18e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002975.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_1740
+MVLSVLADDAAVREVFLDSPALEVMNQGSVHVNLATISPSLASEAAGRHTGAGVGYVAAP
+MFGGVPVAQAGRLNIVTAGQTEVVERVRPYLDAFSAALWPVGEDPAQANVLKVAGQILIA
+SAIQAMSEAVSVVERSGGDVNRAVEVFTSTITPGPVYSMYGAMIAESRYEPARFTPILGR
+KDVDLARSQAAAEGLRLPFGDLLSGLLREALAAGHESRDWAVLGEMQRHRNGGEGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002976.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002976.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf26e1e19843efcc7c1f8019235f95c0b24ca5ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002976.fa
@@ -0,0 +1,7 @@
+>NZ_CP083691.1_1742
+MMRGGEGEKGLGGRAGVEVVPREVLHPARGVANLHGNQIITVGDHMRGEQGDGESVANQP
+EDEIHGHRFESHVSLKIGGLKCQVRLSSTCGATGEINEPFAGDLLKSHVGPPRQPMRSRK
+HCNQTLTGELLGRHLRWWGALGQAQESGIKAAGMNVSQELLATPSAQGDADLRVRLVIAR
+QERRHIDRGHGGDHSEAERATNISRGGRSLGNRTVGRSQTLASGLDKHHTRRSGLHSPRR
+AGKQLDSDLSFQRLDLMTERRLHHKAAFRGPSEAPLLSDRDHVSQLLQFHRPMMHLHPSS
+PKYAARSLTVSGE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002979.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002979.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58f48007a849174576e47b5370a8e61644c47dfa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002979.fa
@@ -0,0 +1,7 @@
+>NZ_CP083691.1_1745
+MSPNLYHLARLLAPGSDRSLGRVAGDLASAHVPVFPCVPGQKRPLTARGFHDASTDLAQI
+EHWWARWPEANLGLPTGASGVVVVDVDVREHVDGRESMRCALNAGRVGMPVFTVVSPSGG
+RHGYYPATPDVVQRSWQVARAGVDFRGDGGYILIPPSHTTAGSYRLATVRQGAASGIDSD
+TLRDFLDPRPALKPRAADRGMAQSEPGVVVWRLAAWVAGLGEGERNRGLFWAACRAAEHD
+ITPATAVETLGAAAAEAGLGPREIAATVRSAYRTTHPTTSTARRATEPAAASPVRVPVGA
+GWGLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002985.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002985.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1dd5e51efbc2e365efbe881d28e49395f605e5b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002985.fa
@@ -0,0 +1,10 @@
+>NZ_CP083691.1_1757
+MGVCDLPVISGVCETAGEAAASLVSAPFDWLAQAMGSAAGWLFEAVWNVFDATTLVDITS
+DGYLSVYNLLFGIAVFVMLLFFCLQLITGLIRRDPTALTRAALGLAKSVLGSFVVITLTG
+LLLEVVDQLCVGIVQAAGETTESMGEKITILAGGLTAINIAAPGVGAIITIFLAGLAITS
+AAIVWLSLLVRKALLLVAIVFAPLALSGSSWDATRGWISKWAMFVVALICSKLVLVVMFL
+VAITQVAAPIDGDLSSISDPLAGVVLMAMAAFAPYLTYRFISFVGFDMYHAIGAEQDAKN
+SLNRPIPLPDRQPGNPQQVLDGNNSGNGGGGGKQPPKPSSPNPSASQGGTEAGAGTGGAA
+GSGASGSGAASGGSAAAAGPAAAAVIGVQVAKDAATAGPKAGAELGQQAETAADAADHTP
+TPNGGAGNGGNTPPAPAPGGTPPQPGTPPASTQPTPPSTPSSQPPGSSSHGGGEQVSPSA
+PVPNPPPADNPPPPSSAWKEPQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002989.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002989.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7df4416ec11c6bbbdf66d8b9f9b5d4ee62100c9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002989.fa
@@ -0,0 +1,11 @@
+>NZ_CP083691.1_1766
+MSASQRQSGSMGEELTNAALIGLIALFLLTLVLRAAGSVAAFLTGAPQPTASWAAGAGVL
+FNPGNPAVALGAPGLSPVAYWVTTIVALGGLVALAGWGWVVWRRRSHAQVVDPHRLAGIA
+TRHEVAQVASEKALLKRASTLRPSLKDPALGEVGYRLGTSKGQGVWASVEDSILLIGPPR
+SGKGLHIVIPAILDAPGPVVTTSTRPDNLTATLRARQRRGPVAVFDPQHLAEGLPAGMRW
+SPVRGCEDSLTAMIRATGLASATGLSAGGVESGGFWEGKTRTALQALLHAAALDSRKPAD
+LFRWTLDPAAAAEAVAILANHPDAAAGWADSLGAMIDADPKTRDSIWQGVALALGALADP
+RVLDAVTPRDNETPFDPETFLRESGTLYLLATGAGAGASAALVAAFIEDLIETARRLAAR
+SPGARLDPPLLLALDEIGNLAPLPSLPTLMAEGGGTGITTLPVLQSLAQARDKWSDHQAG
+AIWDAAIVKLILGGASNSRDLQDLTTLIGERDEYTDSVTLGDHGTRSNQRSVRRVPILPP
+DRIRTLPFGTGVALLRSAPPIITDLTAWPTRPDAEALKRDRARLEQLLQNPRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002994.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002994.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24bf1e4abde158fbe44ae97a3d3a1fd1df3f4ddf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002994.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_1775
+MTTPHESHRPDPDEELLRAVLAEEEAALTEEHGRRDPISPAARTRLRGGTAGAPVPQDRP
+SVEDVYGPVDRPSVGLPGDATADGSVTGAPGAASVPAAGDGSPEVFIGADAETPADVQAG
+RRGARPQRPGPGAAAHRAGHRGAAGRRGVVPVGPPPLARDHGDREHRPVGRPPVGRRGDA
+RRGRDLGGRGAIALTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002997.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002997.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35027747fac6f1a031ac638cbe9454795f8bee56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002997.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_1797
+MTSNATDQPHVILVPGYWLGAWAWDDVVPALKEHGLDVEAVTPPGLDEQDLNRKNATLQE
+QVNALQALVEQAGGDVVLVGHSGANAAVSTVTDRIPQLLRRVIWVDSGPMTDGAAFAPEL
+PQDIEELPLPDFDTLGQQASLEGLSDGQLKTFRARAVPEPAGVARASVSLNNDRRYGVPT
+TLICCSLPSSQVLELAQARHPMFAAVNDLIDVQFIDLPTGHWPMWSRPEDLGKAIATAAL
+AS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003000.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003000.fa
new file mode 100644
index 0000000000000000000000000000000000000000..066c0a723636079a893ae9ddf851daa8ffccc41a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003000.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_1835
+MTEQTPAPGPGVDSVSTGVHREPFSAVGPWKDDPAAAGQVVFTSVHSGHALRPEVAERMV
+LAEADRFREEDPFTDAIGAGVGSGLVMHRSRFEVDLNRPRATSVYTSPEQSWGLDVWRGG
+RLDEDVAERSRQVHDAWYAELGRRLDVLAGRGPYVVFDVHSYNHRRDGAKAAPAPQEQNP
+DVNVGTGSVDREPWAPVVDGFMDSMARPLVAGLGRRLDVRENVKFWGQNEARWAHRRHPD
+QACVLALEFKKEFMDEWTGQPDAAVVRELSAALADAADAVAQALADVKVPTP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003001.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eeb44702e1d5736553ef4aa2c4550fef8c76c8e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003001.fa
@@ -0,0 +1,9 @@
+>NZ_CP083691.1_1836
+MTGNAGRTATEDTHGTMPAEHAAHDDDGGVTPGVRGTSRVVASRMLSRWSGEHPGGGLSL
+ADRAVDHELGMLASTFRFLLDVTPTNVESARRAFLERDELEPFAYRRLEDDPEVLRQVLY
+DIPVQDVEDPVLGTLLRNKEREIDLQLEMLQARDTSDFMPLSIELYGAITPALRETAEHI
+LDQVPVPEPDADEAVDAPTFLALAREEIERYRDQDADIEAHAEIRRDVSGVMVSGDTLLV
+GPESTVQRRRADALVQHEVGTHLVTHVNGSAQPIACLATGLAGYDETQEGLAVLAEIAAG
+QLTAFRLRQLAARVVTVHRMVAGADFRECHRALVDDGIPASSAFTTVMRAFRSGGMTKDA
+VYLRGLLDLVDHVQRGNELDLFLLGKFSLADLPLLEDLRTRGILRPARIRSRWLTDPVHL
+ARLRALADVTDPAALVNA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003003.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003003.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46da2a5a3b8dec6eea199d9537f5d120b9dfc5b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003003.fa
@@ -0,0 +1,9 @@
+>NZ_CP083691.1_1869
+MPRLHSAHDTADNAPGARALSGVGAARHRALRPAAVLFTAGLLLTGCAGPDGAPAGGSPE
+AGASTTEDAGASSGTAGGSAGGQSGASESRAEGSPPVDPADFPASNTTKLTRVETIKDPG
+LTPKSIVSNQHGLAIANNMMYRHNVMLFDTRSREVVQTLEDTVDTDAMGIDGLSGVVNGS
+PVEAAWTQDGRYAYVSNYQLTGGEGTGVKPDDNCTAGSAISPSLVYRYSVEEKKWDAAYR
+VGRVPKYLALSPDDSRLLVSNWCDATLSVLDAETGELQHTIPLDTMPRGIVVLPDNKTAY
+VVAMWADKLYRVDLDAGTAELVMNTGPQPRHLSLSPDGKTLYMTVAGADRIVKLDAATGK
+VLASASAGDEPRSMDVSRDGTALYVVNYEASTLTKIDAETLEILDTAPAGENTVGVTYDD
+PTGQVWVANYGGTVDVYDDTDGVGPGAAGSAQPTADAPGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003004.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09dd4fae0788b3875bf1578188546961962d64b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003004.fa
@@ -0,0 +1,8 @@
+>NZ_CP083691.1_1872
+MEHISGRPLTRRGTLLGLGGAGVAGALGLTGCSSAQTTSAPQTSASPSSSPVAATGIEDL
+AVGQDAVVRASLTTAWLKPDVDRGWTDEPVTQADPRPDEWLPRMDDTLQRGLLGRSDTQA
+ALGSRVTVRELSGDWARVSFLDQAAPNDFGHQTSWVPRAHVVRDLGFLSAQQADGAPIMR
+VTAHSTGVYEGEDMEKTLVVVPLGTRLPLLEEGDEASKVLLPDEREGWIAAADTAVGEPA
+LGTAEQVFETARSFEGTPYLWGGMSRFGIDCSGFTYTVLRAHGILLPRDSGPQLYDSGLP
+RVAADDLTPGDLLFYSHVPGGRRIRHVALYLGKGRGINAPFVGRPVTVETLEQLNAKHDY
+AGAVRPRYAQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003005.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003005.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e1bcdc3be569dd0de0a02c79c78b5825ffde6d6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003005.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_1902
+MKKITRSLASVAAALGLAGAGLVAAPAAQAADLTCSGIISGRTMTGDITVPGGATCTIRS
+STVTADYVYVAPNATLITENSSVSGFISVERGATLRATEGSLGDVLADSQKLIRIHGTSV
+GSLNVSQGGTVTTTRMRVRDDAYFHGMGGTVSHSWGRFSNYVSQYGSARNRFMIRSSVVG
+ADVSVQQSGHVLVGRNTVYGNIFVHDNRGTIYIEGNRADLYLSCDGNRYQPTGGNNTAWD
+KWGQCAAL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003011.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003011.fa
new file mode 100644
index 0000000000000000000000000000000000000000..218a6078f2795d34bbe122dd2c5a95d5b4e92f29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003011.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_1969
+MQHVDKPDEMIGLGLDGADDLESVVLDPVSGIAAYASPEEEFTYVPVLRDDGTVQAHTVI
+DTPGAPTRFEYTVDIPEGGHLEMVGTSVLILDAQGDMVGGIAPAWAKDAVGNDVPTHYEI
+DGATLTRVVEHDSSFAYPVTADPWLRINLFGHVYKDTYRDHPRVNASLSAWGWSVYSGAS
+VGGPAKGQQILNTSGLSEVLSRGQDIRDAFYGKASMYAQYACHALGAVAAGQWNLERIRP
+NLTVPWTTNLANHRCNWNYSNGGV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003012.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f0bc50f85885f0059eeb933ee4f5aa00f043672
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003012.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_1999
+MMGPSHAVTGAAGWLALTGPLADLAGVYVGPQVQLVGALTTAGAALISDWDHPRATIATA
+LPPLSTVLARFIRRAAGGHRRGTHSFVGLAAFTAVTWVLTPLTVTVGSVTFSAGQGVVAA
+FLAAVAARILRVAPGPVTGWAVGLAAGALAGTTAPGATWLTVSVALGVGLHIVGDMLTTR
+GVALLWPALPDPPVPTPFWLPGGRFRLPLLGRAGSWREWVVATACTVYVVGAVSAVVRAL
+LAAADPAAWPLPGPFA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003013.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003013.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ae27bf1d74bed84351a2b5a0b4a4bb4ef1b358f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003013.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_2031
+MDAAFGPRVRFLGLQGSRARGEASATSDIDAVLVLDALTPRDVDAYRELLDGLPHRELAC
+GFLSGRDELLTWDAADLVQFVHDTTPIRGSLAELLPRLDAAAVARAVTAGAGNVYHGAVH
+TLVHTRSPETIAGLAKAAAFVVQARHLQRTGTHVRRQTDLLDVVDPADRDVLALALAVRG
+GAAVDVDRDGRLLFGWAQRVLVG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003015.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ffdfd524c183637082949eb0a7c09c279d8176b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003015.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_2124
+MDPATISGRALGAVLAVVANAPAMLPRRQPLHPRGRTRRATWRVHAAWPESGIAAFAAAG
+DTPVLARTSRAVGLPEPLPDFTGLALRFADGGALLFASTGTGPFTRRLLAPRVPGAVDPL
+TTLLPLHCRLGAVDVGAQVRGDEVGILTSLDGGPWVDRARVVLGGPADVVVRFDPLRPPV
+GLWWSDFWAAARSPAYALARRLTPGAP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003017.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..372ccb41c01970bd7059119a2e6013b402aba446
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003017.fa
@@ -0,0 +1,7 @@
+>NZ_CP083691.1_2127
+MYLVPILCALTGALFLALGSERQASGVRALERGDGARPGRGGALRLLTSPVWLVGGVLML
+AGIVLNVIALAWAPLTVVQPLGAVAVVVTTLVHARVAGLRVDPATWRAVAACTLGSAAFV
+VVTVQATLPNPVPDADQETLTAWIAAGVVVVGLVAALALRGRRSALVPIVAAGVLYGFVA
+VCVRMSAVRLVDGRPPAWGVLAVLVAGAVLGVWFVQTAYRHGPPDLVVAGLTVVDPMVGV
+LVGVLVLGEMRPDAPWWVGPCLLAAAAVATVGIVRLSRSHPDVLARREERRVADTPGETT
+P*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003020.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bdf779264f838f09ce22f8142b7f9b7cb58cee83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003020.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_2163
+MVEGIVYRYRTGIAWRDLPEVFGPWQTVWTWHYRMASDGTWDRVLAKLTAAADAAGLVDW
+SLSVDSTIARAHQHATNTTRLTGGWIELQESAGRAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003021.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84e5070d0bf257c4a73216a1cccea54b8faf1626
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003021.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_2164
+MFLPLMGQLRVGRDRGRPRTRPNAVRADKAYSSRAIRGHLRSRGIKAVIPEPDDQKGHRR
+RRGSRGGRPIGLDAIDYKNRNVIERQYCHLKQWRGLATRYDKHAIVYRAAVVLNAVIAWA
+KTLSDTP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003028.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f84b10ac14a2817d0e30aabd9b7eb83733cfc0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003028.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_2191
+MWSRGLGRGWDLRWVRDVARMQFDLYEEDRTGAWWADQDSGHQLALVSDGGWRMSLNGAS
+YPSRYRVFDFDGVEIVEQTEEVLGRLGHGGHFDPQQEGAGRYQRVREECVSAVEDVLHLG
+GKR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003035.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e16493f9dab0d2d3ed282e3d7f6b585e8b5a3c6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003035.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_2269
+MESTPPVPPLPDGRVGIVIPVYNTGSLALGAAHSARVALGSTENVVVVDDGSKHPDTLAV
+LDSLRVEGFHVIRQPNGGVSSARNTGIQQVTTPYVIALDSDDEIMPEAPHAMAEILDRHS
+DVTIVTGGAFEVVDGAEHLSSPPDGPVTRSAMRAATVLAMASMFRRSDWEAVGGFPEGLS
+VGEDWVFWMRLLRTGGKVEILDIPIARRHLGEHQVTRGYIDPRQSTQAAALVRSENSDLY
+AGQEVELIERLNAAELQLAAYRHAYRHVDRFKAGIRSLLGRARAKR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003042.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003042.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2c792e03e1d1f04c2c9637e4ffeda7504f70b26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003042.fa
@@ -0,0 +1,3 @@
+>NZ_CP097650.1_75
+MRIMTVCLGNICRSPAAEAVLNRKLAEAGLDDVEVTSAGTSDEHVGARPHHLTREVGGEL
+G*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003043.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..104506ae1efa407478f4510bd7a25c2775ec4416
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003043.fa
@@ -0,0 +1,4 @@
+>NZ_CP097650.1_108
+MDFWSTIWDAIWWFFTIFVFVAYLIALFSIISDLFRDRELSGVYKAIWLLFLIFLPFLTA
+LVYLIFRGRGMGDRAERQTREAKATADDYIRTVAGGPASEIAQAKQLLDSGTISEAEFQS
+LKQSALDGSR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003047.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3133924d1392d2acae03b4eef51c6901448906a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003047.fa
@@ -0,0 +1,5 @@
+>NZ_CP097650.1_155
+MMVFPAKFSELNALELSDEARLILTRIIRVAFPHPDFPDGPYERMAQKIIDASEESRWFR
+MALTQGLVTLDSMSDGHFLELPEDRALAVLKRVADLEFFGFIRRTTVLNLYDDPEVQATL
+GYEGESFSKGGYLHRGFNDLAWLPDPRIEESEEQVTEIGPLPYTVAPATPEGGVKPVPDL
+FKGTGTVDEGSKR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003048.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0238bfce369d8f3a00b5792991e5c8661f3c10ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003048.fa
@@ -0,0 +1,10 @@
+>NZ_CP097650.1_156
+MSTQEISASIDHEDDSAVVIVGSGAGGGTLAHELVEKGIKVVLLEAGPYLKNEDYEQDEW
+AAFNQMAWLDPRTTSGSFRLARDFPNLPAWIVKAVGGTTTHWSGATPRFKAHEFKARSTY
+GRIDGANLLDWPITLSDLEPYYERAEMKMGSTHRQGRPPLPANNNYKVLANGAERLGYRH
+YATGPYATNAEPYDGRPASIQDGFNFQGDKHGSKWSIMVSEIPKSLRTGLLDLRPESQAV
+QITHSPEGRVDGVLYSDAEGNLHRQKARIVAVAGNAIETPRLLLLSASPLFPDGLANSSG
+QLGRNYMRHTTGSVYAQFDEPVNMYRGETMAGLIADESRHDVDRGFAGGYYMETISLGPA
+FLASFADPGAWGPDFTALLDGYRNTAGLWIVGEDMPQETNRVSLNTTVTDRLGLPVPNVH
+FDDHPNDVAMREHGYQQGSLLYEAVGSVSAHHAPPYPSTHNLGTARMSERPEDGVVNQFG
+QAHDVPNLFISDGSQFTTGAAANPTLTIVALAIRQAEYIADQMAASEL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003053.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4db13929fda42e8986f3ebc9f292078eb04c98c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003053.fa
@@ -0,0 +1,7 @@
+>NZ_CP097650.1_491
+MTGVESAHSKVPVRSRKSILLANSDMTYRGGTQAWIRQMASTLQSHHDVDVFSLEGAPLE
+FTAFRPEKYYDIALVNHWTTAQALRGARIHTRITTVHGVIPFEEVPVLGSDAYVSVSEAV
+QNHIPYRSMVIRNPIDFAHFSPDPARLMSPVPRRVAFVSNRQGDALPILREACDRAGLEL
+RVVGRETSVEDPREVYLWADVVVGIARVAMEALACGRNVLCFDYQGCHGMATRERLPTLW
+QSNFGGHRPGVWPTADEVARALLEGYDPRRTLRSALLAEHDPERVARSYLRLAETVGSQR
+VARLVRAAPRQVMSPKITRMVAAIRRRPSEVRLAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003056.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a1579d1a1486997e49f5aa8fc92a8cd346b54e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003056.fa
@@ -0,0 +1,3 @@
+>NZ_CP097650.1_973
+MALDIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPIGLDAAAYKGRNVIERQYAHLK
+QWRGLATRYDKYAIIYRAAVVLNAVIAWSKRLSDMP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003062.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9858cd353d38646d9a9a78c57dc686cd6e35180
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003062.fa
@@ -0,0 +1,6 @@
+>NZ_CP097650.1_1499
+MLTLGSFALFRSGERNKFGPLTMLSAQFVSHNLTVQVMQYAHIHDEINEQLFSSRHLGEL
+LLETLGFSYEDFCAVREAIVRVHGEKFFAIRDFIGEMFEQRDEKKNDLAFEKDARSALMS
+MLELPGEGATLTVQEIVEASGVPADRTQAILDRFGLSFNDAEDALAVVTKFLSGDNPFRS
+ASLVKDADGNYILTGKPIGTDCFRQVVEDALKRVPAKFRRYEKRRMLVVVGHEVLDIRTG
+LR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003063.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c57d2c44d35eee0acae7a665d7b76248e0d1f46b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003063.fa
@@ -0,0 +1,3 @@
+>NZ_CP097650.1_1501
+MVTADDEGLAAAFERMGEILGRMNEGENPSEYVRRGPAIIAEHVQAIAESLKDADAFDVI
+ELMRMREMPMILEGYGRVNLSV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003065.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003065.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d6ebd226df6d9f8992d166eaefc1adc39a9f976
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003065.fa
@@ -0,0 +1,4 @@
+>NZ_CP097650.1_1823
+MSSRGNVIKRWGDKGGVGASDGSDARVVEFILNKPTKNFTCTGQYASAPENGVMVAIPAE
+LTLASGAEAAGFRGDFLHPVQFRFVGTDGKTASIDMQTSAALQCVDEKDAPNFNIGDGET
+TSGLITLDLPASEGTLILDNALMDSGWEWEL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003067.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78ae628722954a48de58243cf6a217fa396f2a02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003067.fa
@@ -0,0 +1,2 @@
+>NZ_CP097650.1_1975
+MTMGPSEAAAGALAMLGYVSWLRGEGSLTDDQLALAKARAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003068.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e0e75603151cd8ce67443c5c047856c482a91bf8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003068.fa
@@ -0,0 +1,6 @@
+>NZ_CP097650.1_1978
+MTPSPPSLRSARHALPATTAALTLALTLAGCSGGGGPATASGTTPSPAASSDTTPSPSST
+SETTTPSAGGPASGTTAPSTPAPASGSATQGSGGGSTAGAGFVPEGADPARNGALPLSEG
+FLAALPEAAVTHRAGSPTEDPLARALEGVELPGTPTTDVNVIASELQGLQTPGEGGAAMG
+GERPEGTLRLMLLCDDPDAGPSSVGILGADGFAAYQPLGWSDRCGGYVVMVPESDAEDLV
+VSAEAPEGTRYRLSVITDHDPVAN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003071.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003071.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3e7399d5cf320925e216c6db9b2fb3d2bd74a31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003071.fa
@@ -0,0 +1,8 @@
+>NZ_CP097650.1_2127
+MAGMIITGLLLGLVLGFVFQRGRFCVTGAFRDLFTIRSTRWLTAFMVIVAVQSVGVFALD
+ALGVITLEAETFPWLGTIIGGLIFGFSIVLAGGCATGTYYRAGEGLVGSWFALIFYIVGA
+TAFRKGPLAGTTEAVRSVETQTGSFQQLTGLSPWVFVALLVAGVGLAVRHHLRREAAMTR
+FRLPAAKTGLAHVLTEKAWHPFVTAAIIGVLAILAWPLSWATGRESGLGITGPSANIGAF
+IGTGELELVDWGVLMVTGLLIGSFIAAKASGEFRVRVPDAQTTVRSIIGGLGMGWGAAWA
+GGCTIGNAMVNTATFSFQGWTALVFMVLGTGLAAKLFILNHRGKGTTPAPTSGSGLTSAE
+GAAADAGAARPVKLTPIG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003072.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003072.fa
new file mode 100644
index 0000000000000000000000000000000000000000..665a9753eaf8f72e51052ea1671fe94e898c675c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003072.fa
@@ -0,0 +1,3 @@
+>NZ_CP097650.1_2128
+MAKHLLETDGQVCPFPLVEANQAMQQIPSGDELVIDFDCTQATDSLPRWAAENGHEVTDF
+VKRGAAEWTITVKKG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003074.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003074.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5a2bef915db8bcfbb50aaf657204d907f685281
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003074.fa
@@ -0,0 +1,6 @@
+>NZ_CP097650.1_2155
+MTTPSGAPDVSADPEVRLLTARLNRARTHYLDFAELWAAYLEGRPHSIAREILTDGTVTI
+RLDRVAPIPAELSILLGEFLYEMRAALDNCLYAAAVIASGQNPPPGAERLEWPIRTDQTQ
+WKSQANRYKHLPAELTEALEAIQPYNAELPAWNCLAILHGLARFDRHRRPWPLALFLVKT
+QLQVRPDVVEPLDVACNRVIHPGEKLATLRLSPGHVLSPTNFDFHVEFDVDLADIEPSEG
+PEGLHVRPWGSLAHRLQSVHRAVTEYCDDLLLLAASCRKH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003075.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003075.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a07b9da69bcfb99a9bbc9bc9ffa806094441616b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003075.fa
@@ -0,0 +1,4 @@
+>NZ_CP097650.1_2156
+MNVPERGEARMRDAIHHAMALPQTALGTHCFVWGEVTTVNHTSAEPPHWFLNVRSGTDRL
+FAFHMSAATAKAVVEAMNHQRGLRWQSLFDAVDAQFMVFGYLKVAKNGVPMVSVKELSHL
+SLRVP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003077.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..56f7612ee005adb3de6761cb94f0a788b9399f06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003077.fa
@@ -0,0 +1,8 @@
+>NZ_CP097650.1_2158
+MNPLRPLTIPTYRWLFAAMVLTIFAQGAWALYLAMQTLDLGATPATLSGVVVWSGIGLLA
+GSLPAGVLADRMPNKSVIVGVLSLNLAIATATSTVAVFGMVAFWMLAASAFFIGVSTAFF
+FPAYTALVPVLVESDDLMAVNGLEGATRPLVGQALAPAAVGAVIGVSMPAAGGYLIAAAL
+AVALLAALQLPAPTPAESEADASAASPIGDLLDGFGYAARTRWVRTSVLFAAVMGLVVTG
+PLEVLLPALMRSSHENGPALYGAVLAALGVGGLVGSLLAGSWCTPERFLPAMIGAWALGC
+LPLTIPALTSNPWAIGVGLAIYGALIGIGMVIWGTVLQEHVPLEMLGRVASLDFFISIAF
+MPLSIALTGLLSRHIDTHTLFISAGLVPLVTAVLLATLGQLRMPRTTVGVAGGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000191.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000191.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e199277e3f99b6ef2457e6d4fe2f7b6175b233a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000191.fa
@@ -0,0 +1,46 @@
+>NZ_CP042169.1_20
+MTEVISPARPRRNIELVLLLAALTIALGADLLGMIGTDAPLDSTAWVPLGIFGAATLVLH
+VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAVLVASALVF
+LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA
+IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG
+MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS
+YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV
+TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA
+NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPGGGEER*
+>NZ_CP033200.1_1994
+MTEVISPARPRRNIELVLLLAALAIALGADLLGMIGTDAPLDSTAWVPLGVFGAATLVLH
+VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAVLVASALVF
+LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA
+IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG
+MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS
+YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV
+TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA
+NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPGGGEER*
+>NZ_CP040019.1_360
+MTEVISPARPRRNIELVLLLAALAIALGADLLGTIGTDAALDSTAWVPLGIFGAATLVLH
+VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAIVVASALLF
+LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA
+IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG
+MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRNFGGS
+YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYFLLV
+TRMMRAALGVRDGFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA
+NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPMRGGEAR*
+>NZ_CP083691.1_342
+MTEVISPPRPRRATELMLLLGAVALTLGADLLGTYTTTGALESTAWVPLTVFGCASLVLH
+AVLRLRARYADPFILPIATLLNGLGIAMIHRLSADTAAARPTSQLAWSVLAVLVAAALVF
+LVRDHRMLRRWPYVFLAVSGVLLLLPLVPGLGLSANGARIWINVGVGTFQPGEIAKITLA
+IFFAGYLSTNRDLILLAGRRVGPMTFPRMRDLGPLLVAWAVAMGVLVFQRDLGSALLFFG
+MFMAMLYIATSRASWVLLGLSLVAVGAAVAFLFLPHVTARFEIWLNAFDPEIYRRDFGGS
+YQVVQGLFAMASGGLLGTGLGGGNPTQVPLSFSDMILAAIGEELGLVGLSAVLVLYLLLV
+TRMARAALGVRDAFGKVLAAGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA
+NWIILGLVLRISHAARRPAVVDGMVNASGPGAGHLDPGAALPEPAQRPGPWRAAAPAGGE
+AR*
+>NZ_CP097650.1_20
+MTEVISPARPRRNIELVLLLAALAIALGADLLGMIGTDAPLDSTAWVPLGIFGAATLVLH
+VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLAWSVLAIVVASALVF
+LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA
+IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG
+MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS
+YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV
+TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA
+NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPGGGEER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000207.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000207.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa4e7cf23cccae36149a30533a01c3b09c1e5d54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000207.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_51
+MSTQPPGLTTDAPDTPDDDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP
+RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWM
+EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK
+APATAAALRELVPQYLDSALVSVVAGGKECNTALLAEPWDHILYTGGERVGRIVYEAAAK
+TLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVT
+AELPAALREFYGDDPRASKDYGRLISAEHAERLREMLQADLDAGAELLVGGDVDVAGRYM
+APTVVTGVKPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA
+FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIHGFETFSHLRPSITKSDQVD
+TLKTAYPPYGRMKRALLPKML*
+>NZ_CP033200.1_2020
+MSTQPPGLTTDSSDTPDDDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP
+RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWM
+EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK
+APATAAALRELVPQYLDSALVSVVAGGKECNTELLAEPWDHILYTGGERVGRIVYEAAAK
+TLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVT
+AELPAALREFYGDDPRASRDYGRLISAEHAERLREMLQADLDAGAELLVGGDVDVAGRYM
+APTVVTGVTPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA
+FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIHGFETFSHLRPSITKSDQVD
+TLKTAYPPYGRMKRALLPKML*
+>NZ_CP040019.1_331
+MSTQHPGIATDSPVSSDDDLRPGLDAAPVGPAGEDGDDPVREPLPTEALPLAPAGPRPED
+PRAAVVRLRAAARSRAAHPRAVRVRQLKGLKRLLTEGQDRLVAALGQDLGKPATEALMTE
+VVSVRSEVDHALLHLTDWMEPRPAKLPLALRPASAEVRPRPKGLVLIIGAWNYPVQLTLA
+PLVGALAAGNAVVVSPSEKAPATAAALRELVAEHLDSALVSVVEGGKDCNTALLAEPWDH
+ILYTGGERVGRIVYEAAAKTLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQT
+CVAPDYVLAVGDVAHRQVVEELPGALREFYGADPRASKDYGRLVSAEHAERLRDLLREDL
+DAGAVVLVGGDVDVAGRYMAPTVVTGVRPDGALMREEIFGPILPVLRVDTFQEALDFIAE
+RPHPLAAYLFTDRPSYHRAFDDQVQAGGLGYDVGLLHAGIATLPFGGVGASGIGAYHGVH
+GFETFSHLRASITKSDQVDTLKTAYPPYGWVKRTMIPKML*
+>NZ_CP083691.1_269
+MSTQPPGLTTDSPDSPADDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP
+RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPSTEALITEIVSVRSEVDHALLHLTDWM
+EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK
+APATAAALRELVPQYLDSALVSVVAGGKDCNTELLAEPWDHILYTGGERVGRIVYEAAAK
+TLSPVTLELGGKSPAVVTPSRNTGAMARRITWAKFTNAGQTCVAPDYVLAVGEAALRQMT
+AELPAALREFYGDDPRASRDYGRLISAEHAERLREMLQADLDAGAELFVGGDVDVAGRYM
+APTVVTGVKPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA
+FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIHGFETFSHLRPSIAKSDQVD
+TLKTAYPPYGRMKRALLPKML*
+>NZ_CP097650.1_46
+MSTQPPGLTTDSPDSPADDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP
+RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWM
+EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK
+APATAAALRELVPQYLDSALVSVVAGGKECNTALLAEPWDHILYTGGERVGRIVYEAAAK
+TLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVT
+AEIPAALREFYGDDPRASKDYGRLISAEHAERLREMLQTDLDAGAELLVGGDVDVAGRYM
+APTVVTGVRPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA
+FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGVYHGIHGFETFSHLRPSITKSDQVD
+TLKTAYPPYGRMKRALLPKML*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000210.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000210.fa
new file mode 100644
index 0000000000000000000000000000000000000000..becb163a2ddf334377998b6e4e45e8f7ee505f57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000210.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_54
+MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAPSGEDAAPLDLPL
+TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT
+PALRPAPDGPDTAWLLDGEKPWCSLADRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS
+AWPALGLAPIRTVGLAFDAVPGSAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR
+NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE
+ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA
+LLTGETDGGWTW*
+>NZ_CP033200.1_2023
+MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAASGEDAAPLDLPL
+TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT
+PALRPAPDGPDTAWLLDGEKPWCSLAGRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS
+AWPALGLAPIRTVGLAFDAVPGIAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR
+NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE
+ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA
+LLTGETDGGWTW*
+>NZ_CP040019.1_325
+MAQPEPVRLAPPGRTAEPDAARPAERALLAAASACDGDVAPMLALLGAGRAPDTEASAPD
+AAAPLELPLTGEGRTRQQWELLASVAAQDLSAARVLEPHLDALSILSQASVPAPAGLLGV
+YASESGGRTPRLTPAPHDDDAGSASDGRPDAGPDAWLLDGEKPWCSLADECAAAVITGRE
+ADGTRRAVLVDLDHPGVAETSSAWPALGLAPIRTVGLGFDAVPGTAVGGPEWYLRRPGFA
+WGGIGVAAVWFGGAVGIARTLRDATRSRAAAEAEGRGPGPDQVAQAALGRVDRLLHAMAA
+LLARAAEDVDAGRLDHGRGMVEADRIRGTVAQLCTEVVDVVGQATGPGPLTGSAAHARAV
+ADLQVYLRQHHAHRDDARLGRALLDGDADGGWTW*
+>NZ_CP083691.1_265
+MSETPWVHLPGAEGDGRPAAPTEAEAALLAAARDGEDGEAGIEPILALLSGDDAAASLDL
+PLTGAGRTRRQWELLASVGAVSLPAARVLEPHLDALSILDQAGVPAPRGVLGVYASESGG
+VSPSARPAPGAAVGDEDAVWRLDGDKPWCSLADRCTAAVVTARQEDGLRRAFLVDLGEPG
+MEVADPRWPSLGLAPITTVGLRFADVPAVPVGGPEWYLRRPGFAWGGIGVAAVWFGGAVH
+VARTLRTSLERRTAAASDGSGPGPDQVGLAALGRVDRHLHAMASLLGRAADDVDAGRLDH
+AHGLVEADRIRGTVAQLCTEVLDVVGQATGPGPLTGDAAHARAVADLQVYLRQHHGPRDD
+ARLAESLLAADPAERAELQPW*
+>NZ_CP097650.1_49
+MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAASGEDAAPLDLPL
+TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT
+PALRPVPDGPDTAWLLDGEKPWCSLADRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS
+AWPALGLAPIRTVGLAFDAVPGSAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR
+NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE
+ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA
+LLTGETDGGWTW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000234.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000234.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38dc2253f475bbc008011d94c52e1ed7ff5d0b84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000234.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_86
+MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP
+EQHRHEPSLGDRAHAVVDDARASAYDAAGQAQDRLGDAGDRVSEWADDAQHALHQAPAQL
+RGRTAGNPLAAGLIAFGAGLLLSSLIPASRAEQRAAEGLKDQAAPLVDEAKQAAQQLRED
+LEPAAREAAGSVKESAAEAASHLKEQGTDTAQGLKAESQDAARQVKDTAKDA*
+>NZ_CP033200.1_2055
+MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP
+EQHRHEPSLGDRAHGVIDDARASAYDAAGQAQDRLGDAGDRVSEWADDAQHALHQAPAQL
+RGRTAGNPLAAGLIAFGAGLLLSSLIPASRAEQRAAEGLKDQAAPLVDEAKQAAQQLRED
+LEPAAREAAGSVKESAAEAASHLKEQGTDTAQGLKAESQDAARQVKDTAKDA*
+>NZ_CP040019.1_289
+MTTSNNPDEIRAEIERTRHQLGQDVDALAEKVSPTKAVSRQTNRMKDGLLSVKENIMGSP
+EDHGRQPSMGDRAHAAADDARASMHGAADQARDAMGHASDRVSGWADDAQHAVQQAPAQL
+RGRTAGNPLAAGLIAFGAGLLVSSLIPASRVEQRAAEGLKEQAAPLVDEAKQVAQQLRED
+LEPVARDAAQSVKESATEAVDHVKADGADKAQDLKAESQDAARQVKGAAQDG*
+>NZ_CP083691.1_234
+MTTSSNPDEIRAEIERTRHALGQDVDALAEKVSPTKAVSRQTNRVKDGFITVKENIMGTP
+EHHEGPGAVDRARFAAQDAAGQVQGTAHDVADQARGYAQQAGEAASQWVDDAQHAVQQAP
+AQVRGRTAGNPLAAGLIALGAGWLIGSLIPASPVEKRAAERVKDQAAPLLESAKQEAAQV
+AQDVREQVEPEVRDAAASLKDSAAESVQSLKSEGAEKAQDLKGSSQDAAQQVKHAAKHA*
+>NZ_CP097650.1_81
+MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP
+EQHRHEPSLGDRAHGVIDDARASAYDAAGQAQDRLGDAGDRVSEWADDAQLALQQAPAQL
+RGRTAGNPLAAGLIAFGAGLLLSSLIPASRVEQRAAEGLKEQAAPLVDEAKQAAQQLRED
+LEPAAREAAGSVKESAAEAASHLKEQGTDTAQDLKAESQDAARQVKDTAKDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000304.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000304.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43e48050b4a5bd36b69813c8331c81df5cbd7cf2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000304.fa
@@ -0,0 +1,70 @@
+>NZ_CP042169.1_195
+MTAGDDGGRGAVVGVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAEADRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGAAVPVKANADEAVSGDNAIEHILVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPNPARRDDDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDGIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPAMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPEVIEAGVCPVPHETTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+ALGDTTSLQNEPCVGQIAEVLRAGRRAQDAGTGAVRSASSAST*
+>NZ_CP033200.1_2146
+MTPTEDPARPDPAEEGASGAVRGPNDGVPAAALATLPGPLPQALVDAADPDVHPGRPADR
+LHGGRGDGRPVAEADRLAFWEAAGRRLSWERPFTRTRSLTAPDPAAERGPEIRWYEDGTL
+NVAVNCVDRHVAAGRGEKVALYFEGEPGDRRAVTYAQLQREVAQAANALEELGIEAGDRV
+VVYLPVLVETIVITLACARIGAVHSLVFGGFSAEALRFRVEDTGAKLLVTTDGQFRRGTA
+VPVKANADEAVSGDNAIEHVLVLDRTGHRDIPWTEGRDLWWHDVVDRQPDTHTPRAFDAE
+HPLFIMYTSGTTGQPKGLVHTSGGYLAAASWTHDFLFSHPDPARRDDDVHWCTADLAWVT
+AHTYEIYGPLSNGVTQVIYEGVPNAPHPGRHFEVIERYRVTSYYTAPTLIRSLKGWHPDG
+IPAHADGGPDLSSIRLIGTVGESVNPEAWTWARTQIGRDTPDLPMVDTWWQSETGATVLS
+PRPTDTAFKPGCGSRPLPGVDVAVVDDDGTPTPEGLQGRIVVTRTSPSMARTVWQNPARY
+FHSYWEDYADQSEAGWFLAGDGAKRDEDGDVWILGRVDDVINISGHRLSTIEIESALVAH
+PEVIEAGVCPVPHETTGHAAVAFVVAHESWLAGDDGPGASAADRAEELRRHVGRVIGPVA
+KPAEVVFVPDVPKTRSGKIMRRLLTQLHQGTALGDTTSLQNEPCVGQIAEVLRAGRRAQD
+AGPGAVRSASSAST*
+>NZ_CP040019.1_181
+MTPSPLDAATRARSSAPASPGDAPTAPDAPVRRPNDGVPAEALATLPGPLPQAVVDAADP
+DVHPGRAEDLAHGGRGDGRPVAEEDRLAFWAAAGRRLTWDREFTRVSTGTPADPAAERGP
+ALRWYEDGRLNVAVNCVDRHVAAGRGEKVALYFEGEPGDREAVTYADLQRRVAQAAHALE
+DLGIGPGDRVVVYLPVLVETIVIALACARIGAVHSLVFGGFSADALRFRVEDTGAKLLVT
+TDGQHRRGQVVPVKENADAAVAGDNAIEHVLVIARCGLTGAGEIPWTEGRDLWWHDVVET
+KPTEHAPASFDAEHPLFVMYTSGTTGRPKGLVHTSAGYLAAASWTHDFLFSHPDPARRHE
+DVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRHFEVIDRYRVTSYYTAP
+TLIRSLMGWHPDGIPAEHSLESIRLIGTVGEAVNPEAWTWARTQIGRAALARTGEPVPMV
+DTWWQSETGSTVLSPRPTDHTFKPGCGSRPLPGVEVAVVDDDGAPVPAQTQGKIVVTRTS
+PSMARTVWGDPARYFHSYWEDCAEQGWFLAGDGAKTDEDGDVWILGRIDDVINISGHRLS
+TIEIESALVAHPHVVEAGVCPVPDARTGHAAVAFVVPGREWAPGPEGDEAAAALAAERAE
+ELRRHVGTVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHTGTALGDTTNLQNEVCVG
+QIAQVLADRPGR*
+>NZ_CP083691.1_135
+MTAGDDGGRGAVIVVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAEADRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGAAVPVKANADEAVSGDNAIEHVLVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPDPARRDGDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDGIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPSMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPHVVEAGVCPVPDPKTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+TIGDTTSLQNEWCIPQIAEVVAARR*
+>NZ_CP097650.1_197
+MTAGDDGGRGAVVGVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAESDRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGVAVPVKANADEAVSGDNAIEHVLVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPDPARRDDDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDKIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPSMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPEVIEAGVCPVPHETTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+ALGDTTSLQNEPCVGQIAEVLRAGRRAQDADTGAVRNASSAST*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000313.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000313.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c3dddf93d72ed615c01a84df234a1dfe8f78b6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000313.fa
@@ -0,0 +1,17 @@
+>NZ_CP042169.1_207
+MRSRYTAFARLGEAGPAEAQAMADYLAATWAPEHRPPAAELLPAAGEQAPRFTRLAVLDV
+RDGGPFQDAGTVEFVAVGAGAEGRFRLHEVSRFRREDGVWRYVDGDVR*
+>NZ_CP033200.1_2156
+MRSRYTAFARLGEAGPAEARAMADYLAATWVPEHRPTAAELLPTEGEQAPRFTRLAVLDV
+RDGGPFQDAGTVEFVAVGTGAEGRFRLHEVSRFRREDGIWRYVDGDVR*
+>NZ_CP040019.1_160
+MTDPCPCGAGLPLAECCGRLHARFAADGALTAPTAEALMRSRYAAFALLGEAGADDDGTQ
+GTDGASGPGGTGPGHAGPGHAGPDRARAMAAYLAATWAPEHRPAVEDLLPEAGERAPRFT
+RLAVTDVRDGGPFQDRGIVEFTALGHGEEGRFRLRERSRFRREDGAWLYVDGDVA*
+>NZ_CP083691.1_111
+MTEAPCPCGLGLPYPECCGRLHAAHAADGSLTAPTAEALMRSRYTAFARLGEVEGAGATG
+AADVAATVAYLRATWAPEHRPSTAELTPGPGDPAPAFTRLAVLAVEGGGPFQDVGEVEFA
+AVGRGPEGRFRLHERSRFRRESGVWLYVDGDVTA*
+>NZ_CP097650.1_207
+MRSRYTAFARLGEAGPAEVRAMADYLAATWAPEHRPTAAELLPAAGEPAPRFTRLAVLDV
+RDGGPFQDAGTVEFVAVGTGAEGRFRLHEVSRFRREDGIWRYVNGDVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000334.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000334.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e57d087981b51f254286143a8b1a9d8af0982863
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000334.fa
@@ -0,0 +1,43 @@
+>NZ_CP042169.1_238
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYAEVLPLLEVMGARIVHCGAAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPVNRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA*
+>NZ_CP033200.1_2206
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYAEVLPLLEVMGARIVHCGAAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPANRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA*
+>NZ_CP040019.1_115
+MSEKTATTTTAPVIPHFVHGERVDGSSGRHSDVYHPATGQVEGRVPLASVEEIDAALASS
+EKGFAAWSALNPQRRGRILLKWVDLINENVDELATLLSQEHGKTVPDAKGDIQRGVEVVE
+FAAGAPHLLKGEFSSNAGSGIDVHSIRQPLGIAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKTAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAGRMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPV
+GEETADRLVALLSERIRRLKVGPSLDESSDFGPVVSKDAKERIEGYIAAGAAAARRPGRG
+RPRRRRRGPRGRLLRGRHPLRPRHRGHEHLPRGDLRPGALRGPRRGLRGGAHPRQRARVR
+QRRGHLHPRRRRRPRLRHPRGDRHGGRQRADPRPDRLLHLRRLEGLRLRRPEPARHRRPE
+VLHQDQDHHHALALGRARGRQLRDARRLLTAVHPLPQEDPMTTVLFLGLGHMGGPMAANL
+AAAGHRVLGFDLVPEALEKARMAGIETVTDTAAAAAEADVVLTMLPNGRLVLDVYRGREG
+APGLLDAARPGTVFLDCSTIDVAEAREAAQAAEAAGMRAADAPVSGGQVGAEAGTLAFMV
+GAADEVYAEVLPLLEVMGGRIVHCGGSGLGQAAKICNNMVLGVTQIAVAEAFVLGERLGL
+EHQALYDVMSKASGQCWALTTNCPVPGPVPGSPANRDFQPGFAGALMAKDLGLALAALDE
+QGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHTDRSEA*
+>NZ_CP083691.1_84
+MSQSQTPSASLPGTVAFIGLGNMGGPMAANLVAAGVTVRGFDLVPAAVEAARATGVEIAD
+DAASAVPGADVVITMLPNGALVRGVYEGTADAPGLLGAADPDTLFLDCSTISTSEAQEVA
+ALAEAAGHRAADAPVSGGVVGAQAGTLAFMVGGSVEVFEEIRPLLEVMGSRIVHCGGNGL
+GQAAKVCNNMLLAISQIGVAEAFVLGERLGLEHQVLFDVMSEATGRCWSLTANCPVPGPV
+PTSPANRDFEGGFAGALMAKDLGLALKALDEQHVGAEMGRLAQRTYAAYADGEGARKDFS
+GIIETVREAGKDTAA*
+>NZ_CP097650.1_238
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYTEVLPLLEVMGARIVHCGGAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPANRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000335.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000335.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9e32d31d1806d8e580a33c04f65328bbf46a816
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000335.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_240
+MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDRERETVRADAVAALGPRARFV
+TGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVLAINTVG
+TVAMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVALTLPAARE
+LASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDHALLVEQIVSNPF
+LNGEVIRLDGAVRLEPR*
+>NZ_CP033200.1_2208
+MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDREGETVRADAVAALGPRARFV
+TGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVLAINTVG
+TVSMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVSLTLPAARE
+LASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDYALLVEQIVSNPF
+LNGEVIRLDGAVRLEPR*
+>NZ_CP040019.1_114
+MDLSNQSAIVTGGASGLGHATARRLAEAGAAVVVVDLPDREGETLRADAVAALGPRARLV
+TGDVTAEATAEEAVAAALEAGPLRVLVNCAGVATPGKLVGRGGPLSAEVLTRVLAINTVG
+TVNFMSRAAAAMQGQEPQGEDRGVIVNTASVAAYDGQIGQIAYAASKGAVVSLTLPAARE
+LAASQIRVVTIAPGLMETPMMAGLPEAAREALATKTPHPARLGRPEDYALLVEQIVANPF
+LNGEVIRLDGAVRLEPK*
+>NZ_CP083691.1_82
+MARRESLDLQGASAIVTGGASGLGHATARRLAAAGAAVVVVDLPDREGESLRADAVASLG
+ERARFITGDVTAEATAEQAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLAAEALSRVL
+AINVVGTVTMMARAAAVMKDQELWGEDRGVIVNTASVAAFDGQIGQIAYSASKGAVAALT
+LPAARELAASQVRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGAPDDYALLVEQ
+IVSNPFLNGETIRLDGAVRLEPR*
+>NZ_CP097650.1_240
+MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDREGETVRADAVAALGPRARFV
+TGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVLAINTVG
+TVSMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVALTLPAARE
+LASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDYALLVEQIVSNPF
+LNGEVIRLDGAVRLEPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000337.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000337.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7aa408d1b78ec7136f80faf82abd8e44016c3416
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000337.fa
@@ -0,0 +1,41 @@
+>NZ_CP042169.1_243
+MTAIADRPVPAPGAPAVTPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTDTPGYEATKISGKMGLRIMQNADITLDVRLPA
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV*
+>NZ_CP033200.1_2211
+MTALADRPLPATGAPAVPPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTETPGYEATKISGKMGLRIMQNADITLDVRLPT
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV*
+>NZ_CP040019.1_111
+MTPHADLPHVDLLRLRDGLDPAERTRLEEVEEHLQTAVRPRLAPYWDAEEFAFDLLPGLA
+GLGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMIAHLGSDAHRDRWQA
+RLESFDALGAFCLTEPEHGSDVAGGLATTATLDGDEWVIRGAKRWIGAGMIADVALVWAR
+DTADGEIKGFVVPTDTPGYEATKITGKMGLRIMQNADITLDVRLPADAQLPGAATFDAAR
+DLLRDSRMWVGWQGFGAQMGLLDSLRSYALEREQFGRPLAKFQLIQSAIAEVAGNLAATS
+GMMLQVDALRQEGRMEMMHAAMAKATSTRLARASAALARDALGGNGLLTEYEVSKMMGDV
+EAIYSYEGSYGMNTLIVGRALTGVSAFV*
+>NZ_CP083691.1_79
+MTPSPTPSPASAEPAASPATGVLTVAAAVHPGHAAAPAAAVTDGLPDVDLFDLRSLLSAE
+ERAHLERIEAHLEEHVRPHLAEPWNTETLPMEMLPGLASVGLGELDFLGASRLFQNLVHV
+AIARVDLSFSALVGIHNELNIGSIERFGTEEQKQRWVPALRRFEALGAFCLTEPDHGSDI
+AGGVETTATPDGDGWILRGTKRWIGAGTVAAVALVWAKDVSDGEVKCFLVPTDAPGFSAS
+KITGKTGLRIMQNADMVFDDVRLGPEALLPGAGSFDATREMLRDSRAWVGWQGVGVQQGI
+LRTLREYALTRTQFGRPLAKFQLIQAAIAQVAGNLAAATGLMMQVQRLQDDGTLKMVHAA
+AAKATSTRLARESAALARDAMGGNGIVASYEMARFMGDVEAIYTYEGTQSINALLVGRAL
+TGVSAFV*
+>NZ_CP097650.1_243
+MTALADRPLPATGAPAVPPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTDTPGYEATKISGKMGLRIMQNADITLDVRLPA
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000352.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000352.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f1e2a339e23c958b91f0a9933769353652bfbd1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000352.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_269
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFGQLLYLRARGGSETLTDADLDSRIARELGALRTLADELEAKAATRR*
+>NZ_CP033200.1_2240
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR*
+>NZ_CP040019.1_68
+MAPMTGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRQEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH
+GLNLRSGSQLEDLFGMAERLYLLHEDVEGTLAALGLLTNLPWDGAVGRWKSIQAGLALAS
+QILRDEGEHIVAANLGKRLHEADEVPSEPGRAARVLEVRQRQLNEPQLYDREISRALQAR
+DAEAEYRWRRARFAQLLYLRGRGGSETLTDADLDSRIARELGTLRGLARDLDAKAAARS*
+>NZ_CP083691.1_53
+MSDGGAEVAPIAGGYLRHLKAQDVRPGDSFLTRRGEPAPAVASTRVVRDDFGTPALVIAT
+LVGGREVKIAHGSVIRVRTDRPEEVKAAADTAFSPVDAGSPESRIVAVGQRHLDDAELTA
+TAARLSHGLNLRSGAQLEDVFGMAERMYLLHEDVEGTLTTLGLLTNLPWDGAVGRWKSIQ
+AALGLAALILREDGDHITAANLGSRLKEADEVPSEPGRAARVLEVRQRQLDEPQLYDREI
+SRALQARDAEAEFRWRRARFAQLLYLRGRGGSQTLTDQDLDSRIHRELGTLRQLAKRLAA
+QAARA*
+>NZ_CP097650.1_268
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRAARVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000363.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000363.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4976b672bb3ec2ca5bbcc7c2a8c400b45f8248d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000363.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_285
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHGLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR*
+>NZ_CP033200.1_2
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHDLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR*
+>NZ_CP040019.1_53
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLRENGLVPDAIVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYHADAAKALAIVNETEETTRSLLVVGHMPWVQN
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWVELDGRDAALTHFVVPGR*
+>NZ_CP083691.1_32
+MSPADAKTLVLLRHAKADWPAGVDDHDRPLAPRGHAQAPAAGDWLLEHGIAPEAAVVSDA
+LRTRQTWVWVAQRLGERAPTAYLDRRLYEADAARALAVVNETEETVRSLIVVGHMPWLQN
+LGMRLMSLDSDQDAALEMAEHLPTLGLQVFRVDTPWAELDGRDAALTHFAVPGR*
+>NZ_CP097650.1_292
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPTAGDWLREHDLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000380.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000380.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8af742bcc7511e5abf2e17bec6d10cee36de052
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000380.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_306
+MRELYRADLERLGRDLTEIARLVHRAVMDAQAALEAADVHGAERVISEDARIDQLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEPVRTV
+FTAMCDAAVEVAQEVVLLLETQDLAHGDRIDALNEDVNALHVSVFRAIAAPDWSATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS*
+>NZ_CP033200.1_30
+MRELYRADLERLGRDLTEIARLVHRAMMDAQAALEAADVHGAERVISEDARIDQLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEQVRTV
+ITAMCDAAVEVAEEVLLLLETQDLAHGDRIDALNEDVNALHLSVFRAIAAPDWSATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS*
+>NZ_CP040019.1_15
+MRELYRADLERLGRDLTEIARLVHRAMIDAQEALESADVHGAERVISEDARIDRLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPAPVRPV
+FTAMCDAAVDVAEETVLLLETQDLAHADRIHAVNEDVNALHASVFRFIAASDWTATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWAYHRGSETSGP*
+>NZ_CP083691.1_11
+MRELYRADLERLERDLVGTARLVHRAVLDARAALDAADVHLAEQVISEDARIDLMQEGLD
+EQAVRLLSLQAPVASDLRTVLATLRMSASLERMGDLARHIAQLTRLRYPEHVIPCDMRPL
+FGSMTDAAVEVAQEVVLLLETQDLAHADRIHALNQVVNDHHVSVFRAIAAPSWGSPPATT
+TDVTLASRYLERFTDHGLAVAAKARYLVTGESTRREGSAPA*
+>NZ_CP097650.1_313
+MRELYRADLERLGRDLTEIARLVHRAMMDAQAALEAADVHGAERVISEDARIDQLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEQVRTV
+ITAMCDAAVEVAEEVVLLLETQDLAHGDRIDALNEDVNALHLSVFRAIAAPDWSATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000383.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000383.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5092a7b674fb32502daebc264006ec1cae2aed31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000383.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_309
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH*
+>NZ_CP033200.1_33
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH*
+>NZ_CP040019.1_12
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIEYDASDGINGEEKDFLSYRNLA
+LVGDGDSGPARLIGTLENLSDQAQTYTFQAEGGGSATVQVPAGETFKLEDDANQTVLERQ
+DAWVGELLPVTVSGNGGQTELEVPLLGATQDHYRDLLPEGVSPSDEELGSHLDEETHDYG
+GEH*
+>NZ_CP083691.1_8
+MKSVASRPARRRLAAGALALTAVLGATGCSAVSPVATGIQYSASDGVNATQTGFVEVRNL
+GMVGEGASGPARLIGSLKNDSGADKTYTIAVQDGGQITVPVKAGETVKLEEQQLEVERSV
+WPGQNAQATVSADGTQLQLGVPVLSATQEQYKEYLPAGQSADTEHLDEQTATYGEGEGEQ
+H*
+>NZ_CP097650.1_316
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000440.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000440.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c45e0aa482c5846c08d7b0b070992dae4005447b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000440.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_380
+MSSATPPRPSADGAHPGPAPDVVAPDAALPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGMGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSSGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLTFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD*
+>NZ_CP033200.1_113
+MSSATPPRPSADGAHPGPTPDVVSPDAALPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGVGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSGGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLAFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD*
+>NZ_CP040019.1_2509
+MQGRIFLIGGLGFMFDAWDVALNGVMIPLLREEWALAPADAAWIGTANLIGMAVGAFLWG
+TIADRIGRKAAFAWTLAIFSVFTLAGALTDSLLWFAVFRFVAGVGLGGTIPVDYALVGEF
+TPRRLRGRVLAAMDGWWPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIP
+ESPLFLMSRGREAEARKVIDRMVEATGAERREYVMPPVEQERAGGVLAQLAAVWRFSPRI
+TAVTWALFVAIMVVYYIALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATVLIEV
+TGRRWLLGVSAVVASALLVWLASVLGVPSAVLPLVLAFGFVVQIAIPVLYTYVSELYPTT
+LRASGFGWASAASRVGAGLGPLFFVGTLVPAMGLPAAFAVTGGLVLLACVAMLALAPETR
+GRALEVSAD*
+>NZ_CP083691.1_2375
+MPPTGSHAASAAPTGEQVVQELPWRWPVQGRIFLIGGLGFMFDAWDVTLNGVMIPLLTEE
+WGLSKADAAWIGTANLIGMAVGAFLWGTVADQIGRKAAFTWTLLIFSVFTLAGALTDSLL
+WFAVFRFMAGIGLGGTVPVDYALVGEFTPRRLRGHVLTAMDGWWPIGAALCGVVSAWLVG
+TWSDWRLPLLAMVLPALLVFLVRLGIPESPLYLMSRGREREARAVIDRMVERTGAEPRPY
+VMPAADSRAHGGLLAQLAAVWRFSPRITATAWLLFVAVMLIYYIALQWLPTFLIEAGFAQ
+SRAFITTSGMAAAGLVGVAVSAVLVEATGRRRLLAVSGVVASGLLVWLASVLGVPGAALP
+LVLAYGFVIQIAVPVLYTYVSELYPTTLRASGFGWASAASRVGAGLGPLFFVGTLVPALG
+LPGAFGVTAGLVVVAVLVMFAWAPETRGRALEVAED*
+>NZ_CP097650.1_386
+MSSATPPHPSADGAHPGPTSDVVAPDATLPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGMGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLMAMVLPALLVFVVRLGIPESPLFLMSRGRETQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSGGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLTFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000449.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000449.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7dc1cbb12dfd2e0c68506711a7bc04c0802a112
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000449.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_394
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFDPDPAVAEMLSSLAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAAEERRRQIEMAAERDA
+AEHEADAPRR*
+>NZ_CP033200.1_123
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFEPDPAVAEMLSALAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAGEERRRQIEMAAERDA
+AEHEADAPRR*
+>NZ_CP040019.1_2497
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDISDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPAEEEIDRKVRN
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKEKDGVHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDQGSTFDATLTHLEWLGHEQYGYIEFDPDPAVAEMLSSLAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPKTGENLTRDPEVGAELTRRAAEERRRQIEVAAERDA
+AADREAADTRR*
+>NZ_CP083691.1_2361
+MASITLNHIEKTYDDGYHAISDVNLDIEDGEFVILVGPSGSGKSTLLRMIVGLEDISGGD
+LLIDGRRVNEAAPKDRNLAMVFQNYALYPHLSVYENIAFPLRLAKDGKLSEEELDRKVRD
+AARVLELQDHLDRKPANLSGGQRQRVAMGRAIVRDADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPATVKEQGGQYVLSSPIGDIPVPAEKAQRAAGRDIVFMGLRPEFFEDAELVEDA
+KRPHGSEFDATLTHLEWLGHEQYGYIEFEPDPEVAELLSSLAKDLDADELRPVVVTTLSA
+ESAARPGVPTRLWVDTTRVHLFDPKTGENLTRDAEAGAELTRRTAEARRRQIEAAQARDA
+EGR*
+>NZ_CP097650.1_397
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFEPDPAVAEMLSALAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAGEERRRQIEMAAERDA
+AEHEADAPRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000464.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000464.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca1630eb5fb668ca5ea422966b08ecc51d6d9c63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000464.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_413
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKRAILARQF*
+>NZ_CP033200.1_143
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKQAILARQF*
+>NZ_CP040019.1_2476
+MSHAATETEAPVAQDQTQAAGGGMGAIESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGICGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREVMPFLVAEGHEPSKERYQSQADRARYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAIAEVKQAILARQF*
+>NZ_CP083691.1_2343
+MSHAATETQAPAAPAQQTQGQDGGMGEIESFDITLRVRRFLPESSEESYWDEWRLTMFGT
+DRVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSQPITVE
+PIKGLPVEKDLIVDMEPFFQSYREVMPFLVAKGHEPSKERYQSQADRAIYDDTTKCILCA
+ACTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTE
+ACPRGIQVTKAIAEVKQAILARSF*
+>NZ_CP097650.1_416
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKQAILARQF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000474.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000474.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75ac2e0133c828c107dde000bc35f3860443985b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000474.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_423
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVSGCNIENASY
+GLTLCAECALLAELRMGGGGRLAAFVCVDGAGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP*
+>NZ_CP033200.1_153
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVAGCNIENASY
+GLTLCAECALLADLRMGGGGRLAAFVCVDGAGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP*
+>NZ_CP040019.1_2466
+MAAEGTTTAPGVDWDRLRRAALAATEHAYVPYSGFRVGAAALTEDGRLVTGCNIENASYG
+LTLCAECALLADLRMGGGGRLAAFVCVDGQGVLTMPCGRCRQLLHEFRAPDMVLLTPAGE
+RTMGQVLPDAFGPEDLERAAAR*
+>NZ_CP083691.1_2333
+MTGTTTPPACAAPVAEADWDRLRAAAADAMERAYAPYSGFRVGAAALTEDGRLVSGCNVE
+NAAYGVALCAECALVGQLHMTGGGRLRAFLCVGGDGRLITPCGRCRQLLWEFRAPGLAVL
+TAAGVTTVEALLPEAFGPDALEA*
+>NZ_CP097650.1_426
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVSGCNIENASY
+GLTLCAECALLADLRMGGGGRLAAFVCVDGDGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000480.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000480.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28d274133db38e35bbf17110cf86673b26012b9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000480.fa
@@ -0,0 +1,51 @@
+>NZ_CP042169.1_430
+MTVSPRPAQDRTVTEQDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRFSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVRHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAVADP
+TAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGDEEAALSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVAAARADARRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERSE
+RGFMHPGRVDVIGAGALLWSTVLERVAETAGVTEAWASEHDILDGIVLSLRS*
+>NZ_CP033200.1_160
+MTVSPRPAQDRTVTEKDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVRHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAVADP
+TAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAGLSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVTAARADALRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERAE
+RGFMHPGRVDVIGAGALLWSTVLERVAEVAGVTEAWASEHDILDGIVLSLRS*
+>NZ_CP040019.1_2458
+MTASTRPAHDRAVTEADLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLTNGIPFP
+TTFYLTHPALTAAVSRVEADGEMARMNERLEQDAELAAAHRAAHEAYIAERDRVGADAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDETIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVKHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAGADP
+AAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVEEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAALSFTGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLHSDPPTSDEVAAARADARRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSAYEPAAIHGARLPITEFRAAAQGLVAATRAERSE
+RGFMHPGRVDVIGAGALLWSTVLERVAETAGVTEAWASEHDILDGIVLSLRS*
+>NZ_CP083691.1_2326
+MTTPASRPASQEDALTETPAPQDPRAVTEQDLDTLSRQLGRPVRDVVEVGARCVCGNPLV
+ATTAPRLSNGIPFPTTFYLTHPVLTAAVSRLEAGGLMAEMNDRLAADPELAAAHRAAHEA
+YLAERERIRVASGTGEVPEIAHVSAGGLPDRVKCLHALVGHALAAGPGVDPLGDEAIAAV
+AEWWTPGVCACAGAWDEAAPVPTRDLSRHVKHLERVERLERVTVAGVDCGTNSIRLLIAR
+PAGAEDAAEPAGLPAGAPLEDVVREMRVVRLGEGVDATGAFSEAALERTFAAVDEYAHLV
+KRHHAGRVRFVATSASRDVSNREAFVQGVSERLGVEPEVISGEEEARLSFAGAVSAVDVS
+ALDDDALVLVVDLGGGSTEFVVGTPAGEVVDAVSMDMGCVRFTERFGLAGSAAADGVAAA
+RAAVEQVMDDVAARLPLERVGAAVGVAGTVTTVTAEALGLAEYDPAAIHGAVLPVERLRA
+AAEALLTADREERAARGFMHPGRVDVIGAGSLIWSTVLARVAAASGVTEAVTSEHDILDG
+IALSLRG*
+>NZ_CP097650.1_433
+MTVSPRPAQDRTVTEKDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVKHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAGADP
+AAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAGLSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVTAARADALRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERAE
+RGFMHPGRVDVIGAGALLWSTVLERVAEVAGVTEAWASEHDILDGIVLSLRS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000491.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000491.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92208debbcb2b32174ae018a95feb85deeef1609
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000491.fa
@@ -0,0 +1,26 @@
+>NZ_CP042169.1_444
+MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL
+RWASAVYAVTGLLLFAVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP
+DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL
+IVAGGVAYITGAVCYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVA*
+>NZ_CP033200.1_171
+MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL
+RWASAVYAVTGLLLFAVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP
+DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL
+IVAGGVAYITGAVCYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVT*
+>NZ_CP040019.1_2435
+MDPLTPAREPEAARRLRWRIERIRDPEHPLFKPRLRGWIHAAMAPLTLAAGIVLIVLAPT
+ATLRWASAVYAVTGLLLFGVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLAL
+LPPGKAHLLLTLVWAGAVAGVAFRLLWTDAPRWLYTPVYVVLGLAALLYIGDFFAADVAA
+GWLIVAGGAAYIVGAVFYALRAPTIHREWFGFHELFHVFTVGGFVCHAVAIYRAVLVVA*
+>NZ_CP083691.1_2315
+MWEHGGMVTRAPSVENRTGRPLKWRIERIRDPEHPLYKPRLRGWVHAVMAPLVLVAGIVL
+IVLAPGATLTWACVVYVVTGLLLFGVSATYHLVQWNETVSRVLKRLDHTNIMLVIAGTYT
+PLSLAMLPADKAWTLVTAVWVGAALGVAFRLLWTDAPRWLYTPVYVALGLAAVVYLGDFF
+AASVPAAVLICAGGAAYIVGAVFYALKAPTIHREWFGFHELFHVFTVGGFVCHYIAVMMA
+VLAA*
+>NZ_CP097650.1_444
+MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL
+RWASAVYAVTGLLLFGVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP
+DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL
+IVAGGVAYITGAVFYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000528.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000528.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40634b673f82d8c51176dfe8225b95304e32a5be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000528.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_490
+MTETPLAPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEAHVVVDGDVDGSEGMLAQLA
+AEHPGLDLSWTVFGENRGRVAALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHAGGS
+GGVIGLTANVLPDSAYQRVYGDAQDEAHRRHAYALPAEQQWRHWAGNVSVPRTLHEELGG
+YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTYTKARRALHSGSARQIF
+IAKHGADALGGDRAPGGPWGAAVRAVAALSTERTIQYSSAVVERAAAVLPAPIARKLIAL
+QVEAAAETGRTRPGRARRQF*
+>NZ_CP033200.1_219
+MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEAVLGQLA
+AERPGLDLSWTVFPENRGRVGALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHSGEP
+GGAIGLYLNVLEPTPYQRAYGDTQDVLHREHAYALQADQQWRHWAGNVSVPRALHQQIGG
+YDPDYRQYGWEDIDYGYRLHAAGYPVVIRPELETRHHAAAVTTHSKAVRALHGTAARNLF
+VGKHGAAPLGTIGAPRGVWGAAVRLVAWGTTEATLTRSSALIDAVADHLPRGLARRLIAL
+QVEGAAEAGRAHPHRAQRSI*
+>NZ_CP040019.1_2393
+MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEAVLAQLA
+AEYPGLDLSWTVFGENRGRVAALDAGADATSGRILIRADDDLEPGPHYIRDHVAAHDDVQ
+RGVIGLTANVLPDSAYQRVYGDAQDEAHRRHAYALPAEQQWRHWAGNVSVPRVLHEELGG
+YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTSTKARRALHSGSARQIF
+IAKHGADALGGDRAPGGLWGAAVRAVATLSTERTIQYSSAVIERAAAVLPAPIARKLIAL
+QVEAAAETGRTRPGRARRQF*
+>NZ_CP083691.1_2272
+MSDQTAYEASVIVPSRGGAGRLPRLIGALAAQEEAPPFDVHVVVDGDVDDSASALERLAA
+AHPDLPLTWTVFEENRGRVAALNAGADATTGRILIRADDDLEPGVHYIRDHVAAHAEGPG
+GAIGLYLNILESTPYQRVYGDAQDVLHREHAYALPADQQWRHWAGNVSVPRAVHEELGGY
+DPDYRQYGWEDIDFGYRLHAAGYPVRIRPELATSHHAAAVTTYSKAVRALHGTAARNLFI
+QKHGAEVLGGVDAPRGLWGAAVRLVALGATEGSLTRSSALIDAIADRVPITVARKLIALQ
+VEGASEAGRAYPERAQRPI*
+>NZ_CP097650.1_489
+MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEGMLAPLA
+AEHPGLDLSWTVFGENRGRVAALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHDDVQ
+RGVIGLTANVLPDSAYQRVYGGAQDEAHRRHAYALPAEQQWRHWAGNVSVPRALHEELGG
+YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTYTKARRALHSGSARQIF
+IAKHGADALGGDRAPGGPWGAAVRAVAALSTERTIQYSSAVVERAAAVLPAPVARKLIAL
+QVEAAAETGRTRPGRARRQF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000536.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000536.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb46233a65f6bc13a9fac50ae3b9360708a6b784
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000536.fa
@@ -0,0 +1,110 @@
+>NZ_CP042169.1_509
+MSAPETTPVLAPLLPRLRAERALEAAAASASRPLEARGVELEIGLPDGARAPLLTVLAEA
+LAEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGA
+RLAVLRRLAHPEEHAEGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAAL
+ADAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLED
+TTEDGSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLS
+PLLAEAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDV
+AEADQSAAGGFLTVAELRAAALEQDQGFWSVTALVSDAELLPDAATLRATLGVPQTFSGD
+IEAMVAHTRVRLAEGWHAVVLTDGPGSARRLAELNAEAGLTASVVDGPLPADLAPGRVSI
+ATAPVGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGGHVV
+HSQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDL
+ISTYVGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQ
+GELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGK
+QVAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVIEGLAHGEVDVVIGT
+HRLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGI
+RETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVAKRIA
+ELVPEARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHR
+YGLSQLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDL
+EIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHD
+YVPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGV
+TEVMLLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDV
+PLLEWAQQVVDAIFAPEG*
+>NZ_CP033200.1_239
+MSAPETTPVLAPLLPRLRAERALEAAAASAARPLESRGVELEIGLPDGARAPLLTVLAEA
+LAEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGTAALFPSWETLPHERLSPRSDTVGA
+RLAVLRRLAHPEEHAEGPLRVVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAAL
+ADAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLED
+TTEDGSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLS
+PLLAEAMTSLPRMLPAGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDV
+AGADQSAAGGFLTVAELRAAALEQDQGFWSVTALVSDDELLPDAATLRATLGVAQTFSGD
+IEAMVAHTRVRLAEGWHAVVLTDGPGSARRLAELTTEAGLTAAVVDGPLPADLAPGRVSI
+ATAPVGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGDHVV
+HSQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDL
+ISTYVGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQ
+GELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGK
+QVAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGT
+HRLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGI
+RETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVAKRIA
+ELVPEARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHR
+YGLSQLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDL
+EIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHD
+YVPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGV
+TEVMLLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDV
+PLLEWAQQVVDAIFAPEG*
+>NZ_CP040019.1_2375
+MPPRPPPVVAPLLPRLRAERAIEAAAASAARPLEARGVELEIGLPDGARAPLLTVLAEAL
+AEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGAR
+LAVLRRLAHPEEHAQGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAALA
+DAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDHPVRIEFFGDEVEQMRWFSVADQRSLEDT
+TEDGSGHPTELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLSP
+LLAEAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDIA
+GADQSAAGGFLTVAELRAAALEQDQGFWSVTALAPDDELLPDAATLRSTLGVPRTFAGDM
+EAMVEHTRTRLAEGWHAVILTDGPGSARRLAELHADAGLTASVADGPVPAEPAPGRVTIA
+TAAVGAGFTVPDERLAVITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLALQPGDHVVH
+AQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDLV
+SSYVGGEAPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQS
+ELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGKQ
+VAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGTH
+RLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGIR
+ETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVARRIAE
+LVPEARIAVAHGKMGEARLEQIMVDFWERRFDVLVSTTIIETGLDIANANTLIVEDAHRY
+GLSQLHQLRGRVGRGRERAYAYFLYDAQKPLGEVALERLKAVATHNELGAGMQLAMKDLE
+IRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHDY
+VPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPDPVEALVAVARFRNHARAAGIT
+EVMLLGQNVKFGPAADLPESRQMRLARMYKGSQVKPALNGVLIPRPKTKPVMGQDLVDVP
+LLEWAQQVIDAIFAPEG*
+>NZ_CP083691.1_2253
+MSPADVTAPVPVLAPLLPVLAREPAFEAAAASAARALPARGQELEIGLPDGARAPLFAHL
+ADALAAGHGADAVLLVVTATAREAEDLIGDLAAWADPASVALFPSWETLPHERLSPRSDT
+VGARLDVLRRLAHPGEDGRPPLRVVVAPVRSVIQPLVRGLGELAPVHLRVGQERDFDAVV
+QDLADAAYARVDMVSRRGEFAVRGGLIDVFPPTADHPVRVEFFGDEVEQMRWFSVADQRS
+LQDTSEDGSGHPTELHAPPCRELLVTPSVQERARALMARLPGAADMLERIAEGQAVEGME
+SLSPLLADGMTSLVHLLPEGSLTLLVEPERIRSRADDLLATNEEFLAAAWAGAAQGAQAP
+VDLGADQSAAGGFLTLAELREAVLEERQGHWSTTALSPDAELLPDASALRSSLGVPTTFG
+ADMEAMVRFTRERLADGWSVVLLTDGPGSARRLAELHADAGLTASVLDGPVDPAPAPGRV
+RVATAAVGTGFTDPETKLAVVTEQDLFGRHRTAGTRAAGGKLARRRRNAVDPLALQPGDF
+VVHSQHGIARFVELQRRPVTGGARKRPGEEESYREYLVLEYAPSKRGAPGDRLFVPTDQL
+DLISQYVGGEAPALSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMATRGHSFAPDTP
+WQAELEEAFPYIETPDQLTTIEEVKKDMESPVPMDRLVSGDVGFGKTEVAVRAAFKAVQD
+GKQVAVLVPTTLLARQHHQTFTDRFAGFPVTVAALSRFQTAKESKEVVEGLAAGEVDVVV
+GTHRLLSKEVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLT
+GIRETSTLATAPEERHPVLTSVGPYTDQQVIAAIRRELMREGQVFYVHNRVTTIDKVASR
+LAQLVPEARIAVAHGKMSESRLEQIMVDFWEKRFDVLVSTTIIETGLDIANANTLIVEDA
+HRYGLSQLHQLRGRVGRGRDRAYAYFLYDAQKPLGEVAMERLKAVAQHNELGAGLQLAMK
+DLEIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLP
+HDYVPGERLRLEMYRSLATAVDDAAVDAVVEEMKDRYGPLPEPVQALVAVARFRNRAREA
+GVTEVMLLGQNVKFGPAADLPESRQLRAQRMYKGAQLKPALNALLIPRPKTKPVMGQDLV
+DAPLLEWADQVVQAIFAPEPVSAG*
+>NZ_CP097650.1_509
+MSAPVLAPLLPRLRAERAIEAAAASASRPLEARGVELEIGLPDGARAPLLTVLAEALAEG
+HGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGARLAV
+LRRLAHPEEHAEGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAALADAA
+YSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLEDTTED
+GSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLSPLLA
+EAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDVAGAD
+QSAAGGFLTVAELRAAALEQDQGFWSVTALVSDAELLPDAATLRATLGVAQTFSGDIEAM
+VAHTRVRLAEGWHAVVLTDGPGSARRLAELNAEAGLTASVVDGPLPADLAPGRVSIATAP
+VGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGDHVVHSQH
+GIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDLISTY
+VGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQGELE
+EAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGKQVAV
+LVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGTHRLL
+SDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGIRETS
+TLATAPEERHPVLTSVGPYSDQQVIAAIRRELMREGQVFYVHNRVTTIDKVAKRIAELVP
+EARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHRYGLS
+QLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDLEIRG
+AGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHDYVPG
+ERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGVTEVM
+LLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDVPLLE
+WAQQVVDAIFAPEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000539.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000539.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8bed53948bc34bf0b04c814885504cb3ae45b6aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000539.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_512
+MSRDHRPPIRNPFLPPTPEEPEVPARDGGHPAGDGGDADAPAASTAREDRLAEFRLGPAF
+RPHPADRVPGPVPSARVLVVCTGNICRSAYVEYALQAQLNALLGDRGRAEVTSAGTEPNQ
+ALTVPGPLLDRAPSRRVRAALTQHRPQQLTGRSLAGQDLVLTATDDHLDEVLREDPAAVR
+RTFTILGMGTLLRDHGEELAAAVPPGAGVTALVTALAALRSRLIAHGERPDADLPDPFRG
+PAEGYAAMAQTAQPIVELLAWEIARALDGDLVEEEPTGA*
+>NZ_CP033200.1_245
+MSRDHRPPIRNPFLPPTPEEPEVPARDGGHPAGDGGDADAPAASTAREDRLAEFRLGPAF
+RPHPADPATPRQRATPTERTVAPAPVRAAEPASPASPAGRVPGPLPSARVLVVCTGNICR
+SAYVEYALQAQLNALLGDRGRAVVTSAGTEPNQALTVPGPLLDLAPSRRVRAALTQHRPQ
+QLTGRSLADQDLVLTATDDHLDEVLREDPAAVRRTFTILGMGTLLRDHGEELAAAVPPGA
+GVTALVTALAELRSRLIAQGERPDADLPDPFRGPAEGYAAMAQTAQPIVELLAWEIARAL
+DGDLVEEEPTGA*
+>NZ_CP040019.1_2369
+MSQDRRAPIRNPFLEPGASVPGAPPRRADADPEDRLAEFRLGPAFGGRPAQPRRPQGFGG
+RTAPGEGTTTTPRPDGTAAAEPADTAAEPVDTAAEPAANPKTARPAESAEAADAPAPAPA
+PLPTVRVLAVCTGNICRSAYVQHTLQAQLNALLGDRGRAEVTSAGTEPNQALTVPEPLRE
+LSPSRRVRAALTEHRPQQLTAASLWGQDLVITAADDHLEEVLREDPGAVRRTFTVRGIGT
+LLGEHGEEIAAAVPPGAGLAALVDAMADLRVRLIGRGEEPDADLPDPFRGPAEGYAQMVE
+TARPIVELLAWEIARALDGDLVEDDEPTRV*
+>NZ_CP083691.1_2247
+MSWFERPALRSPFAAAPGMDAPADDGAGGPLRILTVCTGNICRSAWAHHVLQARLDAALG
+ADVVEVSSAGTGPNQALAVPEELLTLAPDAGVRAALAAHRPRRLTARVLAGQDLVLTATE
+AHRDAVVREAPAALRRSATLLDAGALLADPDAVAPGGGGRALVAALEAARREGRGLDAGR
+RGLFPAGRRAADLADPFRGPAEGYTEMTRALEPALAAVEAAVVRAVEPAR*
+>NZ_CP097650.1_515
+MSRDHRPPIRNPFLPPTPEEPEVPTRDGGHPAGDGGDAGAPAAATAREDRLAEFRLGPAF
+LPHPADPAAPRQHATPAERAVAPATAAAAEPASPAAPADRVPGPLPSARVLVVCTGNICR
+SAYVEYALQAQLNALLGDRGRAVVTSAGTEPNQALTVPGPLLDLAPSRRVRAALTQHRPQ
+QLTGRSLADQDLVLTATDDHLDEVLREDPAAVRRTFTILGMGTLLRDHGEELAAAVPPGA
+GVTALVTALAELRSRLIAQGERPDADLPDPFRGPAEGYAAMAQTAQPIVELLAWEIARAL
+DGDLVEEEPTGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000548.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000548.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0acd8080980002c988bf66628367c49083e76be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000548.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_522
+MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALELQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA
+AGGFFPGLVERAEAADVVDDALAARIRSGADAAAQAYRDFADTLEAELRPHAPEADGVGI
+EYYRLASRDFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLSKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA*
+>NZ_CP033200.1_256
+MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQSIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA
+AGGFFPGLAERAEAADVVDDALAARIRSGADTAAQAYRDFADMLEAELRPHAPEADGVGI
+DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLTKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA*
+>NZ_CP040019.1_2357
+MTQNTPVAADRGARTPSAIDALAERYVADVLALHPDEATTLGFPGHETEYADFSPAGTRA
+DDELNARLLADLEALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVIEQARAHGA
+AGGFFPGLVERAEATDVVDAALAERIRAGADAAAQAYRDFADTLQAELRPHAPEADGVGI
+ELYRLGSRAFLGAEIDLEETYRWGQEELARIIAAQEADAERIKPGATIEEARALLDADPE
+RTLNGTAALQAWMQRLSDEAVQAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRTEHEEREGEGFDLK
+AFHTRALRLGGMGLDTLRAALA*
+>NZ_CP083691.1_2236
+MTQTTSAPEGARTPSAVDALAERHVAAYLALRPDEATSLGMPGHETEYPDLSPAGAAALD
+ELNRTTLEELAGLEPADDVDRVTVAAMRERLGLEREIHATGRTELNNIASEAQGIRAIFD
+LMPTDTAEQWGHIAGRLENLPAALRGYAESLLASRDAGHVAAVRQVEIVVEQARAHGAEG
+GFFPGLVERAEAADVVDAALAERIRTGAAGAAAAYAEFADTLEAELRPHAPEADAVGIEH
+YRLASRVFLGAEIDLEETYRWGQEELDRIIAAQEADAERIKPGATIEEARAILDADPART
+LTGTKALQEWMQRLSDEAVEAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSRPG
+RMWWSVPAGEEEFTTWAETTTVYHEGVPGHHLQIATAMMNRGTLNLWRRNFAWTSGHGEG
+WALYAEKLMEEFGFLDDAGDHLGMLDMQRMRAARVVFDIGYHCGFEMPASEGGGEWTPEK
+GYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEAREGADFDLKAF
+HTRALRVGGMGLDTLREALA*
+>NZ_CP097650.1_525
+MTQHTSEAAADGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGG
+AGGFFPGLVERAEAADVVDDALAARIRSGADTAAQAYRDFAATLEAELRPHAPEADGVGI
+DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLAKHLMISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000560.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000560.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a544c3fceee5a600b55aaa28e3cbee6c66a0554
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000560.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_536
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLASALAERDVSWAVPVALSDPVSAG
+PGAAVLQRFLPGGPYPPHEGDPDVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPAR
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAALTDAVTTWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDLACAWGPALNVAYLALWHGEQKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG*
+>NZ_CP033200.1_270
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG
+PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAALADAVTTWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDLACAWDPALNVAYLALWHGEEKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG*
+>NZ_CP040019.1_2339
+MASDPVDSELELVHRALGRLRPHVSPADARALHEADWSAGTVEEGGQFNRVLVCAGAGVL
+RMTRAHEVGAAPAARWSPERDPARQLGRRMALLDGLDAALAEQGVAWTVPVALSDPVPAG
+TGAAVLQRYLPGGPHPPHEGDPAVLRRLLDEIAAVDVADPRIAPHLGRPFSFRGPWTAQR
+AEHVAGIPGRLAPRLGAWPGDDVDARTGADAWADAVARVTRAVTAWTEEPPVPPSLVHGD
+LAGHNMRWRAMPAADDAPGEVRWELAGVLDWDLACAWDPALNVAYLSLWHGEDQVERLAV
+DAGEAARARVWLGAMALETLDDAAARDELVGGLPNGSWRRLLRKALPRVARALTALG*
+>NZ_CP083691.1_2219
+MASDPARSELDLVAAALQRLRPGLDDGVAARLRGADWSAGRVEEGGQFHRVLVLEDVGVL
+RMTRVHEAGAAPAARWTPERDPAVHLPRRLALLDGLAAVLAEAGVRWSLPTALSAVVEDG
+PGAAVLQRYVPGFPHPPHEGDPAVLRGVLADLAAVDVADPRVAPHLGRPFTFRGPWTPER
+AAHVAGLPARLAPRLGAWPGDALGHAGDETAAGEAAVRLRADAWGESVTALTGVVSAWTR
+EPPVPPALVHGDLAGHNMRWRVVPAAATPDAEVPDAPVRWELAGVLDWDLACAWDPALNV
+AYLGLWHGEDLVEAIAADPAEARRARVWLGAMALETLDDAGARDVLVGGLAESSWRRLLR
+KTLPRVGRALAAAAA*
+>NZ_CP097650.1_539
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG
+PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAAVTDAVTAWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDFACAWDPALNVAYLALWHGEEKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000564.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000564.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef3ad3706e9ca90b0ca667746f3a6df286aad25a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000564.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_540
+MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELTYETWGTLAADGSNAVLVLHA
+LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP
+WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA
+ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ
+RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLADRFDANSYLVVTEALMGHDV
+GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTIASPIGHDGFL
+TEYGQVADTLKRTLAL*
+>NZ_CP033200.1_274
+MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELAYETWGTLAADGANAVLVLHA
+LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP
+WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA
+ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ
+RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLTDRFDANSYLVVTEALMGHDV
+GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTITSPIGHDGFL
+TEYGQVADTLKRTLAL*
+>NZ_CP040019.1_2335
+MTATVSRPPRAALPEGGRHRLRIGELRTETGGVLPDVELAYETWGELDADGSNAVLVLHA
+LTGDSHVAAHAADPTPGWWDALVGPGRAVDTDRWFVVAPNMVGGCHGSTGPSSPAADGRP
+WGSRFPFLTLRDAVAAERRLADHLGVGAWQAVIGGSMGGARALEWAATHPERVAGVGVLA
+ATARSSADQIAWGQAQTAAIRLDPGFLGGDYYEGAGPAAGLGIARRIAHTTYRTAGELER
+RFGRSPQGAEDPFGAVVGVPGGRGRYAVESYLDHQATKLTGRFDANSYLLLTEALLGHDV
+GRGRGGVEAALAGYRGRAFVAAVDSDRLYLPAEAQALAAVLPARPPVHTIVSPIGHDGFL
+TEYGQVADALRDSLAL*
+>NZ_CP083691.1_2215
+MTAIDPRILPGHAAHRPHQGPQGEAAPSARSAAPHDARPADRLPAGEFRTLSVGPLELEA
+GGRLPGVELAFETWGTLAEDGANAVLVLHALTGDSHVASHRRDESAGWWEELIGPGLAVD
+TDRWFVVAPNMLGGCDGSTGPSSPAPDGAPWGGRFPFVTIRDAVAAERRLLDALGVTALQ
+AVIGGSMGGARAIEWAVSHPDLVRGVAVLASTASSSAEQIAWAQAQTHAIRLDPEWRGGD
+YHPGPGPVTGLGIARRIAHTTYRSAAELQHRFGREPQGAEDPLGTASGERVGRYQVESYL
+DHQASKLVGRFDAGSYVALTEALMSHDVGRGRGGVEAALASYPGRAFVAAVDSDRLYFPA
+ESERLASLLPGEVPVHTIHSPIGHDGFLTEYGQIADELRRTLEL*
+>NZ_CP097650.1_543
+MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELTYETWGTLAADGSNAVLVLHA
+LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP
+WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA
+ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ
+RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLTDRFDANSYLVVTEALMGHDV
+GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTIASPIGHDGFL
+TEYGQVADTLKRALAL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000565.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000565.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61b0a97cb743c0ef10e324d64a352438488efd07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000565.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_541
+MGNPSSSQPPHASDATPVDDPAAHPWRRYVAIGDSFSEGIGDPDPDRPGYHRGWADRLAE
+ELSRLTPPGEDLAYANLAVRGKLLDQIAEDQVEPAIALRPDLISVCAGGNDILRGADPDE
+IAARLDAVVERLASAGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPD
+MWSLKDLARREMWAEDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWRAARA
+SDAAWVRTHLAPWVVRRLRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTEPLDIVEP*
+>NZ_CP033200.1_275
+MGNPSSSQPPHASDATPVDDPAAHPWRRYVAIGDSFSEGIGDPDPDRPGYHRGWADRLAE
+ELSRLTPPGEDLAYANLAVRGKLLDQIAEDQVEPALALRPDLISVCAGGNDILRGADPDE
+IAVRLDAVVERLASDGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPD
+MWSLKDLARREMWAEDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWREARA
+SDAAWVRTHLAPWVARRIRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTESLNVVEP*
+>NZ_CP040019.1_2334
+MRAESPDGDDFPSESTGGGGRGRRGRLTDDGGASRLLLVSNQQESAPQHPAAAEAEPPAD
+VVTRAETAAHPWRRYVAIGDSFTEGIGDPDPDRPGYHRGWADRAAEELARRTPDGEDLAY
+ANLAVRGKLLDQIAADQVEPALALRPDLISVCAGGNDILRRADPDDVAVRLDAVVERLSA
+NGATVLLFNATDTKDTPVLGRIRGTVAIYNENVRTVALRHDALVADMWSLKELARREMWA
+EDRLHFSATGHHTIAAMVLDTLAVPHGLEPLRPEPAAPRTWRQARASDAAWARTHLAPWV
+VRRIRGVSSGDGVSAKRPVPAPLFGAEMPHGSDPTEPLDVVAR*
+>NZ_CP083691.1_2214
+METMSPLTNTADSEPPHAEGHASAEPAHPWRRYVAVGDSFTEGIGDPDPERPGYHRGWAD
+HLAEELARLTPAGEEFSYASLAVRGKLMDQIRADQIDPAVELAPDLVSICAGGNDILRRA
+DPDETALHLDDAVGRLAETGATVLLFNVPDIKETPVLARIRGRVAIYNENIRTVAARHHA
+VVADMWSLKDLARPEMWAPDRLHFSPVGHHTIAAMALDTLGVEHELEPLSPKRAAPRTWR
+EARVDDARWARTHLVPWVGRRLRGVSSGDGMQPKRPLPAPLFGADMPHGSDYTEHAAD*
+>NZ_CP097650.1_544
+MGNPSSSQPPHASDATPVDDPAAHPWRRYVAIGDSFSEGIGDPDPERPGYHRGWADRLAE
+ELSRLTPPGEDLAYANLAVRGKLLDQIAEDQVEPALALRPDLISVCAGGNDILRGADPDE
+IAVRLDAVVERLASDGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPD
+MWSLKDLARREMWAEDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWREARA
+SDAAWVRTHLAPWVVRRLRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTEPLDVVEP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000589.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000589.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f76790e577d77d8268f83af1ddf3220007fbd6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000589.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_628
+MTPRTHLPRPLPRPHIAGCVAAALLAWLVLASGVGGLDAVPRATSAPSGRDALLLVAASP
+AGPGSTAAPVAWHAPVAGAAPDDVLRAFVAPERPWGRGHRGVDLAVPSGAAIRAPAAGRV
+VFAGVVVDRPVLTLEHEDGTRSSLEPVEADVAVGAVVAAGDPVGRLAGAPPHCTRACVHW
+GVREPDGWRVGDAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP*
+>NZ_CP033200.1_374
+MTPRTLLPRPLPRPRIAGCVAAALLAWLVLALEMGDLGPASRATPAPSTRDALLLVAASP
+AGPGATAAPVAWHPPVAGAAPDDVLRAFVAPERPWSRGHRGVDLAVQTGAPIQAPAAGRV
+VFAGVVVDRPVLTLEHADGTRSSLEPVEADVAVGAVVDAGDPVGRLAGAPPHCPRACVHW
+GVREPDGWRVGDAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP*
+>NZ_CP040019.1_2268
+MTARSPAPRRARPAASPHRLLAVLLLCVLGLALAFALGPGIGAATPSSIRAEDGPTADAR
+LAVAATPARAWTAPAAGVRPGDVLRPFAAPERPWGRGHRGVDLAVSPGAAVLAPAAGTVV
+FAGTVVDRPVVTLEHADGTRSSLEPVEAAAPVGARLERGAPLGTVADAPAHCAVPCVHWG
+VRVPDGWRFGDATFDRYLDPLVLIGWSGPSVLWPHAAPPPAGPAPARE*
+>NZ_CP083691.1_2121
+MNEASTPPPRLRAAAVLAVALLATASAARAEDAPAAPPVTGALLAPTPGAGPSDVLRGFA
+GPERPWSRGHRGVDLATSSGLVTAPAAGTVRFVGSVAGRGVLTLAHPDGTLSSFEPVTSD
+LTAGQAVAAGQEVARVQEGAAHCPVRCVHWGVRREDAWAVGAARFDRYLDPLLLLGWSGP
+SVLWPVGDAG*
+>NZ_CP097650.1_597
+MTPRTLLPRPLPRPRIAGCVAAALLAWLVLALGMGDLGPVSRATPAPSTRDALLLVAASP
+AGPGATAAPVAWHPPVAGAAPDDVLRAFVAPERPWSRGHRGVDLAVQTGAPIQAPAAGRV
+VFAGVVVDRPVLTLEHEDGTRSSLEPVEADVAVGAVVAAGDPVGRLAGAPPHCTRACVHW
+GVREPDGWRVGEAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000599.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000599.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ac7e1c1c4a4892b5c0c3de2a55cea97fe3bef02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000599.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_639
+MPAADPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP
+AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI
+RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPREDQATAVFRAQAVLGLLNSTP
+RSVRRTAADRAARRATLVAMAWAAATAPGPLSGED*
+>NZ_CP033200.1_385
+MPAVDPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP
+AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI
+RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPHEDQATAVFRAQAVLGLLNSTP
+RSVRRTAADRAARRATLVAMAWAAATAPGPLSGED*
+>NZ_CP040019.1_2257
+MPAAVDPSAPAASAAAPTSRVAAKARRREDLLAAAARLFAARGFDAVRLEDIGAEVGISG
+PAIYRHFAGKAAVLVAILATASQDLLEGALATEREHDAGEDALRALIAFQTDFALAQRDV
+IRVQDRDMSALPEDERAAVTGTQRAYIDVWARQLRVVHPSEDQATAVFRAQAVLGLINST
+PRSVRRTAADRAARRATLVAMAWAAATAPGPAADRP*
+>NZ_CP083691.1_2109
+MPHAPDTAAPGPTGTPRERAKARRRAELLAAAARLFAAHGYEATRLEDIGAAAGISGPGI
+YRHFAGKAAVLVEILSSASLFLLDGAEAVAARGLSGAEAVHDLIAFHTDFALANRDVIRV
+QGRDMSSLPPADGAEITRVQRRYIDLWGAQLRRLHPGEDHATARFRTQALLGLINSTPFS
+VRRSRADRGARRDALIGMAWAAARTPGGTARPEPPVVP*
+>NZ_CP097650.1_608
+MPAVDPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP
+AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI
+RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPHEDQATAVFRAQAVLGLLNSTP
+RSVRRTAADRAARRATLVAMAWAAATAPGPLPGGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000619.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000619.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c511ec32b344b7e0b3b96fc48a90595a576f0780
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000619.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_664
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK*
+>NZ_CP033200.1_410
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK*
+>NZ_CP040019.1_2226
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK*
+>NZ_CP083691.1_2089
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK*
+>NZ_CP097650.1_633
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000621.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000621.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ba4750ba2ad27d31d76841c8421bb7d37be7d54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000621.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_666
+MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES
+PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA
+VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG
+TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTQGALP
+APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM
+SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD
+VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR
+AVAARLAAGDRARVVVAPA*
+>NZ_CP033200.1_412
+MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES
+PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA
+VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG
+TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTQGALP
+APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM
+SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD
+VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR
+AVAARLAAGDRARVVVAPA*
+>NZ_CP040019.1_2222
+MAGMSIHREIPLDFTGVLADEGHGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSR
+DESPEGYGSTHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDL
+PMAVEVLTDMLTSSLLDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRP
+IGGTPETIRAVTREHVAGHYARWYRPDELVVTAAGNLDHDEVCRLVLAALQASGWELAPG
+ALPAPRRAVDTEGAAASRVLTGTHTVAKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLG
+GGMSSRLFQEVRERRGLAYSTYSFSAGYSDAGYWGLYAGCQPDRVDEVSALMEAELDRMA
+AEVVTEEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLERVRAVDAA
+QVRAVAARLAAGERARVVVAPA*
+>NZ_CP083691.1_2087
+MAGMTVQREIPLDFSGVLAEDRGAVVCRSVLPGGVRVLTESMPDQRSVTVGYWVAVGSRD
+ESPEGYGSTHFLEHLLFKGTPTRTAMDIASAFDRVGGESNAGTAKESTVYHAHVLDEDLP
+MAVEVLTDMVTSSLIDADELETERGVILEELAMDADDPVDVAHERLAAVLMDGHPLGRPI
+GGTPETIRAVTREHVVAHYRHWYRPQELVITAAGNLDHDDVCRLVLDALERSGWDLAEGA
+APAPRRTADAAGAGAVLAGTHTVAKQVEQANVIVGGQSLSTTDPDRFALGVMMSVLGGGM
+SSRLFQEIRERRGLAYSTYSFSAGYSDGGYFGLYAGCQPERVDEVAALMEAELERMAAAE
+VTAEELDRAHGQICGGTVLGMESTGARMSRLGRAELVTGEFVDLSASLARVRAVDAGRVR
+AVAARLAAGERARVVVAPA*
+>NZ_CP097650.1_635
+MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES
+PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA
+VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG
+TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTPGALP
+APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM
+SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD
+VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR
+AVAARLAAGDRARVVVAPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000643.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000643.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0d28e77e8f4fe4d4fab64c8b2b9ecc9996a4e9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000643.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_696
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL*
+>NZ_CP033200.1_436
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL*
+>NZ_CP040019.1_2195
+MAAELISGRRARMTRTTSESDVHVEMDLDGTGRAEISTSVPFYDHMLTALARHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMSGVPSTKGAL*
+>NZ_CP083691.1_2063
+MAAELMSGRRARMQRTTSESDVYVEMDLDGTGTSEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKRGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFEAITYHASICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRVHDVPSTKGAL*
+>NZ_CP097650.1_659
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKAALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000645.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000645.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dda416f50981560b744743344b91030a8bda0f5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000645.fa
@@ -0,0 +1,10 @@
+>NZ_CP042169.1_698
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA*
+>NZ_CP033200.1_438
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA*
+>NZ_CP040019.1_2193
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVAR*
+>NZ_CP083691.1_2061
+MPYWSVLYLGLGGILLGAAWSMRTQKAPTWAVVIALVLAAMAVAAAFLTV*
+>NZ_CP097650.1_661
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000652.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000652.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acb53b55693b46be977c92969c98e1388d098107
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000652.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_705
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG*
+>NZ_CP033200.1_445
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPLAHLVRQFAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG*
+>NZ_CP040019.1_2185
+MNTAFDAGRLGRTDVLTLQQVTSFMSNDMQVTGPDGQTVATVVTTGGGLGRMVLGSRTFD
+VVDGEDGRVLFRLADPATFGRDRYAIVDADGLPLANLVREFALFRTSVSVEVVDGTRFAV
+TGNLWDHDYTMTVGQAPIARATATFGGFMNALAGRSRYELRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRRNN*
+>NZ_CP083691.1_2054
+MTTFDAGRLALVNSLALQQVTSFLSNDMQVLGPDGEVVATVQTQGGGLSRMLMGSRRLLV
+CDGDDGRPLFELQDPATFGRDRFQVLDPAGLPLANLRREVAFFRTAVSVEVVDGTVFRVE
+GDLFDHDYRMIAGEVPIARAVSQWSGFGNALLGRSRYRLELDPAMPPVVRCAVLGTAIAL
+DLLRAKDARRND*
+>NZ_CP097650.1_668
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000659.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000659.fa
new file mode 100644
index 0000000000000000000000000000000000000000..811626bb54766bf74eb5f55c2fdf19c49188b2d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000659.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_713
+MPRGAAHGAQAPRGGHTGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI
+DAASAGARYGALADRSPEDGVQRARELLSAGVPGQSGADVAAELTSQDGVPVLRVTVSSS
+LPGLGFLPGPIPVEVSGHAFRQ*
+>NZ_CP033200.1_453
+MPRGAVHAVPVPRGVHMGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI
+DAASAGARYGALADRSPEDGVQRARELLSAGVPGQSGADVAAELTSQDGVPVLRVTVSSS
+LPGLGFLPGPIPVEVSGHAFRQ*
+>NZ_CP040019.1_2150
+MTAGSGAAAAAPRRRRPRWRDDRGAAVAESTMVMTLVVLLFAALLQAGLVIHTRNVMIDA
+ASAGARYGALADRVPEDGVQRARELLAAGVPGQSGARIVAEPTSQDGVPVLRVTISSSLP
+GVGFLPGPIPVEVSGHAHRL*
+>NZ_CP083691.1_2045
+MEPAARPAVQGRPGPDRRAGDRGSVVAENAMVTALLVLLFAAVLQVGIIVHVRNVMIDAA
+SAGARYGALADRDPAEGAARARDVLSASVPGQSGAQVRSEPTTVGGVPVVRVTITSSLPG
+LGFLPGPVPIEVHGHAFRY*
+>NZ_CP097650.1_676
+MPRGAAHDAPAPRGGHTGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI
+DAASAGARYGALADRNPEDGVQRARELLSTGVPGQSGADVAAELTSQDGVPVLRVTVSSS
+LPGLGFLPGPIPVEVSGHAFRQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000704.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000704.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2bc0ad947df0200e32e625473e6532ebd29a81c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000704.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_766
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH*
+>NZ_CP033200.1_506
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH*
+>NZ_CP040019.1_2098
+MLTLVLANASFVPPTISDGNLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+QLVPGKAQWLAESGYSFVRNGIAKDILGEKNFRQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PSFSHAGAAYGIALIVYAIWIGVGLKRHGIRYLKLAVVPSGVPSWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVIIGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH*
+>NZ_CP083691.1_1987
+MLPLVLANAEFVPPSVSDAHLPDLLPWGAEYGTGFGKQMLLVLLSVVLITGFFAWAMRKP
+KLVPGRAQWIAESGYAFVRNGIGRDVMGEKHFKQWVPLLFAIFFFVLLNNLFGAIPLLQM
+PSFSHAGSAYAIALIVYAIWIGVGVKHHGVKYFKLAVVPSGVPGWILPLLVPLEFISNFI
+VRPLTHSLRLMAVMLAGHMIVMLAGAGAAFLITQTGNPLLAGTGVLVILASVALYLLEIL
+LMYLQAFVFTLLTALYIQGAIDANDH*
+>NZ_CP097650.1_732
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFSIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000713.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000713.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f920d4844b94219a36cee0694b1ee948a6a5b69c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000713.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_775
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF*
+>NZ_CP033200.1_515
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF*
+>NZ_CP040019.1_2088
+MRLVIARCSVTYEGRLNAHLPPATRLLMVKADGAVLVHSDGGSYKPLNWMSPPATLHTTA
+PTAEQAEQGVVEVWRVQAAKSDDRLMILIEEILADQSHELGADPGLVKDGVEADLQRLLA
+EQIGLLGDGHTLVRREYMTAIGPVDILARDPEGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF*
+>NZ_CP083691.1_1977
+MRLVIARCSVTYEGRLNAHLPSATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PTEEQAAAGVTQVWRVQAKKSDDRLLVLLEEVLADETHELGVDPGLVKDGVEADLQRLLA
+EQIGLLGDGHTLVRREYMTAIGPVDILAKGPGGQTVAVELKRRGDIDGVEQLTRYLDLMN
+RDPLLAPVTGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDADARLF*
+>NZ_CP097650.1_741
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PFPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000723.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000723.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c367217ebedff78e7120c86f514d0595605a27d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000723.fa
@@ -0,0 +1,19 @@
+>NZ_CP042169.1_786
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
+*
+>NZ_CP033200.1_527
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
+*
+>NZ_CP040019.1_2077
+MSVLTSHDPTAPRAAGPAPGEAVPGGATDTAVLERPREDLALDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSESRAHRLMLEVHERGRSVVATGTREKAELHVGAMHGYGLWATLEQAED
+*
+>NZ_CP083691.1_1964
+MPHPAPPAPGADTALLERPREDLAAARPWHVVVWNDPVNLMSYVAYVFRSHFGYSAARAQ
+SLMLEVHERGRSVVFTGSREVAEGHVTAMHGFGLWATLEQAED*
+>NZ_CP097650.1_754
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000730.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000730.fa
new file mode 100644
index 0000000000000000000000000000000000000000..268d947812a7cab85c1e8701c6d37f226b340673
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000730.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_793
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQEGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLTGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAAAYALVIAALLRGLDLAAAVAHAR
+AWLDTLGEEAEETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAAHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGAAHGTAVFGAHDPADRAAAEA
+SVPGWIAEREVVLEAARRWSAATT*
+>NZ_CP033200.1_534
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQQGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLSGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAAAYALVIAALLRGLDLAAAVAHAR
+AWLDTLGEEAEETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAAHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGAAHGTAVFGAHDPADRAAAEA
+SVPGWIAEREVVLEAARRWSAATT*
+>NZ_CP040019.1_2070
+MTETPAAPSLPGPEHATRVAALLAAGAAGDALGYTVEFDADAAVRARHGAEGLTTGEAAL
+AVVGGEALPISDDTQMTLYVLDGLLEWIEWQNDGQAADPAACVWLACLRWWATQHGGALP
+DGAPPVPPRWLEDHPELRARRAPGNACLSGLDSAAMGLPGDPRNPDSKGCGTVMRSAPYG
+MVPGLEDVHVVSFARQGAVLTHGHPTAWVAAAAYSLMIAALLRGAGLEDAVAHARVWVDS
+LDPAEGGETAAALASAVELAASPADDAGRPGTLPAALGEGWVAEEALAIAVHAALVAQAR
+HEDPADMLALALRIGANHAGDSDSTASLAGQLLGAAHGPAVFGADAAADGPAGLVPAWVA
+EREVVAEAARRWSAATT*
+>NZ_CP083691.1_1957
+MTDAAPSPRTDVSYPSRVLGLLAAGAAGDALGYAVEFDSVDRILGRLGAAGVTDGPALAA
+VSGVSALPVSGDTQMTLYVLDGMLEWIEWQNAGQASDPAACVWLACLRWLRTQDGALPDG
+APPAQDRWIDAHTELHAQRAPGMACLSGLRSSGMGVVPDPKNPDSKGCGAVMRSAPYGMV
+PGLEDHHVASFARQGAVLTHGHPTGWTAAAAFALTVSALFDGAELRGALEHPRTWLDSTG
+EDGAETRAALDGALAEAARAVEAGDDVGAPGTLPASLGEGWVAEEALAIAAYAALVAEAR
+AEDPAAALGLALRIGANHDGDSDSTAALAGQLVGARHGMAVFGSRGQDADSVPAWITERE
+VVAEAARRWIAATT*
+>NZ_CP097650.1_761
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQEGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLTGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAGAYALVIAALLRGLDLAAAVAHAR
+AWLDGLGEEAAETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAVHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGVAHGTAVFGAHDPADRAAAEA
+SVPGWVAEREVVLEAARRWSAATT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000752.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000752.fa
new file mode 100644
index 0000000000000000000000000000000000000000..114be7834c1ac44afb71e8aa9747abf451757295
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000752.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_830
+MTVRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGSASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLCRTPAAA
+DRDRVLAEGADLVHAQAVPDGPRAAAPPGPGWAAAGLAVLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAQAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARAPAGHRPLPGSGWDPFAG*
+>NZ_CP033200.1_561
+MTVRDPAAAAGATVGDLTESELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLPRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLCRTPAAA
+DRDRVLVEGADLVHAQAVPDGPRAAAPPGPGWAAAGLTLLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARPPAGHRPLSESGWDPFAG*
+>NZ_CP040019.1_2037
+MTPAGGRPADGRTVGEVTEAQLLRVVLDGLAPAVRPGHWPPGTVAPGDDAALVPAPRGGT
+LVSTDAMGEGTDFLHRWPAGVRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PLAWVRSFAAGVVGAVDRLGAPGCRVAGGDLGTGERVHAAVTVLGDPHPAGVLRRAPAPA
+ARERVLAEGADLVHAQDAPGSSGAARSGALRPSAARPGPGWAAAGLALLLTDRDELARRA
+AALPPEDRPGARDLARAVRAQLRPRPPLALGPAAVEAGILTLMDVSDGLGRDAHRMAAAT
+GAAASAEAPPPVPWIDAAWLAEAAAPLRGVAALAGVSAESLVTGGGEDYGLLGLAWPETA
+LPAGFVRIGRLEPAGAPAPAGHRELPEAGWDPFGG*
+>NZ_CP083691.1_1928
+MSTPASTASAGGRPAPARTVGEASEAELLDLIQDALAPVARDVPWPAGTVPPGDDCAVVP
+APRGLVAVSTDAMGEGTDFLRRWPAGVRTRGHDVGWKAAAQNLSDVNAMGATPSALVTAL
+ALPAPTPLDWVASLAGGFTAAVRALGADRCRVAGGDLGAGESVQVAVTALGDPDPAGALR
+RAAGGERGARIARRGADLVLAAGSPRAAAAGEGQDSAWGPAGPGWAAAGLALLLTDRAVL
+TRRWADLAAHERPSARELARAVRGQLRPRPPLAAGPAAARAGLAALMDVSDGLGRDGHRL
+ARASSAPGAPLVPWVDRRWLAEAAEPLRRVASLAGTTPEALVLGGAEDYGLLGLAEPGLA
+LPSGFRRVGRLAPAGETPDGHVRLPEAGWDHFDAGRG*
+>NZ_CP097650.1_788
+MTMRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLRRTPAAA
+DRDRVLAEGADLVHAQAVPDGPRAAAPSGPGWAAAGLTLLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARPPAGHRPLSESGWDPFAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000805.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000805.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9b7954dd46c9376eace386a95f0079b3c3ecaef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000805.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_897
+MLTIMSSSTESLRAPVTPSRWAEVRSGVAVTLGAGLGLFPLGMAFGMLVVQAGLPAWVAP
+LFSVVVFAGSVELLLVSLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRFARIYS
+MGALIDEAYAIAAARPRGWTGPRLVAMQVALHAYWVLGGLAGVAVAWLLPGPVEGLEFAL
+VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR
+GTALPLPEPVPVTGPVPVVAATGERAGTDAEPGAGEDPR*
+>NZ_CP033200.1_625
+MLTIMGSSSASSRASAPPSRWAEVRSGVAVTLGAGLGLFPLGVAFGMLVVQAGLPAWVAP
+LFSVVVFAGSVELLLVSLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRLARIYS
+MGALIDEAYAIAAAQPRGWTAPRLLAMQIALHAYWVLGGLAGVAVAWLLPVPVEGLEFAL
+VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR
+GTALPLPEPVPVTGPVPVVAAAGERAVTDAEPGVEEDPR*
+>NZ_CP040019.1_1975
+MNAPSLQPSPYPAPPPSRGAEVRAGVRLSLAAGLGLFPLGVAFGMLVVQAGLPAWVAPLF
+SVVVFAGSVELLLVSLAVAATPLLTIAVTVFLVNFRHVFYAFSFPLRVVRHPLARLYSMG
+ALIDEAYAIAAAHPRGWTAPRLIALQVALHAYWVLGGLAGVAVAWLLPGPVEGLEFALVA
+LFIVLALDAARTRAQAPLVLAAALAVGVGLLVAPGQLLVAAFAVYAAVLIALHVLARRGV
+DLPLPAPTPATGPVPVVAGPAPGEEPR*
+>NZ_CP083691.1_1871
+MTEITPPSPAASGVPDALPTRRAEVAEGVRLSGPAGLGLFPLGVAFGMLVVQAGLPGWAA
+PLLSVVVFAGSVELLLVSLLAAGTSLAGIAVTVFLLNFRHVFYAFGFPLRVVRNPLARLY
+SMGGLIDEAYAITAAHPRGWTAPRLLATQVSLHLYWVVGGLVGVVAAGLLPAPVEGLEFA
+LTALFIVLALDAARTRRHVLLVLAAAAAVGVGLVVAPSALLVASFLGFVAALMAAHVAAE
+RGARLPLPAVKELGATSPGAAEAAELTTVDAEAGR*
+>NZ_CP097650.1_844
+MLTIMGSSSASSRASAPPSRWAEVRSGVAVTLGAGLGLFPLGMAFGMLVVQAGLPAWVAP
+LFSVVVFAGSVELLLVPLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRLARIYS
+MGALIDEAYAIAAARPRGWTGPRLVAMQVALQAYWVLGGLAGVAVAWLLPGPVEGLEFAL
+VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR
+GTALPLPEPVPVTGPVPVVAATGERAGTDAEPGAGEDPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000811.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000811.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32f534a372a4c9967e9a27b5fd76cdf7d11233d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000811.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_903
+MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS
+QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPSEGK
+PLVDPAEYVDPALWI*
+>NZ_CP033200.1_631
+MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS
+QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPAEGK
+PLVDPAEYVDPALWI*
+>NZ_CP040019.1_1968
+MGLLARIKEDLDNVRSHDPAARGDLEVALVYSGLHAVWAHRIAHRMWRHERLRMPARILS
+QATRAATGIEIHPGATIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGAGSAVGANAVVVKDTPADAIATGIPATYRLRRSPAEGK
+PLVDPAEYVDPAMWI*
+>NZ_CP083691.1_1862
+MGIRSRIKEDIATVRSHDPAARGDLEVVLAYSGLHAVWSHRVAHRMWQVGRLKTPARLLS
+QAARALTGIEIHPGATIGRRLFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLEKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTSVGANAVVVKDTPPDSIATGIPASVRLRTSPAEKK
+PLVDPAEYVDPAMWI*
+>NZ_CP097650.1_851
+MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS
+QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPAEGK
+PLVDPAEYVDPALWI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000826.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000826.fa
new file mode 100644
index 0000000000000000000000000000000000000000..997fa7bab1ff2c2d94cce564c371d6bc63b1db1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000826.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_929
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDRETAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGERSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDDASGGRAGAVGDGFSAGLPDGFQGGDAPASPGPDESDAGAPGREPAAA
+GVA*
+>NZ_CP033200.1_652
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDREAAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGERSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDASGGRAGAVGDGFNVGLPDGFQGGDAPASPGPGEPDAEAPDREPAAAG
+VA*
+>NZ_CP040019.1_1891
+MQDIITVRGFVATDPVTRTTASGATVAGFRLATTERRFDREAGAWVDAHTNWYSVSAFGQ
+LGSNTAQSVRKGNPVIVTGRLRVRDWSTEERSGTTVDVVADAVGLDLAFGSAAFQRSQRA
+ASARPEGADEQDGQGQAGAVASAGPAEADGTAAGTGDGYVTELPPALRGGDAPATPPPPS
+SEEGDEADEADDDAHGVRALCGGVSAA*
+>NZ_CP083691.1_1839
+MQDTVTIRGFVATDPTTRHTASGAAVVGFRLASTERRFDRDAGMWVDAHTNWYSVSAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSTEDRSGTSVDVVADAVGLDLAYGASAFMRNGRR
+ADAVERADAPVDADAGASLDAAPADGFGLALPPAFTGGDAPASSAEDAHEAAGALAVA*
+>NZ_CP097650.1_874
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDRETAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGDRSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDASGGRAGAVGDGFSAGLPDGFQGGDAPASPGPDESDAGAPEREPAAAG
+VA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000841.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000841.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e84a51f796db99e7aa56e6808d5e3f809f242dfd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000841.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_948
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR*
+>NZ_CP033200.1_672
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGVGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR*
+>NZ_CP040019.1_1873
+MDVSHTTENQSPRAAVVTGATTGIGRATALELARRGWRVYAVGRRAERLDALAAQAREEA
+VPGEVVPAPLDVTDEAAVAGLVARVDTDGGIDTLVNIAGGARGTDFVGAGNREDWEWMYR
+ANVLGTLAMCQAFLPGLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTAALRLE
+EAEHNVRVIEVLPGMVHTEEFSLMRLGGDAAAAEKVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVIRPVAQAAQHKVIRR*
+>NZ_CP083691.1_1817
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAPLDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRTHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR*
+>NZ_CP097650.1_890
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000843.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000843.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e885b747fdb27d54a6837b2b9fe47dcd411973f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000843.fa
@@ -0,0 +1,48 @@
+>NZ_CP042169.1_950
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAHEG
+FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEISNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERVVRRYDEQREPGETFARWAHRVDEEALR*
+>NZ_CP033200.1_674
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTTPLNHNEEFKQQDDGLNVRERIEQVYAREG
+FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEVSNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERLVRRYDEQREPGETFARWAHRVDEEALR*
+>NZ_CP040019.1_1871
+MVLDVEGDRVDAVVAGLKELGLDPEPSVFRRSTIACTGLEFCKLAIVDTKDTATAAIAQL
+EERLADLADRLPERLSLHVNGCPNSCARIQTADIGLKGQLLPDDDGGQTPGFQIHLGGGL
+ASVDRAEAGLGRSVRGLKVRADGLVDYVERLVRRYDEQREPGETFARWAHRVDEEALR*
+>NZ_CP083691.1_1815
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAREG
+FDSIPSDDLHGRFRWWGLYTQRKQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEVSNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERLVRRYDEQREPGETFARWAHRVDEEALR*
+>NZ_CP097650.1_892
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAHEG
+FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEISNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERVVRRYDEQREPGETFARWAHRVDEEALR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000858.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000858.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ed8cacda6c53e5a9f8b0a8ed4250c05cacc49f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000858.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_968
+MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID
+RLVDVLAAERQKGTQVVLVSSGAIAAGFPHLGLSRRPKDTATQQASAAVGQSKLMAHYTT
+SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALARLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLCKADLLVLLSDVDALYTGHPSNPDARRIPEVTSDDDLSGVDVRVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGEDVGTWFSATGRRRSARAAWLGLT
+AEVRGRLIIDDGAVAGAIDRGRSLLAAGITGCTGAFTPGDVVEIVDAHGRVRARGLVQYS
+SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR*
+>NZ_CP033200.1_692
+MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID
+RLVDVLAAERQKGTQVVLVSSGAIAAGFPHLGLGRRPKDTATQQASAAVGQSKLMAHYTT
+SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALSRLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLCKADLLVLLSDVDALYTGHPSHPDARRIPEVTSDDDLAGVDVRVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGEDVGTWFSATGRRRSARAAWLGLT
+AEVRGRLIIDDGAVAGAIDRGRSLLAAGITGCTGAFTPGDVVEIVDAHGRVRARGLVQYS
+SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR*
+>NZ_CP040019.1_1854
+MSARRTVVTRYPTPATRGAEDPRANPVTTRDTMAAARRVVIKIGSSSLTTATGLDVAAID
+RLVDVIAELRGRGTQVVLVSSGAIAAGFPHLGLDRRPKDTATQQAAAAVGQGRLLAHYTH
+SFGRHETEVAQVLLTAEELMRRTQYTNAHRALARLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLVKADLLVLLSDVDALYTGHPSLPDSRRIPVVATDADLEGVDVHVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAPNAGSAFAGEDVGTWFEATGRRRSARAAWLGLT
+AEVRGQLVIDDGAVAGAIDRGRSLLAAGIIGLSGRFTPGDVVEILDATGRVLARGLVQYS
+SSQLPRMLGRSTSDLKEDLGAGYDGVVVHADDWVRLAPPRR*
+>NZ_CP083691.1_1779
+MARRPSTVHRHATPSSRGAEDPKANPVHTRADIGAARRVVIKVGSSSLTTGTGLNTDAID
+ALVELVARLRGRGTQVVLVSSGAIAAGFPALGLSRRPKDTATQQAAAAVGQNRLVAYYSQ
+SFARFDTTVAQVLLTAEELMRRGQYINAHRALARLLTLDVLPIVNENDAVATREIRFGDN
+DRLAALTANLVKADLLVLLSDVDALYTGHPSRPGSRRIDTVTAETDLGGVDVRTPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAALASAALDGEDVGTWFSAAGRRRTARAAWLGLT
+AQVRGRLTIDDGAVAGAIDRGRSLLAAGITAAEGDFTAGDVVEIADAQGTVLARGLAAYS
+SSQLPRMLGRQTAQLKEEIGAGYDGVVVHADDWVRLAPTHSAFR*
+>NZ_CP097650.1_910
+MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID
+RLVDVLAAERQKGTQVVLVSSGAVAAGFPHLGLGRRPKDTATQQASAAVGQSKLMAHYTT
+SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALSRLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLCKADLLVLLSDVDALYTGHPSNPDARRIPEVTSDDDLAGVDVRVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGQDVGTWFSATGRRRSARAAWLGLT
+AEVRGRLVIDDGAVAGAIDRGRSLLAAGITGCTGDFTPGDVVEIVDTHGRVRARGLVQYS
+SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000875.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000875.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d6c3c5cbd20eae0aa6c9906298d1898534c98b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000875.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_990
+MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTPEIDEAFRWSRENRNLQAKARLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL
+SGHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDEDWDF*
+>NZ_CP033200.1_715
+MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTPEIDEAFRWSRENRNLQAKAGLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL
+SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDEDWDF*
+>NZ_CP040019.1_1827
+MTEVTDTVKTNHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAITPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTKEIDEAFRWSRENENLQRKASLIVERYDGEDPYKRKIASTLLESFLFYSGFYWPMYL
+SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRNIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLSEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDADWDF*
+>NZ_CP083691.1_1711
+MTEPHHGPSVHDHLVEAINWNRIQDEKDNEVWQRLVNNFWLPEKVPLSNDVQSWNQLTDD
+ERLLSMRVFTGLTLLDTIQGTVGAVSLIPDAITPHEEAVYTNIAFMESVHAKSYSSIFST
+LASTKEIDEAFRWSRENPNLQRKAQLILERYDGEDPYKKKIASTLLESFLFYSGFYWPMY
+LSSHARLTNTADLIRLIIRDEAVHGYYIGYKYQRNIETLPEERREELKAFTFELMFELYE
+NEVEYTHSLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTDVNPAILSALSPNSD
+ENHDFFSGSGSSYVIGKAEATEDEDWDF*
+>NZ_CP097650.1_933
+MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTPEIDEAFRWSRENPNLQAKARLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL
+SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDEDWDF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000888.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000888.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f32f0f5b1f68b52f32f853cf2dc5af2dbdac4ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000888.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1012
+MGQRKKDRGARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL
+FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL
+GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVRVTGAVVAEIAAG*
+>NZ_CP033200.1_735
+MGQRKKDRGARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL
+FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL
+GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVQVTGAVVAEIAAD*
+>NZ_CP040019.1_1806
+MAKTGRGRGRAHGAATPAVAALETAGVPYTLHTFEVDLDAGGERFGVQVARAMGVPPERM
+FKTLMVAAPDGGLAACVVPVSGQLDLRAAAAVLGVKRLALADLALVERRTGYVRGGVSPL
+GQRHRHPVLLDSSALDAPVMYVSGGQRGLDLELAPADLAAATDAVVAPIAAR*
+>NZ_CP083691.1_1693
+MGRRKAADAAHGAATPAIRALVDAGVPHRVLSFDVHLDAVGERFGVQAAKALGVPPERTF
+KTLMVALPDGSLAACCVPVSGQLDLRAAATALGVKKVAMADLAVAERRTGYVRGGISPLG
+QRQRHPVVVDSSALDGDVLYVSAGQRGRDLELAPADLVAVTDAVVAPIAAR*
+>NZ_CP097650.1_952
+MGQRKKDRSARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL
+FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL
+GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVQVTGAVVAEIAAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000904.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000904.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c962691f2e26aefa20d70ea4fa72a47b569c9b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000904.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1041
+MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA
+WSRYSFIGAGSSVTLTSRNGEAHWQGTPPEGLPTQGRALDVLAACLRLLRTDVRAEVGGV
+LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGADRAYDDALARLDAMVERLAAPAADPVSDVPRRWLEADADEVAAQAEDRWG
+AEGFREAVAKAQRAIRDGDVFQAVVSRRLSVTTDATGLDVYRVLRTVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATEKDDRLLGKDLLEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA*
+>NZ_CP033200.1_770
+MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA
+WSRYSFIGAGSAVTLTSRDGEAHWQGTPPEGLPTQGRALDVLAACLRLLSTDVRAEVGGV
+LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGADRAYDDALARLDAMVERLTAPAADPVSDVPRRWLEADADEVAAQAEDRWG
+AEGFREAVGKAQRAIRDGEVFQAVVSRRLSVTTDATGLDVYRVLRMVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATAEDDRLLGKDLLEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA*
+>NZ_CP040019.1_1787
+MSAATTPSREEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESAAPGAV
+WSRYSFVGAGSAVTLTSRDGQAHWQGVPPEGLPTEGRALDVLAACLRLLRTDARTHLDGA
+LPHLVSGMAGFLGWNTVRAWERLPNPPQDDLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGAEGAYEDALARLDAMVDQLAAPAAEPVSTVPRRWLDADADEVAAQAEDRWG
+AAGFREAVGKAQEAIRDGEVFQAVVSRRLSVTTGATGADVYRVLRMVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVQDRRVVTHPIAGSRRRGATLEDDRLLGKDLMEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMREDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGVVADSDPDAETAETVTKATAPLRSVLTAGEMGRA*
+>NZ_CP083691.1_1673
+MSGVVPSREEFLAVAPTSRVIPVVRRVLADGLTPLAIHRRLADSRPGTFLLESATPGAAW
+SRYSFIGAGSAATLTARGEDAVWLGEPPEGLPTEGRALDVLAESLRLLSTDARTRVDAAL
+PHLVSGMAGFLGWPAVRAWERLPHPPEDHLGLPLLAMNLISDLAVHDAQDGTVTLIALAI
+NGDGLATGAERAYDDAVARLEDMVARLRAGAEDPVDEVPRRWLDATAEEVAAEAEDRWGA
+AGFRDAVGRAQQAITDGEVFQIVVSRRFSVDTAASGVDVYRVLRMVNPSPYMYLFSFQTP
+DGEPYEIVGSSPEALVTVQDRRVVTHPIAGSRRRGATPEDDRLLGKELAEDEKERAEHLM
+LVDLSRNDLSRVCEAGTVEVTQFMELEAFSHILHLVSHVEGRLRDDVTSLDALRSAFPAG
+TLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSVTLAGRQAHVQAGA
+GIVADSDADAETAETVTKATAPLRAVLTAAELRGA*
+>NZ_CP097650.1_989
+MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA
+WSRYSFIGAGSAVTLTSRDGEAHWQGTPPEGLPTQGRALDVLAACLRLLSTDVRAEVGGV
+LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGADRAYDDALARLDAMVERLTAPAADPVSDVPRRWLEADADEVAAQAEDRWG
+AEGFREAVGKAQRAIRDGEVFQAVVSRRLSVTTDATGLDVYRVLRMVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATAEDDRLLGKDLLEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000940.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000940.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1642ffb9040dd5a41d4c9f1a6e6f8fa633ec4500
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000940.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1083
+MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM
+AHLGRPKGEPDPAYSLRPVAARMAELLGTDVALAADVTGDDARAKAAALQDGQVLLLENV
+RFDARETSKDDAERAALAGEMAALAGDDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL
+VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA
+HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG
+GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA*
+>NZ_CP033200.1_812
+MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM
+AHLGRPKGEPDPAYSLRPVAARMAELLGTDVALAADVTGDDARAKAAALQDGQVLLLENV
+RFDARETSKDDAERAALADEMAALAGEDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL
+VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA
+HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG
+GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA*
+>NZ_CP040019.1_1740
+MPAQTLNDLLEAGVAGRTVLIRSDLNVPLDGETVTDDGRIRASLPAIRQLADAGARVIVM
+AHLGRPKGEPDPKYSLRPVAARMGELLGADVALAEDVTGPSARAAAEALADGDVLLLENV
+RFDARETSKDDAERAELAAEMAALAGEDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL
+VAGELEVLTRLTQSPERPYAVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLDTVRAYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLPVDALTSGA
+HGASAMGLDIGPETARAFAEQIRGAETVFWNGPMGVFEFEAFAEGTRAVAQALTEATAAG
+GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALSGEGEA*
+>NZ_CP083691.1_1632
+MTAQTLTDLLEAGVAGRTVLIRSDLNVPLDGQTVTDGGRIRASAPAIKDLADAGARVVVM
+AHLGRPQGEPDPQYSLAPVARRLGEVLGADVQLASDVTGEDARAKAAALQDGQVLLVENV
+RFDARETSKDAAERGELAREMADLAGEDGAYVGDAFGAVHRAHASVADIAGLLPAYQGPL
+VAAELQVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLMEKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLETVRGYLERSGKDGAAEIVLPTDIVMASAFAKDAEHEVLPVDALTTG
+AHGADALGLDIGPGSAAAFGERIRGARTVFWNGPMGVFEFPAFAEGTRAVAQALTEATQA
+GGLSVVGGGDSAAAVRSLGFTDEQFGHISTGGGASLEYLEGKELPGVSALSGTDT*
+>NZ_CP097650.1_1032
+MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM
+AHLGRPKGEPDPAYSLRPVAARMAELLGADVALAADVTGDDARAKAAALQDGQVLLLENV
+RFDARETSKDDAERAALAGEMAALAGDDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL
+VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA
+HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG
+GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000949.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000949.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a75e94d88b8a575982e68d75cda33c0875f885d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000949.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1092
+MSTTTPAAGTAPAGLAARLPQRLTKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW
+PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL
+AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG
+ATTVRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRIHVIPVYLL
+LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA
+LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG*
+>NZ_CP033200.1_821
+MSTTTPAAGTAPAGLAARLPQRLTKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW
+PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL
+AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG
+ATTVRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRIHVIPVYLL
+LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA
+LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG*
+>NZ_CP040019.1_1731
+MASLASEIGIIVTGGAVRLTGSGLGCPTWPKCTPESLTNTPEMGIHGYIEFGNRTLTFVL
+VVIAAAMFLSLWRLRRTHRSPFWLSVGLLAGIPAQAVVGGIVVLTELDPWWVAGHFIVSS
+VMVAVATLLVIRIGAERRAGRAGVRIVDGVTTGASRAAAWAAFAFTWAAVYLGTVVTGTG
+PHGGDPDAPRHAFDPLLVTRVHVIPVYLLIAAALVLLFTVRRAEGASRLQRAAVLRLLLA
+IAVQAAIGYTQHFTGLPVVLVILHMLGSALLVAAATEVWDRQRSRYVTAGPAALLDADPT
+PVTANAR*
+>NZ_CP083691.1_1623
+MTASPTTARPAAGGSSARRPPDRVTGVTVGLALASLISQMVIVVTGGAVRLTGSGLGCPT
+WPKCTPESLTTTAEMGIHGIIEFGNRTLTGVLGVIALLMIATLWRLRRSHRQAFTLSLLL
+LAGIVLQAVVGGVTVWMHLDPRIVGVHFVISGALIALATMLWVRLRAEHRHGAGAPVADG
+TTTPASRTASRVAYAALWLALVVGTLVTGTGPHSGDPAAARHGFDALMITRLHVVPVYIT
+VAATLVLLWQVLRTPGSGAGQRVAAWSLLGAVLLQGLLGYWQHFTGLPVGVVAAHLAGAT
+VAVVAGTLAWQRQTSRYRAPAVA*
+>NZ_CP097650.1_1041
+MSTTTPAARTAPAGLAARLPQRLSKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW
+PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL
+AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG
+ATTGRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRAHVVPVYLL
+LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA
+LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000960.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000960.fa
new file mode 100644
index 0000000000000000000000000000000000000000..450dd3f7c5c0dccf46f75fbdee1e1f347baf6974
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000960.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1104
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMRVYLVQMLVRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDDTAAPEPVV
+LTGDLVDDPRDRAPRALGRGSSSAGSPGLPGRGGA*
+>NZ_CP033200.1_833
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDDTAAPKPVV
+LTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA*
+>NZ_CP040019.1_1719
+MTSSAAGSRAGRPARAGRSTGPQVQGVTTASAARSEDREARMKVYLVQMLIRTVCFGAAL
+FTTGWWQLLFILGAVALPYVAVVQVNNAGPRQAGSLRAVPAEGPELTARPADAPGPASPV
+VLTGDVVDDPREVGPRALPPGSPSEGARRLPGRGAA*
+>NZ_CP083691.1_1611
+MAAIVREPDAVQGVTTAAAPRSADRDARTRVYVVQMAVRTACFIAALFTHGWWQILFILG
+AVVLPYVAVVRVNNTGPREAGRRRDVARTAPAVPALPAEPSPVPTGPVVLVGEVVEDDDP
+AARRALPAGSPGETGRGRP*
+>NZ_CP097650.1_1053
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLHAVPAQGPALAPRPDDTAAPKPVV
+LTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000970.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000970.fa
new file mode 100644
index 0000000000000000000000000000000000000000..055ed5ca1e108aace463bfbbbe43c3f804a08d96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000970.fa
@@ -0,0 +1,65 @@
+>NZ_CP042169.1_1117
+MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK
+DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD
+PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT
+ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR
+RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ
+EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQFVGKRLLTDYSKEFGRLNVGA
+VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA
+GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL
+RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR
+MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG*
+>NZ_CP033200.1_846
+MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK
+DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD
+PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT
+ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR
+RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ
+EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQLVGKRLLTDYSKEFGRLNVGA
+VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA
+GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL
+RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR
+MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG*
+>NZ_CP040019.1_1703
+MTVHEKLAPQSPTHTTEVPSDVAEIAPEHPEPGSLDSAALQDALLGAWAEDRRTARALVR
+DPRLHRDPLLGMDEHRERVLGQLGVLVENGAVHRMFPKEFGGDDNHGGNIAAFADLVLGD
+PSLQIKAGVQWGLFAAAILHLGTEEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIGTT
+ATYDEAAGEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITKGVNHGVHCFYVPIRDED
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFDQVRVPRTNLLNRYGDVAEDGTYSSPIESPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGAIAYGEQRRQFNASDPEREEVLLDYQNHQR
+RLVDRLARAYADAFASNELLERFDGVFSGRADSDADRQELETLAAAIKPLATWNALDTLQ
+ETREACGGAGFMARNRIPQMRADLDVYVTFEGDNNVLLQLVGKRLLTDYSHEFGRLNVGA
+VSRYVVAQASDAIHRAGLHKAVQSVSDGGSERRSANWFKDPEVQRDLLTDRVRAKTADIA
+GTLAGVRGKTQAEQAAAFNTRQHELIEVARNQGELLQWEAFTRAVQATRDESTRTVLTWL
+RDLFALRVLEEDLGWLVAHGRLSSQRARSLRGYVNRLAERLRPFALELVEAFGLEPEHLR
+MDIATQAEAERQAEAHAWFEARRAAGEEPEDEKAVRAREKAARGRRG*
+>NZ_CP083691.1_1599
+MTDIRTDAASAAEALPATDAVPHDVAEIAPEDPTPGALDAAALQDLLLGSWAEAHRTARG
+LVKDERLHRDPALGMDEHRARVLDQLGILVEEKAVHRAFPADLGGQDDHGGSIAAFANLV
+LADPSLQIKAGVQWGLFSSAILHLGTREHHEKWLPGAMDLSMPGAFAMTEIGHGSDVASI
+ATTATYDEATQEFVIHTPFKAAWKDYLGNAALHGRAATVFAQLITKGVNHGVHCFYVPIR
+DESGAFLPGVGGEDDGLKGGLNGIDNGRLHFDHVRVPRTHLLNRYGDVAEDGTYSSDIAS
+PGRRFFTMIGTLVQGRVSLSLAASIASFMGLHGALAYAEQRRQFGGPEGSETLLLDYQNH
+QRRLIDRLARTYADLFAANELLEKFDHVFSGAGDTDKDREELETLAAAIKPLTTWNALDT
+LQEAREATGGMGFMAGRNRLPHLRADLDIFVTFEGDNNILLQLVGKRLLTDYSAEFGKLN
+VGAVSRWAASEASDALHRVGLHKAAQSVHDRGDQRRAANWFKDPQVQRDLLTDRVRTRVA
+DIASTLGSARGKSKAEQAAAFNSRQHELIEVARHHGELLQWEAFTRQVESLPAGQTRTVL
+TWLRDLFALRLIEDDLGWLVAHGRVSSARARVLRGYVNRLAERLRPFALELVEAFGLEPE
+HLRMEIATDAESVRQQEAADWFAARRAAGEEPVHEKTLHAGKR*
+>NZ_CP097650.1_1066
+MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK
+DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD
+PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT
+ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR
+RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ
+EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQLVGKRLLTDYSKEFGRLNVGA
+VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA
+GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL
+RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR
+MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000971.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000971.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b15ecfd6dfa41fb1a0791073b2c41a3dcee59a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000971.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1119
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTMKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQTQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR*
+>NZ_CP033200.1_848
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEAVGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLTTAKTMKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPVFGRQLGDEATMTAGNSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR*
+>NZ_CP040019.1_1702
+MTQPETTARPAVAGGALRPAVVVGGNRIPFARANTAYAEVGNQEMLTAALEGLVARFGLQ
+GERVGQVSAGAVLKHPRNFNLTREAVLGSALASDTPAADLQVACATGMEAIGTLADKIRL
+GRIDSAIGGGVDSISDAPVSLSDGARRALLRLNAAKTMKDRLAALKDLRPGHLAPEPAGA
+GEPRTGMSMGDHQALTTHRWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFRGLDRD
+NNLRPDSTPEKLAGLKPAFGRHLGEEATMTAGNSTPLTDGASAVLLSSEDWAAERGLPVL
+AEFVDVENAAVDFVDGDEGLLMSPAYAVPRLLARHGLTLQDLDFVEIHEAFAGTVLSTLA
+AWEDEEYCRERLGLPGALGSVDRAKLNVHGSSLAAGHPFAATGGRIVALLSKMLHEKGEG
+SLGLVSVCAAGGQGIVALLRGR*
+>NZ_CP083691.1_1597
+MSTESPRVPAETARPAIAGGELRPAVVVGSNRIPFARAFTAYAEVGEQEMLTAAIDGLVA
+RLGLQGERLGQVSAGAVMKHPKDFNLTREAVMGSALSSETPAADIQVACATGMEAIGTLA
+DKIRLGRIDSAIGGGVDSISASPMTVSESARRVLLQLNSAKTVKDRLKALSSLRPGQLVP
+EPAAAGEPRTGMSMGEHQALTTHQWGITRQAQDELAAASHRNLGASYASGYQDDLVTPFR
+GLAKDNNLRPDSTVEKLAGLKPAFGRHLGDEATMTAGNSTPLTDGASAVLLSSEDWAVQR
+NLPVLAEIVDMENAAVDFVDGEDGLLMSPVYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LATLAAWEDEEFGRTRLGLPGAYGSVDRAKLNVNGSSLAAGHPFAATGGRIVGLLSKMLH
+EKGEGSLGLVSVCAAGGQGIVALLRGR*
+>NZ_CP097650.1_1068
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLIA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTTKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000975.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000975.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c693dae8c4f9c5e201c2e28c4acdbe418b30e7c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000975.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1123
+MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDEADPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPEVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE
+RVPVDALEFGCRVLERMLEPR*
+>NZ_CP033200.1_852
+MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDSEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE
+RVPVDALEFGCRVLERMLEPR*
+>NZ_CP040019.1_1697
+MIQNAHDTPVSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAALCARLMEEAGMRPRL
+FESSPGRVSVVGHLPGWDEDAPGLVVHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLSVLLHLTRTGRRPRRPLTVAFFADEEAGGVYGARWLVEHHPELFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGIAWLNLRAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDEQDPTPQLDALGQARSWVAGTLRTSSNPTGMT
+SGYKHNVIPSTATGTVDARLLPGEEEAALATLQELAGPGVSIEPEHRDVALETPFSGDLV
+ELMVASLQAEDPGAEVLPFMLGGGTDNKSLARLGITGYGFAPMRLPADLAFTSLFHGIDE
+RVPVDALEFGCRVLERMLEPR*
+>NZ_CP083691.1_1593
+MDASTPSTAPSTADADVVEICRDLIRIDTTNHGGGRSVGEPEAAELCAAWMRKAGMEPEL
+IESAPGRVSVVGRLEGWDPEAPGLVLHGHTDVVPAEPDEWTVDPFGAEFRDGMIWGRGAV
+DMKGMDAMILSVLVHLARTGRRPRRPVVVAFFSDEEAGGVFGAQWLVAHRPELFAGCTEA
+ISEVGGFSTDVAGTRAYLVQTGEKGLAWLNLRAQGAPGHGSAPHTDNAVTRLAGAMERIG
+RHPWPLTYTKTTRQLLEEVAEITGTPFDERDPTPQLQALGHARDWVAGTLRTSSNPTGLT
+AGYKHNVIPSTATGTVDVRLIPGEEEQTLAELADLAGDGIEISPEHQDTGLEVPFSGDLV
+ERMASALDAEDPGAHVLPFMLGAGTDNKSLHRLGIAGYGFSPLQLPSGLEFTRLFHGIDE
+RVPVESLRFGCRVLEHVLEPRA*
+>NZ_CP097650.1_1072
+MVENIENPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMTEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHGIDE
+RVPVDALEFGCRVLERMLEPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000976.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000976.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9823f1ee4698e6d8151cb541cc494bf6d4acf11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000976.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1124
+MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA
+RRYWMRRRVMRVASTLQTL*
+>NZ_CP033200.1_853
+MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA
+RRYWMRRRVMRVASTLQTL*
+>NZ_CP040019.1_1696
+MREQLMSSTLDSIARGQKWEYLVITVSPDESLGDARRRLVEHAEYGRWELQRSVHFRGGA
+RRYWLRRRVVRVASTLASA*
+>NZ_CP083691.1_1592
+MDGMREQLMSSTLDSIARGEKWEYLVITVAPHESLADARRRLVDHAEYGQWELQRSVHYR
+GGTRRHWMRRRVIRVRSTLQS*
+>NZ_CP097650.1_1073
+MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA
+RRYWMRRRVMRVASTLQTV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000994.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000994.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93527f8e483c428d42fbceb8325509f5ffd890bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0000994.fa
@@ -0,0 +1,90 @@
+>NZ_CP042169.1_1143
+MAHHPASATPHDEPELSPAERYARARAARHHAGSELGRFAARVGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADFARVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLIDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHVMAGGRLYDLFAE
+DIAFEDTADRDGEALLNPELKRLGEETERRFQRADWGRPGRQQHRDGRGGGPKGRVRGGR
+RTTRDGGRGRNGSSALDRERPVSGRPGGHDGGQRRGPRLSTSRPEMIRALDRDGLLPCIT
+FIFSRTGCDAAVEQCLRAGLDLTTAREKALVAERVEEAARLLPVEDLEILGFWAWRDGLS
+RGFAAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGINMPARSVVIEKLVKFNGENH
+VDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVAGLASRRTYPLRSSFRPTYNM
+SANLLAQVGAERARGILESSFAQFQADRSVVGLAREVRSKQASLEKYEEAMQCHLGDFAE
+YLTLRKELAAAEKSGSQGRRRAHLAAVKDSLANLAVGDVVELDAGRALGRAVVVFPAGNL
+QNPRVGVVTDKAQLRRITVDDVAGPVEPVAGAALPQVVQVKTPAQRKDVAALMREAVRTG
+RPPAGGRRTAGFRLREDPAAPRVEELRRALRRHPCHGCQDREEHARWGDRWWAMRREVSV
+LRERIAGRTNTIARTFDRVVGLLRAYGYVQEDASSPRAALTERGEALRRIYGERDLFTSL
+VLQDPATDGLTPEEWAAVAALLVYQGRGEAEPGLVPMPTPRLARVAEAAERIEERLRTDE
+AQARLEPTPRTDPGLVAPMHRWVRGATLRRTLDGADLAAGDFVRWARQVIDVLGQLANVP
+GDTRRSRACRRAADLVSRGVVATSLPAASAPRADED*
+>NZ_CP033200.1_872
+MAHHPASATPHDEPELSPAERYARARAARHHAGSELGRFAARVGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADLARVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLIDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHIMAGGRLYDLFAE
+DIAFEDAADRDGEALLNPELKRLGEEAERRFQRADWGRPGRQQHRDGRGGGTKGRARGGR
+HTGRDGGRGRTGSSALDRERPVSGRPGGHDGGPRRGPRLSTSRPEMIRVLDRDGLLPCIT
+FIFSRTGCDAAVEQCLRAGLDLTTAREKALVAERVEEAARLLPVEDLEILGFWAWRDGLS
+RGFAAHHAGMLPPFKEAVEDLFTAGALKAVFATETLALGINMPARSVVIEKLVKFNGENH
+VDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVARLASRRTYPLRSSFRPTYNM
+SANLLAQVGAEQARGILESSFAQFQADRSVVGLARELRSKQASLEKYEEAMQCHLGDFAE
+YLTLRKELAAAEKSGSQGRRRAHLAAVKDSLANLAVGDVVELDAGRSLGRAVVVFPAGNP
+QNPRVGVVTDKAQLRRITVDDVAGPVEPVAGAALPQVVQVKTPAQRKDVAALMREAVRTG
+RPPAGGRSTAGFRLREDPAAPRVEELRRALRRHPCHGCQDREEHARWGDRWWAMRREVSV
+LRERIAGRTNTIARTFDRVVGLLRAYGYVHEDAPSPRAALTERGEALRRIYGERDLFTSL
+VLQDPAMDGLTPEEWAAVAALLVYQGKGETEPGLVPMPTPRLARVAEAAERIEERLRTDE
+AQARLEPTPRTDPGLVAPMHRWVRGATLRRTLDGADLAAGDFVRWARQVIDVLGQLANVP
+GDTRRSRACRRAADLVSRGVVATSLPAASAPRADED*
+>NZ_CP040019.1_1676
+MSHAPASATPPEEPQLSPAERFARAKAARHHAGSELGRFASRLGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADLSRVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLTDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHVMAGGRLYDLFAE
+DIAFEDTADRDGEALLNPELKRLGQEAERRSERPDWGRPGRHRGRGGRDGGQRGRGGRGG
+DGRKGGRDADRRGRHGSHAMDREQPATGRVRGQEDGERRGPRLSTSRPEMIRALDREGLL
+PCITFIFSRTGCDAAVEQCLRAGLDLTTAHEKALVAERVEQAARLLPVEDLEILGYWAWR
+DGLSRGFAAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGINMPARSVVIEKLVKFN
+GENHVDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVAGLASRRTYPLKSSFRP
+TYNMSANLLAQVGAERARGILESSFAQFQADRSVVGLAREVRSKQASLEKYEKAMQCHLG
+DFSEYLALRKELASAEKSGSQGRRRAQLAAVKESLADLAVGDVVELDAGRSLGRAVVVFP
+AGNPQNPRVGVVTDKAQLRRITVDDVTGPVEPVAGAALPQVLQVKTPTQRKDVAALMREA
+VRTGRPPAGGGRRTSGFRLREDPAAPRVEELRRALQRHPCHACQDREEHARWGDRWWGMR
+REVSVLRERIAGRTNTIARTFDRVVGLLRSYGYVHEDASSPRQALTARGEALRRIYGERD
+LFTSLVLQDPTVQGLTPEEWAAVAALLVYQGKGEAGHGVVPMPTARLAEVADAAERIEER
+LRADEAQARLEPTPPTDPGLVGPMHRWVRGASLRRTLEGADLAAGDFVRWARQVIDVLDQ
+LANVPGDARRSRACRKAADLVSRGVVATSLPAATAREADED*
+>NZ_CP083691.1_1573
+MAPHTHHDLPPEEPALSPAERFARSRASASRPGTELSRFAARLGFPLDEFQLEACREVEA
+GHGVLVAAPTGAGKTVVGEFAVHLGLARGRKAFYTTPIKALSNQKYADLAAVHGADRVGL
+LTGDTSVNPDAPVLVMTTEVLRNMLYADSEALTDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVVVSEHRPVPLWQHVMAGGRLYDLFAE
+DVAFEAAADADGTPLLNPELQRMAQEASRRVERPDWGRTGHRGRGRGGPGGRGAGRGRGK
+GGPRGGREGASSGWDRERPHRADASPGDGERRALGLSTSRPEMIRALDREGLLPCITFIF
+SRAGCDGAVEQCLRAGLDLTDRREKALIAERVEQAAAALPPEDLEILGFWAWRDGLSRGF
+AAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGVNMPARSVVLEKLVKFNGESHVDV
+TPGEYTQLTGRAGRRGIDVEGHAVVLWRPGLDPSAVAALASRRTYPLRSSFRPTYNMSVN
+LLAQVGAERARGILESSFAQFQADRSVVGLAREVRAKQSSLEKYADAMACDRGDFAEYLS
+LRKELAAAEKSGSRGRRREHLRAVKESLADLAVGDVVELHDGRALGRVVVVAAAGNPQNP
+RVAVVTDKAQLRKVAVEDLVDPVEPVAGAALPQTVQVKTPSQRKDVAAAMREAVRAHRPP
+TGGTRRGTGFRLREEVASPRLEELRRALQAHPCHACPDREDHARWGERWWDMRREVSLLR
+ERIAGRTNTIARTFDRVVELLGRLGYVGDDPDAPSRALTERGQTLRRIYGERDLLTSLVL
+HDPSTRSLTPEEWACVAALLVYQGKGDTQGLPVAMPTARLQALAEAVDRIEGGLREDETA
+ARLEPTPPTDPGLVAPLHRWVRGASLRDSLHGADLAPGDFVRWARQVIDVLGQIAQVPGD
+ARRTRACRKAADLVGRGVVAASLPAAAAGADGVEGEEPDRVDR*
+>NZ_CP097650.1_1092
+MAHHPASATPHDEPELSPAGRYARARAARHHAGSELGRFAARVGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADFARVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLIDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHVMAGGRLYDLFAE
+DIAFEDTADRDGEALLNPELKRLGEETERRFQRADWGRPGRQQHRDGRGGGPKGRVRGGR
+RTTRDGGRGRNGSSALDRERPVSGRPGGHDGGQRRGPRLSTSRPEMIRALDRDGLLPCIT
+FIFSRTGCDAAVEQCLRAGLDLTTAREKALVAERVEEAARLLPVEDLEILGFWAWRDGLS
+RGFAAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGINMPARSVVIEKLVKFNGENH
+VDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVAGLASRRTYPLRSSFRPTYNM
+SANLLAQVGAERARGILESSFAQFQADRSVVGLAREVRSKQASLEKYEEAMQCHLGDFAE
+YLTLRKELAAAEKSGSQGRRRAHLAAVKDSLANLAVGDVVELDAGRALGRAVVVFPAGNL
+QNPRVGVVTDKAQLRRITVDDVAGPVEPVAGAALPQVVQVKTPAQRKDVAALMREAVRTG
+RPPAGGRRTAGFRLREDPAAPRVEELRRALRRHPCHGCQDREEHARWGDRWWAMRREVSV
+LRERIAGRTNTIARTFDRVVGLLRAYGYVQEDASSPRAALTERGEALRRIYGERDLFTSL
+VLQDPATDGLTPEEWAAVAALLVYQGRGEAEPGLVPMPTPRLARVAEAAERIEERLRTDE
+AQARLEPTPRTDPGLVAPMHRWVRGATLRRTLDGADLAAGDFVRWARQVIDVLGQLANVP
+GDTRRSRACRRAADLVSRGVVATSLPAASAPRADED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001011.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001011.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e99c6acc16b0d12174afbd915a3408a4f6b3ad17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001011.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_1161
+MTTYEYATDEVRSQAQPRVVPRSLGKIVVSWLTTTDHKVLGYMYLITSFIFFCIGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTLMLLMFATPLFVGFANVLVPLQIGAPDVSFP
+RLNALAFWFFLFGSLIATAGFLTPQGAASFGWYAYAPLSNTTFSPGVGGDLWVFGLALQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILILMAFPPLAAALFALGLDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGIVSEIIPVFSRKPIFGYKSIVFA
+TTAIGALSFSVWAHHMYVTGSVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFENPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQLNDTYFVVAHFHYVVFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWMLFVGFHGTFLIQHWLGVTGMPRRYADYMVEDSFHAMNAFSSV
+FSFVLGASLIPFFWNVYITARYGKKVTVDDPWGFGGSLEWATSCPPPRHNFHSLPRIRSE
+RPALDLHHPELFPHSPQHTTEAFGEKVAQ*
+>NZ_CP033200.1_890
+MTTYEYATDEVRSQAQPRVVPRSLGKIVVSWLTTTDHKVLGYMYLITSFVFFCIGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTLMLLMFATPLFVGFANVLVPLQIGAPDVSFP
+RLNALAFWFFLFGSLIATAGFLTPQGAASFGWFAYAPLSNTTYSPGVGGDLWVFGLVLQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLASALFALGLDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSIVFA
+TTAIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVVFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWMLFVGFHGTFLIQHWLGVIGMPRRYADYMVEDSFQAMNAFSSV
+FSFVLGASLIPFFWNVYITSRYGKKVTVDDPWGFGASLEWTTSCPPPRHNFHSLPRIRSE
+RPALDLHHPELFPHSPQNTSEAFGEKVAQ*
+>NZ_CP040019.1_1657
+MTTYEYATDEVRSQAQPRVVPRSLGKIAVSWLTTTDHKVLGYMYLIVSFMFFCIGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTIMLLMFATPLFVGFANVLVPLQIGAPDVSFP
+RLNALAFWFFLFGSLIATAGFLTPQGAASFGWFAYAPLSNTTYSPGVGGDLWVFGLVLQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLAAALFALGMDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSLVFA
+TTSIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVIFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWLLFVGFHGTFLVQHWLGVIGMPRRYADYMIEDGFTAMNQFSTV
+FSFILGASLIPFFWNVYVTARYGKKVTVDDPWGFGASLEWATSCPPPRHNFHSLPRIRSE
+RPALDLHHPELFPHSPQHTPEAFGEKVAQ*
+>NZ_CP083691.1_1553
+MTTYEYATDEVRTQAQPRVAPRSLGKIVVSWLTTTDHKVLGYMYLIVSFVFFCVGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTIMLLMFATPLFVGFANVLVPLQIGAPDVAFP
+RLNALAFWFFLFGSFIACAGFLTPQGAASFGWFAYAPLSDTTYSPGVGGDLWVFGLVLQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLAAALFALGMDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSLVFA
+TTSIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVIFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWLLFVGFHGTFLVQHWLGVIGMPRRYADYMIEDGFTAMNQFSTV
+FSFLLGASLIPFFWNVYVTTRFGKRVTVDDPWGFGSSLEWATSCPPPRHNFHSLPRIRSE
+RPALDLHHPELAAYSPQAEPEVFGEKVASK*
+>NZ_CP097650.1_1117
+MTTYEYATDEVRSQAQPRVVPRSLGKIVVSWLTTTDHKVLGYMYLITSFIFFCIGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTLMLLMFATPLFVGFANVLVPLQIGAPDVSFP
+RLNALAFWFFLFGSLIATAGFLTPQGAASFGWFAYAPLSNTTYSPGVGGDLWVFGLVLQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLASALFALGLDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSIVFA
+TTAIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVIFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWLLFVGFHGTFLIQHWLGVIGMPRRYADYMVEDTFTAMNAFSSV
+FSFVLGASLIPFFWNVYITSRYGKKVTVDDPWGFGGSLEWATSCPPPRHNFHSLPRIRSE
+RPALDLHHPELFPHSPQHTTEAFGEKVAQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001038.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001038.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1392194ea03d552ab6ae12ff7f015af3b21b8d6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001038.fa
@@ -0,0 +1,43 @@
+>NZ_CP042169.1_1189
+MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI
+LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW
+AGSTLMTLLVLVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ
+ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTALLLMAST
+LLYLGYAEIGRADVPMLRLFASIAPWLGWAMVVVIYLMIFNTAIGMFYALGRRLTADRPG
+RYRPVFAGVTLLAFAVSFVGFGDLINVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL
+RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPDAVTEALEDEVAQVLEEDDALTS
+EGARPGPDAGPERPAGGSHSA*
+>NZ_CP033200.1_918
+MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI
+LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW
+AGSTLMTLLVLVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ
+ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTVLLLMAST
+LLYLGYAEIGRADVPMLRLFASIAPWLGWAMVVVIYLMIYNTAIGMFYALGRRLTADHPG
+RYRPVFAGVTLLAFAVSFVGFGDLMNVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL
+RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPGAVTEALEDEVAQVLEEDDAVTP
+DEVHPGPDAGPERPAGGSHSA*
+>NZ_CP040019.1_1630
+MVFRSVSHPVMARILDVTVTVTLFAIGFVMLAGAGSTLAQQLGWPTWAGAGLMTALVLVT
+GMLDVEKVSAIISLITPLIILAVVAGFVHVLLTHEGSFTANEALAVQAATPVAPWWLSSV
+NYFGLVVVMAVSMCLVIGGSITNPREAFAGGLTGGVLYTVLLLLASVLLYLGYAEIGRAD
+VPMLQLFASIAPWLGWTMVVVIYLMIYNTAIGMLYALGRRLTAERPGRYRPVFIGVTLLA
+FAVSFVGFGDLMNVVYPALGYLGIVLALVLIAWWVLHRRQISAESGLRLRLRALLRLREH
+PEKTFTAQHAVLLQEAADESVAATAVVTEAVEEEVVQAIEADEPYGDPRRS*
+>NZ_CP083691.1_1525
+MQKSAALRSVQLALAFVGLLVGAGFATGAEVIQYFVGFGEVGIGGALLAGVLVAVGGAVA
+LQLGSLFLAADHKVVFRSVSHPVMARILDAVVTVTLFAIGFVMLAGAGSTLAQQLGWPVW
+AGAALMTAMVIVTGMLDVEKVSAIIGMITPLIIIAVVAGFAYVVATHEGPFTVNDSLAVQ
+AVTPVSPWWLSSINYFGLVVVMAVSMCVVIGGSTSSPREAFVGGLVGGVVYTVLLVLASV
+LLYLGYAELGTADVPMLQLFASIHPALGWAMVVVIYLMIYNTAIGMFYALGRRLTAERPG
+LYRPAFVGVTLAAFAVSFLGFGDLMNYVYPALGYLGIVLAVVLLVWWAAHRDDIAAESGL
+RLRLLALLRLREHPEKTFTRQHAVILQETAEESVAPTETVTEMMEADAVAVIEAEDPDLL
+PAADETAGRGGADHGGADGSAAARG*
+>NZ_CP097650.1_1146
+MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI
+LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW
+AGSTLMTLLVVVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ
+ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTALLLMAST
+LLYLGYADIGRADVPMLRLFASIAPWLGWAMVVVIYLMIFNTAIGMFYALGRRLTADRPG
+RYRPVFAGVTLLAFAVSFVGFGDLMNVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL
+RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPGAVTEALEDEVAQVLEEDDALTS
+GGARPGPDAGPERPAGGSHSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001065.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001065.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54406c072f82f0afb942da4a963759fd31f928e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001065.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1216
+MDDLFSAAHTGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLEDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTEEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVATAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD*
+>NZ_CP033200.1_945
+MDDLFSAAHNGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLQDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTDEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD*
+>NZ_CP040019.1_1602
+MADLFSAAHESDDDGPSGTVAAPRASAPLAVRMRPRTLEEVLGQRHLMRPGSPLRKLAEP
+DPGSPAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRER
+DLYDRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLLT
+LRPLTDEDIVGLVERAVADERGLNGAVDLADDARDYVVRMAGGDARRALTVLEAAAGVAL
+DKARQAGADEDAGGDGGARAGAAAPVTVTEEDAAQAMDHHVQRYDKDGDQHYDVISAFIK
+SIRGSDVDAALHWLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLI
+GMPEGRIILGQAVTHLATAPKSNASYAAVNEALADVRAGGTGQVPPHLRDAHYPGAAALG
+HGKGYVYSHDEPHAVARQQYAPDPLVGKDYYRPKPIGAEKRLVDQVAALRRITRGE*
+>NZ_CP083691.1_1498
+MDDLFSAAHADPDDDAPVTASGRARASAPLAVRMRPRSLDEVLGQAHLKQPGSPLRKLAE
+PAASAQAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQARR
+EREMYDRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLL
+LTLRPLDDTDLAALVDRAVADERGLNGTVEPTPNARDYVVRMAGGDARRALTVLEAAAGV
+ALDRAEARGETTGPGSAPVEVTEEDAAQAMDAQVQRYDKDGDQHYDVISAFIKSIRGSDV
+DAAMHWLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRI
+VLGQAVTHLATAPKSNASYTAVNEAIADVRAGGTGVVPAHLRDSHYPGAKALGHGQGYVY
+SHDEPHAVARQQYAPDPLVGRDYYRPKPIGHERQLGPQVDALRRIIRGD*
+>NZ_CP097650.1_1173
+MDDLFSAAHNGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLQDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTDEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001082.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001082.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2362fdc26da722d5fe9fbb1aa728c868b4b66a33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001082.fa
@@ -0,0 +1,44 @@
+>NZ_CP042169.1_1234
+MAARPRRPRPHPADLPPALAAAVTVAARRAGSRESRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAAYAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIAPYPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSALAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTAVRGWLRAVLSAPRPGGRGR*
+>NZ_CP033200.1_963
+MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRGR*
+>NZ_CP040019.1_1584
+MRTGVKAASPLARWTPPVLSVLASSAFVLAGASSALAGVFARTVVTPVRRHTETTAVLAV
+VDTPTGPEVILKADEYTTVPGVYSLTFDGGAGCARIGRISSFDPRDGTVQRVVEEVYFGD
+LAAATRGRLTGFVYPTPADAGLDAEEVLVPVPGGHAPAWLVGPDPDDDGAARPAAGIWAI
+MVHGRGARRNEGIRTVPTAQRLGMTSLLISYRNDGDAPDAADSRYGLGTTEWEDVEAAIR
+YALDNGASDVVLFGWSMGGAVVLQAVDRSDLAPQVRGVVLTGPVVDWVDVLQHQARLNRI
+PEAVGVLGQWLLSNRAGRFITGLAAPVDLKSLDWVTRAEHVRVPTLIIHSEDDEYVPVGP
+SQDLAERNPGLVRFVRFHQARHTREQNVDPKRWDTTVRGWLRAVLNADRPGAAER*
+>NZ_CP083691.1_1477
+MACPRRHSPRLRARPDLRDALLGSLRGSAAVARPAARLAPAAASVAASAAFVLAGASAGL
+AGVFARTVVTPVRSRPEHTAVLAVLDTGDGMDVILPADEHTTVPGTYSLTFHGGEGCARI
+GAIRSYDPRDGTVQRVVEEVYSGDLRSAVRGRFTAFIWPGPAEAGLEAADVEVPVPGGAA
+PAWRIDPPPAEDGEERAGEGMWAVMVHGRGAVRNEGLRAVPTAARLGMTSLLVSYRNDGD
+APDAEDARYGLGTTEWEDVEAAVRYALDHGARDVVLFGWSMGGAVVLQTADRSDLTSRVR
+GIVLTGPVVDWMDVLRHQARLNRIPEGIGLLGQWLLSNRAGRLVTGLAAPVDLKALDWVT
+RADHVRVPTLILHSEDDEYVPVGPSQDLAERNPALVRFVRFHQARHTREQNVDPVKWDRS
+VRGFLRAVLTAPRPGAVSPPGAPQAPSGSSPRRRSSGSSSASRPRNAR*
+>NZ_CP097650.1_1191
+MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001102.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001102.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27e4c6e79387b99179d200db55b5694a30d0f96c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001102.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1262
+MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDEAEAAEGFELPGADLSGEELMV
+RVLPAQSDEFTCASCFLVRHRSQAAREKNGLIYCTDCEG*
+>NZ_CP033200.1_995
+MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDEAEAAEGFELPGADLSGEELMV
+RVLPAQSDEFTCASCFLVRHRSQAAREKNGLIYCTDCEG*
+>NZ_CP040019.1_1561
+MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDETEAAEGFELPGADLSGEELMV
+RVLPAQSDEFTCASCFLVRHRSQAAREKNGMTYCTDCEG*
+>NZ_CP083691.1_1455
+MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDETEAAEGFELPGADLSGEELMV
+RVLPAQSDEFTCASCFLVRHRSQAAREEGGLVYCTDCEG*
+>NZ_CP097650.1_1219
+MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDEAEAAEGFELPGADLSGEELMV
+RVLPAQSDEFTCASCFLVRHRSQAAREKNGLIYCTDCEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001135.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001135.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f39266ec9c5bb51e0e259d2133d31f0292c1093e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001135.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1301
+MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLEDGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDED*
+>NZ_CP033200.1_1031
+MGMRPGLTERLQVAEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYATLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDED*
+>NZ_CP040019.1_1522
+MEPIPGATARIEVTPDRAGRRADAVLAEVLGLSRSALADWFSRGLVRAESRTGRRDRVLA
+KSAKAVAGEVLAVDVPDDPDPLEVRAERVDALRILHEDEHLIAVDKPTGVAAHPSPGWAG
+PTVVGALAALGHDISTSGAPERQGIVHRLDVGTTGVMVVAKTEQAYAALKDQFRRRVPEK
+VYHALVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDGGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLSFPHPVTGEPVSV
+TSEHPDDLAHALARLRRDGS*
+>NZ_CP083691.1_1416
+MGLRPGLTERLAVTEDDAGRRADAVLADAFGVSRASLADLFSRGLVRAESRTGRRDRVLA
+KSAKAVAGETLAVDVPVDPDPLEVRAERVDAMTVLYEDDDLLAVDKPTGVAAHPSPGWFG
+PTVVGGLAGLGRRISTSGAPERQGIVHRLDVGTTGVMVVAKSERAYTALKDQFRERVPEK
+VYHAVVQGMPDPLEGTIDAPIGRDPNHHWRFAVLEGGRPSVTHYETVEAFGRATLLEIHL
+ETGRTHQIRVHTSALRHPCAGDLTYGADPRLAAELGLTRQWLHAHRLALPHPATGERLEI
+VSPYPDDLAHALRVLRGEDRGAAPDA*
+>NZ_CP097650.1_1255
+MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGRDISTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRMAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001153.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001153.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a30356eb13488db27ecd38f452e39871f1103a11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001153.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1320
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCIYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF*
+>NZ_CP033200.1_1050
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCVYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF*
+>NZ_CP040019.1_1504
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCVYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NAYLAEQEAAFSETDEDVLPGVF*
+>NZ_CP083691.1_1397
+MFLGTYTPRLDEKWRLILPAKFREELADGLVLTRGQERCVYVFSAAEFERVHEQLRSAPL
+SSRQARDYIRVFLSGASDETPDKQGRITVPSPLRQYAGLDRDVTVIGAGTRAEIWDTAAW
+AAYLAEQEAAFSETDEDVLGGIL*
+>NZ_CP097650.1_1274
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCIYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001162.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001162.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cc5e207d4113c886b84749a170f41fd5541ed53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001162.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1330
+MHEISEPYHHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRAL
+AKGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSDV
+RAVVTGNEDLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGADVTDEELET
+RRSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVREDTSTVLFIP
+LAHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQ
+SGGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALVYRRIRTAMGGRLAYAVSG
+GGPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDG
+EILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKN
+VAPAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAAR
+EDAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQ
+IADIYGEPAPQN*
+>NZ_CP033200.1_1060
+MHEISEPYHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRALA
+KGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSHVR
+AVVTGNENLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGTDVTDEELETR
+RSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVRQDTSTVLFIPL
+AHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQS
+GGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALVYRRIRTAMGGRLAYAVSGG
+GPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDGE
+ILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKNV
+APAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAARE
+DAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQI
+ADIYGEPAPHN*
+>NZ_CP040019.1_1493
+MREISEPYHPRLSPESNITDFLERQAEERPDHGLFAVADEQDQWTDVSARDARERVRALA
+KGLIAAGVGAGDRVGLIAATRLEWTLVDFAIWYAGAVTVPIYETSSATQVAWIVEDADVC
+AVVAGDESLVKTVRDAVHREHLPELRGVWVMDVAGGEPGSGLDELAALGADVSDEDLEAR
+RSAANLEDLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGEVVRPDTSTVLFIPL
+AHVFARFVSVLTVAAGARCGHVTDLKRLSNSLQTFQPSFVLAVPRVFEKIYNAALLNAQS
+GGKDKIFRRGADVAVRWSRALDSGKMTAPLRLQRAFYSALIYRRIRAAMGGRLEYAVSGG
+GPLSPDLAHFFRGVGLTILEGYGLTETTAPITVGRPGRLKIGTVGLPLGGNAVRIAEDGE
+ILTRGTSLMRGYHDRPEANEEAFEDGWFRTGDLGSLDEDGFLTITGRKKELIVTAGGKNV
+APAMLEDAIRSDALISQVMVVGDAKPFIAAIVTLDADTLPSWLAAHGLPKDLDVAAAAKE
+ERVRRHVQEIVDKASSAVSRAEGIREFRILDRDFSMEEGHMTPSLKMKRAVIMQDFAAEI
+ADIYGEAPAQG*
+>NZ_CP083691.1_1386
+MRQISEPYLPRLSPDAAITDFLRDQAVQHPERALFAVPREDGSWDDVTAAEAWDRVRALA
+RGLVAAGVGPGDRVAIVSATRLEWTLADFAIWTAGAVTVPVYETSSASQIAWIFEDAGVG
+AAIADTPARAKSVSDAVHREGLPELKGLWVMDEDGGAPGAGLDRLTDAGADVPADELDAR
+REGVTLESLATIIYTSGTTGRPKGCELTHGNFAELVNQTLRSSLGEVVDEGASTLLFIPL
+AHVFARFVSVLTVAAGARCGHVPDLSRLATSMDTYHPTFLLAVPRVFEKIYNASLLKAQA
+GGKEKIFRRGADVAVRWSRALEEGRMTAPLRLQRAFYSALLYRRIREAMGGHLKYAVSGG
+GPLSPDLAHFFRGVGVTILEGYGLTETTAPITVGRPGKLKIGRVGQPLGGNEVRIDDDGE
+ILTRGTSLFRGYRNRPEANAEAFTEDGWFRTGDLGELDDDGFLKITGRKKEIIVTAGGKN
+VAPAQLEDAIRSDALVSQVMVVGEAKPFVAAIVTLDADTLPSWASAHGLDPQISMAEAAR
+EPQVIAHVQKAVDRANDTVSRAEGIREFRILDRDFSADEGHMTPSLKMRRTAILKDFQPV
+LDEIYGAGPARG*
+>NZ_CP097650.1_1284
+MHEISEPYHHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRAL
+AKGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSHV
+RAVVTGNENLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGTDVTDEELET
+RRSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVRQDTSTVLFIP
+LAHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQ
+SGGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALIYRRIRTAMGGRLAYAVSG
+GGPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDG
+EILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKN
+VAPAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAAR
+EDAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQ
+IADIYGEPAPHN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001166.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001166.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0018cb3f794d42ca943e2488b10693bd2f2343b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001166.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1334
+MTEPRPVPADDAGDVPLSVLGVRVELPEQHHVILLVDPPGRTMIPLWVGAPEAAAAALAL
+EGVRAPRPLTHELLLAAVDALGAEVVRVRLTEVRDEVVHAELVLSTGARVDARASDAVVV
+ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA*
+>NZ_CP033200.1_1064
+MTEPRPVPADDAGNVPLSVLGVRVELPEQHHVILLVDPPGRTMVPLWVGAPEAAAAALAL
+EGVRAPRPLTHELLLAAVDALGAEVVRVRLTEVRGEVVHAELVLSTGARVDARASDAVVV
+ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA*
+>NZ_CP040019.1_1489
+MTEPRPEDAPEAGDVPMSVLGVRVELPEQHHVILLVDPPGRIMVPLWVGAPEAAAAALAL
+EGVSAPRPLTHELLLSTVAALGAEVVRVRLTEVRNDVVHGELELSTGARVDARASDAVVL
+ALRANAPVLASPAVLAEAGMSARSGEEDGQERTVEDFRDFLDSVRPEDFA*
+>NZ_CP083691.1_1382
+MAEPPEPAGDVPLTVLGVRVELPEQQHVILLLDPPGEIVLPLWVGSPEAAAAALALEGAP
+SPRPGTHALLLAALAAAGSRLRGVRLTRIEDETVHAALLLDGGAEVDARASDAVVLAVRA
+QVPVLCAAEVIAAAGMAARDAAAGDEDEVDDFRAFLDSVDPEDFA*
+>NZ_CP097650.1_1288
+MTEPRPVPADEVGDVPLSVLGVRVELPEQHHVILLVDPPGRTMVPLWVGAPEAAAAALAL
+EGVRTPRPLTHELLLAAVDALGAEVVRVRLTEVRDEVVHAELVLSTGARVDARASDAVVV
+ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001183.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001183.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91d66e26ec245ead4a54122ab25a7dad8f81624c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001183.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1377
+MPYTPGRRILVLTHTGREDAISAALQATRMFAEEGLVTVMLEQDVAAIRAAAGDPPEFAP
+ETLGVDCELEDITLGLVLGGDGSVLRAADFVRGYNVPLLAVNLGHVGFLAESERTDLHRT
+VQAIASESYVVIERMALDVVVHVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT
+SFGCDGVVLATPTGSTAYAFSAGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARVEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQERAGVLHEVETVEPRHAGPRPDVVEPATMPLSVPSPADIQRHRDRGARHPGE
+DA*
+>NZ_CP033200.1_1118
+MPYTPGRRVLVLTHTGREDAISAALQATRMFAEEGLVSVMLEQDVAAIRAAAGDPPEFAP
+EALGVDCELEDITLGLVLGGDGSVLRAADFVRGHNVPLLAVNLGHVGFLAESERTDLHRT
+VQAIASESYVVIERMALDVVVLVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT
+AFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQERAGVLHAVETVEPRHAGPRPDVVEPATMPLSVLSPADIQRHRDRGARHPGE
+DA*
+>NZ_CP040019.1_1452
+MPHNPGRRVLVLAHTGREDAISAALQATRILEEEGLVSVMLEQDVAAIRENADAPAGFAP
+QTLGVDCGLEDIVLGLVLGGDGSVLRAADFVRGYDVPLLAVNLGHVGFLAESERTDLQRT
+VQAIASEAYVVIERMALDVVVRVEDREVARTWALNEASVEKSNRERMLEVVISVDNAPIS
+SFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQEREAVLREVETVEPRHAGPRPDVVEPATMPLSVLSAADIQRYRDRGARYPGE
+DA*
+>NZ_CP083691.1_1359
+MSETPSRRVLVLAHTGRADAIAAALQATAMLAEEGLDTVMLAEDVAAILESGTDAVGFRP
+LTLGRDCTLDDVQLGLVLGGDGSVLRAADFVRGHGIPLVAVNLGHVGFLAESERTDLHRT
+VKAIADGAYVVIERMALDVTVRVEGREVARTWALNEASVEKSNRERMLEVVVSVDDSPLT
+SFGCDGVVLASPTGSTAYAFSAGGPVVWPGVEALLCVPISAHALFSRPLVVGPHSTVAVD
+VLTRTRETGVLWCDGRRTVELPPRARIEVTRSAEPVRLARLRPTPFAERLVRKFRLPTEG
+WRGPVTEADRRTGPLAEVETVEPRHAAPRPDVVPPPSEPLTVLSPEALARYRGRDGREGD
+RTS*
+>NZ_CP097650.1_1326
+MPYTPGRRVLVLTHTGREDAISAALQATRMFAEEGLVSVMLEQDVAAIRAAAGDPPEFAP
+EALGVDCELEDITLGLVLGGDGSVLRAADFVRGHNVPLLAVNLGHVGFLAESERTDLHRT
+VQAIASESYVVIERMALDVVVLVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT
+AFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQERAGVLHAVETVEPRHAGPRPDVVEPATMPLSVLSPADIQRHRDRGARHPGE
+DA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001186.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001186.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d465912872aa687ef68bd5bc8ce2e7199757d23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001186.fa
@@ -0,0 +1,39 @@
+>NZ_CP042169.1_1380
+MTGKELDRGTLKEINGLDERAASWVAKHLVMAGRYLDVDPTLAFQHALAASRKGGRLSRV
+REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS
+RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG
+RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRNRRPSPRERRHERYAAEAG
+AEPTADGSPAEEPEAAAEPTLVPRQEAVAQPPAAVDTPDEVDPNQLSLFDALEAPEADER
+*
+>NZ_CP033200.1_1121
+MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALAFQHALAASRKGGRLSRV
+REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS
+RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG
+RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRDRRPSPRERRHERYAAEAG
+AEPTADGSPAEEPEAATEPTEAPRPEAAAEPPAAVDAPDEVDPNQLSLFDALEAPEADER
+*
+>NZ_CP040019.1_1449
+MAEDTPRGRRDDRRSPGDGAGRSRGGSGDARRFGGPRDGRRSGGSGEGRSGQDRRDRSSE
+GFRGGRSGDGPRRERSSDGPRRERSSDGFRRDRSSDGPRGERSGDGPRGPRAGGDRRQSG
+AGSARGGFEGRRGGERREGAGGERRDRRSASSSPRWEGRGQDRTERTERRERPAHNPRDL
+RAANRVDQERSPDIDADVTGQELDRGTLKEVNGLDERPASWVAKHLVMAGRYIDVDPALA
+FQHALAASRKGGRLSRVREAVALTAYAAGEYADALREFRTYRRMTGDDTHVAAQVDSERA
+LGRPAKALQLAAEIDTARLDRAARVELAMVVSGIREDAGDLQGAHDALQIPELDRRRGYP
+FSPRLFQRQADVLLLLGRADEARLWARAVRVAEKALGIGGFAEPEIVDVDTEPVDDRRER
+GPSPRERRYAENAAPAAEEVPDTPEADDEVAADADTEAPASTESELDAPPAAVAQADEVD
+PNQMSLFDELDGGEGEGR*
+>NZ_CP083691.1_1356
+MAERSAREPRDDRRGDGHDGTRSGTPRGRRDGDGGRRQGEGRPFRPHRDGEGVGRSRNVG
+GRDGAAPRPGRPERAQRERPAHSPSDLRAANRVDQQRSPDIDGDVTGKELDRGTLKEIGG
+LDERPATWVAKHLVMAGRYIDEDPELAFQHALAASRKGGRLARVREAVALTAYAAGEYHE
+ALREFRTYRRMTGDDTHIAAQVDSERALGRHEKALQLAGEVDTSRLDRAARVELAMVVSG
+VREDLGDLEGALAALKIPELDRRRGYPFSPRLFQRQADVLTALGRTQEAAVWQRSVHVAE
+RALGIGGFAEPEIVDVEVEPAEDDRPVRGHRERHTGPRVSDASQSSAESAPVGEGSAEEH
+GQAAPAERES*
+>NZ_CP097650.1_1329
+MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALAFQHALAASRKGGRLSRV
+REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS
+RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG
+RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRDRRPSPRERRHERYAAEAG
+AEPTADGSPAEEPEAATEPTEAPRPEAAAEPPAAVDAPDEVDPNQLSLFDALEAPEADER
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001197.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001197.fa
new file mode 100644
index 0000000000000000000000000000000000000000..297c04d5b8de87ef8033ec4fb23b5cc92f95ce6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001197.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1391
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMPR
+GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAVLDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP*
+>NZ_CP033200.1_1133
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTADVLAGHDVVILALPHEASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR
+GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP*
+>NZ_CP040019.1_1437
+MTHTVAVSGASGYAGGEALRLLAGHPDVAVGAITAHSNAGERLGALQPHLHSLADRVLEE
+TTADVLAGHDVVILALPHGASGALAAQIAERSPETLVIDAGADHRLESAADWEAFYGSEH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLSQAAGERVQISFTPTLAPMAR
+GILATATARLRPGADPAAVRGAWERAYADERFVHLLPEGLWPATKSVLGSNHVQMQLAVD
+ERAGRVIVTAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP*
+>NZ_CP083691.1_1344
+MTFTVAVSGASGYAGGEVLRLLAGHPEVQIGAISAHSNAGERLGSLQPHLHALADRVLDD
+TTADVLAGHDVVVLALPHGASAAVAAELAERSPRTLVIDAGADHRLESAADWERFYGTDH
+AGTWPYGLPELPGQRERLAGATRIAVPGCYPTTSILALAPGFAAGLLETRDVVIVAASGT
+SGAGRAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVQISFTPTLAPMPR
+GILATATARLKEGVTADRVRAAWEDAYGPERFVHLLPEGQWPTTKAVVGSNHVVMQLAVD
+PHAGRVIVTAALDNLTKGTAGGALQSMNIALGLPEQLGLEIQGVAP*
+>NZ_CP097650.1_1340
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR
+GILATATARLRPGVAAADVRDAWAEAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001224.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001224.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a734392b89bc5b6f112ed72d27f1f9a420644af9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001224.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_1422
+MTTVDPQPPRPPRVAVVAVIVALVLALSGCTQIPQSSEVRSADPVDGASAAADAPQFHPP
+GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD
+GDGDYQIQVEVDSEIDEYGLRTVAPPGTTRAWAVTVQERPQGMRITSTENGTLLSQAQFG
+QLFAPHELAFYDTAKRYIVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVETAFPLRTG
+TDLAAPTVPVDDDGVAHVDLTQAAAEGADAERRHRMREQLELTLRGLQSVKEVEVTVAGA
+QLSTSGDDGPAPVQTDPAVRSVQVGIDAATGGLVYVQGSSVTPVGGAPDVTALDPVRPTM
+SGDRSRFAFVTGDRTAVHVAGTDGSLREVLRGTGLTVPSLDLLGWVWAADRGTTSRIRAV
+SAQPGGQERIVTATWLRPGERIVDLRLARSGARAAMLVDDGQRTTLRVSGVVRGSDGVPN
+ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAEKPDERVVPRIVSIDGTVRELNPLGGLRG
+ISAGDDGAYYAETEELVFLLVGSSWRAQELDRGVRDLSFPD*
+>NZ_CP033200.1_1164
+MTTVDPQSPRPPRLAVVGVIVALMLALSGCTQIPQSSEVRSADPVDGATADADAPQFHPP
+GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD
+GAGDYQIQVEVDSEIDEYGLRTIAPPGTTRAWAVTVQERPQGMRITSTENGTLLSQAQFG
+QLFAPHELAFYDTAKRYVVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVDTAFPLRTG
+TDLAAPTVPVDDDGVAHVDLTQAAAEGADAERRHRMREQLELTLRGLQSVKEVEVTVAGA
+QLSTSGDDGPAPVQTDPAVRSVQVGIDAATGGLVYVQGSSVTPVGGAPDVTALDPVRPTM
+SGDRSRFAFVTGDRTAVHVAGTDGSLREVLRGTGLTVPSLDLLGWVWAADRGTTSRIRAV
+SAQPGGQERIVTATWLRPGERIVDLRLARSGARAAMLVDDGQRTTLRVSGVVRGSDGVPN
+ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAAKPDERVVPRIVSVDGTVRELNPLGGLRG
+ISAGDDGAYYAETEEFVFLLVGSSWRAQELDRGVRDLSFPD*
+>NZ_CP040019.1_1408
+MSPTRPTGPRRARRLAGVGLAAALALALGGCTQIPQSSDVRSAEPLDGATAAPEAPQFRP
+PGPSADDTAEDVIRGFLLAGTSPQDDYAVAREFLDGPAAARWAPGQRTLVYSAQPRITRG
+EGTGNYQVQVEVDSEIDEFGLRTIAPEGTTRAWQVSVQERPEGMRITATENGTLLSQSQF
+GQLFAPHELAFYDTAQRYAVPDVRWFVNRGTTVTAVTRALLRGPAPYLTGAVETAFPLRT
+GADLAGPTVPVDEDGVAHVDLTEAAAEGADADRRHRMREQLEITLLGLQSVSDVRVTVDG
+AELSASGENPPPPVQDEPTTGSVQVGIDSATGDLAYFQGMSVGPVGGAPDVSALDPVDPT
+MSRDRSRFAFVTRDRTAVHVAGTDGSLREAMRGTGLTSPSIDGLGWVWAADGAETSRVRA
+VPAEPGQEARIVTATWLRPAERIVDLRVSRSGARAALLVDDGDRRTVRVAGIVRGSDGVP
+SALTEPILLPSTGRAASVEWAGDTNLLVSPRAATPDERVVPRIVSIDGTVRELNPLGGLT
+GVSAGDGGALYAETDELVFLLVGSSWRAQELERGVRDLSFPG*
+>NZ_CP083691.1_1309
+MRPSGPARPRRRLCAAALAGALALAGCAQIPQSSPVRSGAPLDVGSRAADAPQFRPPGPA
+EDATAEQLVRGFAQAGIAPEDGYAIARQYLSAEASDGWEPDRGVVVYSGEPTVTRGLGEG
+TYEVQLEVESEVDEFGQRTMAPPNTTQAREVTVEEVDGVLRITGVQDGVLLSRSQFAQLY
+APHPLYFFDQSQAFAVPDVRWFVNRGTAVTALTRALLRGPAPYLTGAVATAFPLRTGADL
+TGPSVPVAEDGTAAVDLTGATVDGADPARLSRMREQLERTLTGVSGVERVEVTVEGRSLT
+SSAPSGSVPSARIGEDPGTVQVGVSDAGELVFFQGLDAVPVGGLPSVADLGPEDPAMDRE
+RRRFVFLDRTRTVLHGVGTDGGEHRLLDGGRLTAPSLDSSGWAWTVDRARSSRISVVRAD
+GSEPARVVTTPWLAEGESIVALHIGPAGARAALIVDDGQQRTLRVAGVVRGGDGVPTALT
+PPVYIPTLDPPDDVEWMGDGSLVSTPLAPDAETRVRPEVVSLDGTSRQLNPLAGLTGISA
+REEGTLYAETAEDVFLLVGSSWRAQDVATPVHDLAFPD*
+>NZ_CP097650.1_1371
+MTTVDPQPPRPLRVAVFAVIVALVLALSGCTQIPQSSEVRSADPVDGATAAADAPQFHPP
+GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD
+GAGDYQIQVEVDSEIDEYGLRTVAPPGTTQAWAVTVQERPQGMRITSTENGTLLSQAQFG
+QLFAPHELAFYDTAKRYVVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVDTAFPLRTG
+TDLAAPTVPVDDDGVAHVDLTQAAAEGADADRRHRMREQLELTLTGLQSVKEVEVTVAGA
+QLSTSGDDGPAPVQTDPAVGSVQVGIDTATGGLVYVQGTSVTPVGGAPDVTALDPVRPTM
+SGDRSRFVFVTRDRTAVHVAGTDGTLREVLRGTGLTVPSLDLLGWVWAADRETTSRIRAV
+PAQPGGQERIVTATWLRPGERIVDLRLSRSGAQAAMLVDDGQRTTLRVSGVVRGSDGVPN
+ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAEKPDERVVPRIVSIDGTVRELNPLGGLRG
+ISVGDDGAYYAETEELVFLLVGSSWRAQELDRGVRDLSFPD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001297.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001297.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bdb6bdacfaee22210861465e7643ca8c7bce816
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001297.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_1525
+MSETRRARPGVDPASTPPSDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT
+VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE
+GGLIVFLVPAVALILGVGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA*
+>NZ_CP033200.1_1246
+MSETRRARPGVDPASTPPSDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT
+VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE
+GGLIVFLVPAVALILGIGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA*
+>NZ_CP040019.1_1328
+MPRLSAVSEPLTIAPRSDDAPSVPSSSSDAPRGPGGRRALVRRRVFRSPLQRRIVYAVVF
+ELLAILFTTGILAAFGNSGGSSLAVAVVSSTVALLWNIAFNSMFEAVERRAGITGRPWWL
+RALHAVAFEGGLILFLVPAVALILGVGLWQAFLIEAGLLVFFLVYAAVYAYAFDSVFGLP
+DSAAGATR*
+>NZ_CP083691.1_1220
+MTPPHDDAPRGPGGRRALVGRRVFRSPLRRRIVFAVVFELLAILFTTLILRAVGNEGAAS
+FAVAVVSSTVALIWNVVYNSLFERLERALGVHGRPWWARVGHTVGFEGGLVLFLVPAVAL
+LLGVTLWEAFLIELGLIVFFLVYNAVYTYLFDAVFGLPDSAGVTAPGTP*
+>NZ_CP097650.1_1452
+MSETRRARPGVDPASTPPFDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT
+VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE
+GGLIVFLVPAVALILGVGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001300.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001300.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f40d2e9a80f57812631ba33790983530f0ebe84d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001300.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1528
+MNTTAAASDPSDAPLASTRIGEGPRGVAFLHGLMGRGRNFTGPAKELGDDFTVELIDLPD
+HGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPELVDRLI
+VEDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRR
+TAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHPVLWLAGAESDYVQDEDVPRM
+KELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD*
+>NZ_CP033200.1_1249
+MNTTAAASDPSDAPLASTRIGEGPRRVAFLHGLLGRGRNFTGPAKELGDDFTVELIDLPD
+HGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPDLVDRLI
+VEDISPRVSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRR
+TAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHPVLWLAGAESDYVQDEDVPRM
+KELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD*
+>NZ_CP040019.1_1324
+MTISDQGSPRRLPDSLERVSTPDPSASAAPSDAALASDVIGDGPHRVAFLHGLMGRGRNF
+TGPAKALADDFTVELLDLPDHGRSPWTDRVDYQEIADRVAEHLRAGLAADGPVHVLGHSM
+GGKVAMVLALRHPDLVDRLIVEDISPRLLPQATDEFVHLLGTMLRMDLDSYESRAEADAV
+MAKHVHDARVRGFLLQNLRREGGRFAWQPNVAMLFEHLEAVGSFPDPAAPEDPDRVFDRP
+VLWLAGANSDYVRDEDVPRMKDLFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD*
+>NZ_CP083691.1_1216
+MPTWSRASLSRVNTTAASAPSDAPLASTRIGEGSRRVAFLHGLMGRGRNFTGVATALADD
+FTVELIDLPDHGQSPWTDAVDYQDMADRVADHLRAGLAADGPVHLLGHSMGGKVAMVLAL
+RHPELVERLVVVDISPRMSPSATGEFVHLLGTMLRMDLASYTSRAEADAAMAEHVHDARV
+RGFLLQNLRREDGHFAWQPNVRMLFEHLDEIGAFPDPVVPEDPDRVFDRPVLWLGGADSD
+YIRDGDAPEMKALFPRVVRVTVRGASHWVHADQPEAFVSAVRTFLTAD*
+>NZ_CP097650.1_1455
+MNTTAASAPSDAPLASTRIGEGPRRVAFLHGLMGRGRNFTGPAKELGDDFTVELIDLPDH
+GASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPELVDRLIV
+EDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRRT
+AGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVVDHPVLWLAGAESDYVQDEDVPRMK
+ELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001333.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001333.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ce2a28a6cc3dbf338dbd786e13b006120156c1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001333.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1592
+MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAELESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD*
+>NZ_CP033200.1_1308
+MDTPQDPPRRDDPSGGPVEPAVDAALDRVHALLRQARVIAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALVPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAGLESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDTALELTRRVIAVLGGLRAAGALLPIGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTVLPAARAVLASATTVRAIAAHELDRPTAALDLAFEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD*
+>NZ_CP040019.1_1232
+MDAPQQTPAPADVGPTAVLARVRTLLAEARTSGAPEDAVDAAPVDHDARQWWELSLEAAL
+RDEPRESARCAESGLAALGPGEDGVRLSLLRALAVAADRLGDETGLTRWVEARAALLRTL
+GRPRQAALETQLGASLVREPDGFEAAVLAGVVEEEPGVPGEDPGDTVLPEAALALAVHRV
+HASDLDGALAAARRAVESLRGLRAAGAVLPVGSWSSAHLLLSRLHLWRGEHAEADEAAAV
+VTSLPAARAVLASATTVRAIAAHEQDRPTAALALALDAADRMARVGLRRGAASAAALAGR
+VAGDLEGHEEAAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRPDEAEPLLARLVR
+REAAQGHDVEQARALVDLGHAHHDQDRSENALPLWREAAGLFEAHGRWEDAARTLLAAGA
+LVNRERDELTRPSALDLFERAVAAARRAVDEDPAVLPAALHAHGYLLCESGRPEGLELLD
+EAVALVREAEAPWQVADYTDTRARALWSLEQGAEAVSTALHAADLFTAAQDPEGAAQAEL
+FAASVVAEDGSPEQAATLFRLVSESTQSTLVRLGALTGLHQCLSAVGDHDGAARVRDDLD
+AVREQLGAD*
+>NZ_CP083691.1_1140
+MAEDAPALLAGRDPLAAVEALLAAARDDAALPLPAGSDAPSLRERALEALLREDPASAAR
+AAEDGLDAPGGQDPALRLALLRLRATAAAHAGDEPALEEWTARRADLLRRLGRPRQADLE
+VQLGASLLREPDAFEATVLAGVAEDERGRITADPAALEDTVLPDALLALCAQRVQAHDLD
+AALEAAEEALAVIRAQETAGVVLGEAAEPHALLMLARLHLWREEHRASDDAARAVLARPC
+AAVVRASATLVRALAAHGQDRPEAALDFALRAAEAMSRAGLRRGAASAAALVGRVAGARA
+DRQDLAVAAWELSCVHAEKAEAPEAPSLAYWWAHQLLIAGRAEEAEPVLTALVRREAAAG
+DEAAQARALVDLGHACHELDRPSEALPLWREAAELFTRRGHHADAAHTLLAAGALCHRDP
+HDAAHAGALDLFEQAVDAARRSEGDSAVLASALHALGYLRCETGRGDGLELIDEAIALAE
+GSGAAWQKADYLDTRARSLWALHRGDDAVSAALTSADLFTDAGDPSGAAQAELFAAHVVA
+EDGRPEQAATLFRLVSESTHSDLVRLGALTGLQQCLAALGEHAEADRVRADADAVRRALG
+GRD*
+>NZ_CP097650.1_1522
+MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAGLESQLGGALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRYAGADWQVANYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001379.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001379.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0ce9202c0050abfbc47c57ccf70bb1e35b9759f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001379.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1646
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK*
+>NZ_CP033200.1_1364
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK*
+>NZ_CP040019.1_1161
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK*
+>NZ_CP083691.1_1090
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDRDIRVKDLTDDQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK*
+>NZ_CP097650.1_1575
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001384.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001384.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28cdd56c0f76adbc3071271db5164a6355d1e959
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001384.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1651
+MLKAIARIVRTPDLLRKIAFTLALIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPSILIQFNTPQDGSAPAPW
+ITWLSRYFGPGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR*
+>NZ_CP033200.1_1369
+MLKAIARIVRTPDLLRKIAFTLALIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPSILIQFNTPQDGSAPAPW
+ITWLSRYFGPGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR*
+>NZ_CP040019.1_1156
+MFKAIARIVRTPDLLRKIAFTLGIIAVYRMGAFVPSPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSIFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQSTLTQYTRYL
+TLALSLLQATTMASLARTGALLGCQLPLLRNDSILTVLLVVVVLTAGCIIVMWLGERVTE
+NGVGNGMSLLIFASIAAGFPAGLGQVVQTQGWRVFAIVMLIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTFIPIKVNMANVIPVIFASSVLMLPGILIQFNTPQDGTAPAPW
+IAWLSRYFGNGDHPVYMAVYFLMIIGFTYFYVSITFNPQEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLAGALYLGIVAMIPLIAFVVIGASQNFPFGGTSILIMVGVGLQTVKQ
+VNAQMEQRHYEGLLR*
+>NZ_CP083691.1_1085
+MFKAIARIVRTQDLRRKILFTLALVAVYRLGAFIPAPGVDYAAVRQCLAAGSAQGGLYSF
+VNMFSGGALLQVSIFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TIALAVLQGTTMASLARTGALLGCRVPLLHDQSIATVLLVVVVLTTGCVIVMWLGERITE
+NGIGNGMSLLIFASIAAGFPAGIGQVLQTQGWRTFAIVMVVGLLTMLAVVFVEESQRRIP
+VQYAKRQIGTRTVGGTSTFIPIKVNMANVIPVIFASSVLMLPGILAQFNTPQDGSAPPAW
+VSFLSTYFVGGDHPLYMALYLLMIIGFTYFYVSITFNPQEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLPGALYLGIVAMIPLIAFVLIGANQNFPFGGTSILIMVGVGLQTVKQ
+ISAQMEQRHYEGLLR*
+>NZ_CP097650.1_1580
+MLKAIARIVRTPDLLRKIAFTLGLIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPGILIQFNTPQDGSAPAPW
+ITWLSRYFGSGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITFVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001413.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001413.fa
new file mode 100644
index 0000000000000000000000000000000000000000..897f5d6bee03f08141f05725b8834585d7976ea9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001413.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1680
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRAITSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK*
+>NZ_CP033200.1_1398
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK*
+>NZ_CP040019.1_1127
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAAGAAGGDAAAAEEKD
+EFDVVLESAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLEG
+AGATVTLK*
+>NZ_CP083691.1_1055
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAMAAAGAPAGGDAAAAEEKD
+EFDVILEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLEG
+AGATVTLK*
+>NZ_CP097650.1_1609
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001421.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001421.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2af93dcd8891a5d4b797de2bb58511091c3943ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001421.fa
@@ -0,0 +1,42 @@
+>NZ_CP042169.1_1688
+MPTPSAPAPAPRPPLMRHGADRPVSGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALY
+VWLWLLVPEEGPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG
+LAVDWALVGPVAVLVIGLGLAWMQLDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGA
+VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVL
+QSLALIQRRAQDADAVARVARAQERELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGAR
+VEVVAVGRAAGAWLEPLAAAAREAMQNAARHAGDAQVFAEAGEDDRGRTVAEVFVRDRGP
+GFDLPTVPADRLGVRESILGRMGRAGGTARIRSGPGGTEVHLTLAEPEGARARTGQEHP*
+>NZ_CP033200.1_1406
+MPTPSAPAQAPRPPLMRHGADRPVSGVAAGLARHLGVPVGRVRAALALLSLMGGAGLALY
+VWLWLLMPEEGPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG
+LAVDWALVGPVAVLVIGLGLAWMQLDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGA
+VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQVQRAEIAAHLHDSVL
+QSLALIQRRAHDADAVARVARAQERELRQFLALDSRGGPRSLAEALEEHAAAVEDAHGSR
+VEVVAVGRAAGAWLEPLAAAAREAMQNAARHAGDAQVFAEAGEDDHGRTVAEVFVRDRGP
+GFDLHTVPADRLGVRESILGRMERAGGAARIRSGPGGTEVHLTLTEPEGARARAGQEHP*
+>NZ_CP040019.1_1119
+MPASAVPPSAPSGRAGPRRAAADDARTRPIGADPRTSEARASGTRAPLMRHRADRPVSGV
+AAGAARHLGLSPRTARAGFAVLALAGGAGLALYVWLWLLMPEEGADGAPTGEAPSLRGRA
+PEVLERVREGGWPVLLAAVVLGVGVITIADGLGLAVDWALVGPVAVLVIGLGLAWMQLDL
+AGGPPAGRVGRVVRLALGTALVLLAVLAIVLGGVTSGDLWLGLLVAVALIAGVAMVAMPY
+ALSWLRRRDAERTAFAVQAQRAEIAAHLHDSVLQSLALIQRRAHDPEAVARAARAQEREL
+RRFLALDDRGGHDSLAATLREHAAAVEDAHGRRVEVVAVGEASGAWLEPLTAAAREAMLN
+AARHAGDAQVFAEVAEDDDGRTVAEVFVRDRGPGFDPGAVPADRLGVRESVVGRMERAGG
+AARIRSGPGGTEVHLTLTRPDRVPPHAAQERP*
+>NZ_CP083691.1_1047
+MPAPAIPPPADLSARPALLRHAADRPVSGVAGGVARHLGLDPRLARAGFAVLALAGGAGI
+ALYAWLWLLMPEEGPDGAPAGPAPTLRGRAPEVLERLREGGWPILLAVVVLGVGVLTVAD
+GLGVPVDWALVGPVAVLVIGLGLAWMQLGAADGPEGGRWARRARLGLGTALVLLGVLAIV
+VGAVTAGDLWLGLLVAVALLAGGALVAMPFVLARRRRRDEERTGAAVRAQRDEIAAHLHD
+SVLQSLALIQRRADDPETVARVARAQERELRQFLALDSARAHGTLAEAVEDHAAAVEDAF
+GRRVEVVSVGEASGPWLEPLASAAREAMVNAARHAGDVQVFVEVSEDDGGRTLAEVFIRD
+RGTGFDLADVPADRLGVRESILGRMRRAGGTARIRSGPSGTEVQLSLADPGAPGVGLREG
+RGRA*
+>NZ_CP097650.1_1617
+MPTPSAPAPAPRPPLMRHGADRPVSGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALY
+VWLWLLMPEERPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG
+LAVDWALVGPVAVLVIGLGLAWMQLDLAGGSRAGRSGRLVRLVLGTALVLLAVLAIVLGA
+VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVL
+QSLALIQRRAQDADAVARVARAQERELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGAR
+VEVVAVGRAAGAWLEPLAAAAREAMQNAVRHAGDAQVFAEAGEDERGRTVAEVFVRDRGP
+GFDLHTVPADRLGVRESIVGRMERAGGTARIRSGPGGTEVHLTLTEPEGARARTGQEHP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001437.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001437.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f761f32adf83530b63e232c873a40e7606d3c25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001437.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1704
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPSFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA*
+>NZ_CP033200.1_1422
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPSFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA*
+>NZ_CP040019.1_1102
+MSTAPRLSELSKGETIGTRTVPLTRADLVAYAGASGDHNPIHWSPSFAERVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGQTGDDGAPVPGATLQVVGKVG
+AVDEAAGTVRIDLDVTNPDAEKPRVLTKAQAVVRLAEPAPAAGESA*
+>NZ_CP083691.1_1026
+MRAQSARPVLAELAKGQSIGSRTVPLTRAGLVAYAAASGDHNPIHWNQAFAASVGLPGVI
+AHGMLTMGAAVQLVTDWAGDPGAVVDYQTRFTAMVPVADTTGQTDDAGAPVPGAVLEVSG
+AVGAIDAEAGTVRIDLTVNDPAQAKPRVLTKAQALVRLTRAVETPEETA*
+>NZ_CP097650.1_1633
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPTFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTVRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001441.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001441.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89faadefdec73399d4edfd10dafe01079f529b2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001441.fa
@@ -0,0 +1,26 @@
+>NZ_CP042169.1_1708
+MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR*
+>NZ_CP033200.1_1426
+MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR*
+>NZ_CP040019.1_1098
+MPQNSEDRPLARGLGRAAGRAARSFQESQRADDARLRAERARLAAEDEERLSRRREDRER
+GLAERDAAESDAGLVHPLLRIARMYWLALTVVLAVVAGAFVWNGMRARESGEPVVDPLTG
+IESVGVLGGATGQFTMGVTVALFAAAALWGWIGLLRRRRSAIGTLTFIALLLAAPAFLRA
+NGLLIVLAVIMLVGAALLWLPPVRSRLRR*
+>NZ_CP083691.1_1022
+MADNSAENSSDRIARAAGRAARAFREGQDAERIRREQARAEAPRTADADGSRATGLRERA
+VRAAAQAAERAEPLKERVGHAAGEAGRSFKENQAQDAARLRGVREQVRADDDAARAERQA
+ERERALDARDETEAGRVHPLLRLTRLWWLAVSLLLLGLATAFVYNGVRADRDGGEVIDPV
+TGLQSIGPLGGATGQYTVGGVLAALALVTLWGWVGLLRRRRASLGTLTTVAVLLAIPAVL
+RPNPLFIVLGAAMAIGAVLLWLPPVRSRVRR*
+>NZ_CP097650.1_1637
+MPQNSEDRPLARGLGRAAGRATQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLAARDAAESDAGLVHPLLKVARLYWLAVTVVLVGIAGAFIWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001459.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001459.fa
new file mode 100644
index 0000000000000000000000000000000000000000..653547186e6b94f388369397161192e81014ac10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001459.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1731
+MSDPTPAVPGAARTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+EDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA*
+>NZ_CP033200.1_1449
+MSDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+EHDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQITRDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA*
+>NZ_CP040019.1_1076
+MSDPTPAVSGSARTDQAEARPNAGAAFGISLEEYLLPATRRIQLIGEDGTLLSPEEQGAE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+KQDWLFPTYRDTVAVIARGVPPLEVMVSYQGTWHQGYDPNEHHVSVQSTPLTTQLLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVDLCRQGQGPFLVEADTYRMQAHTN
+TDDPTRYREDAEVQEWEARDPLRRMTAYLESTGALTEEVSAEIAQAAEDVAKDLRDAMNA
+EAELDPLELFDHVYSVQTPQLAAQRAQLTEELSRSENQEA*
+>NZ_CP083691.1_998
+MTSTRPGPATPDTRTEAAAAFGITLEEYLLPAARRIQLISPEGELLPAEEQGTAPGHEYP
+LPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLGQDDWLF
+PTYRDTVAVIARGVAPLDVMVSFQGTWHQGYDPKEHRVSVQSTPLTTQLLHAVGMAKAAR
+LRGEDVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFLVQNNKFAISVPFAKQSAAPSL
+AHKAVGYGLAGERVDGNDLAALLAVLGRAVDLCREGKGPFLVEADTYRMQAHTNTDDPTR
+YREDSEVKEWEVRDPLRRMTAYLESTGALTAEVSTSIAKDAEDVAQQLRDAMNADVELDP
+LELFDHVYSVQTPQLAAQRAQLAEELSRSENKEA*
+>NZ_CP097650.1_1660
+MSDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVSLG
+EDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001463.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001463.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e471d75cce9f372aedc1e4e388322b0555adf82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001463.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1746
+MSTPQPDAARPDRDRLPEQVSDLFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF*
+>NZ_CP033200.1_1454
+MSTPQPDAARPDRDRLPEQVSDVFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF*
+>NZ_CP040019.1_1056
+MTETTPAAARDRLPEKVSDLFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPTVRI
+AFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQRIR
+GRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHVVAD
+LTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVALGAV
+NEAVDHERLEEVALEYAADINAQSPQALRMLKFAFNLADDGMAGQQVFAGEATRMAYMTD
+EAVEGRDAFLQKRDPDWSAFPYHF*
+>NZ_CP083691.1_991
+MPAVRFSNDSIPGGIHVTNENAVVATTVLSMTESTPHHDRDRLPEKVSDVFDPTRWRVVE
+GFEFEDMTYHRQVERDADGRWVRDLPTVRIAFDRPEVRNAFRPGTVDELYRALDHARMTP
+DVGTVLLTGNGPSPKDGGHAFCSGGDQRIRGRDGYRYAEGETAETIDPARAGRLHILEVQ
+RLMRNSPKVVIAVVNGWAAGGGHSLHVVADLTLASRQHGKFKQTDATVGSFDAGYGSALL
+AREVGQKRAREIFFTAREYSAEEMVAMGAVNEAVDHERLEEVALEYAADINRQSPQAIRM
+LKFAFNLPDDGMAGQQVFAGEATRMAYMTDEAVEGRDAFLQKRDPDWSAFSYYF*
+>NZ_CP097650.1_1667
+MSTPQPDAARPDRDRLPEQVSDIFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYHALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEKMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001471.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001471.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4419d3b4e6cfb3924b69233628b651de82e3d252
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001471.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1758
+MTADLPAATARVQLLVKPGCHLCAEAEATVVQVCDARGEAWEAVDGAAHPDLLERFVDEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRA*
+>NZ_CP033200.1_1466
+MTADLPAATARVQLLVKPGCHLCAEAEATVAQVCDARGEAWEAVDGAAHPALLERFADEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRA*
+>NZ_CP040019.1_1045
+MSTLLPASAARVQLLVKPGCHLCEDAAATVAQVCGARGEAWEAVDGAAHPDLLERFVDEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRP*
+>NZ_CP083691.1_979
+MAAMMTPPASAARVQLLVKPGCHLCAEAEAVVAEVCDARGTAWERVDGPAHPDLLETYAE
+EVPVLFVDGVQRDFWRVDAQRLGRLLDGPAA*
+>NZ_CP097650.1_1679
+MTADLPAATARVQLLVKPGCHLCAEAEAAVAQVCDARGEAWEAVDGAAHPALLERFADEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001481.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001481.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b68904d91bc29ff69b9ffcaf22f8f4d1046e9e9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001481.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1768
+MSTAALSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYVRGTREHPAFRDLEVKWSDGSAADFPRLSVKLKPELVAFGAPERVTVDADGVVGTGER
+LTPAQVDALVAERAGSANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCEAPTSALRNCADPACTTLEVRCAACAVDDPERRCPVCVHH
+PHPAERTEA*
+>NZ_CP033200.1_1476
+MSTAPLSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYMRGTREHPAFRDLEVKWSDGSAADFPRLSVKVKPELVAFGAPERVTVDADGIVGTGER
+LTPVQVDALVAERAGTANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCHAPTSALRNCADPACTTLEVRCAACAVDDLEHRCPFCAHR
+PHPAERTEA*
+>NZ_CP040019.1_1030
+MSPAPVSRIALYYRFAPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+QYVKGTREHPALKDLEVKWSDGSAADFPRLSVKVRPELVAFGVPERITVDEHGVVGTGER
+LTPERLEALVAERAGTENPVRFLDGRNTVEAQIGRFDGAVVPAAHTTRDLLAAVDSGSLD
+HLRDAPLVTYCTGGVRCEVLSALLKDRGFREVYQLDGGIVRYGEAFGDAGLWRGELAVFD
+RRIALRFSEDAETIGRCVTCEAPTSALRNCSDPACTTLEVRCAACAAADPDRRCPVCTER
+SAA*
+>NZ_CP083691.1_968
+MTAAAPAAPTPLPAPGGPGRIALYYRFTPLADPEAVRLWQRTLAVSLGLAGRIIVSPQGI
+NGTVGGPAEAVKRYVRGTREHPAFRGLEVTWSDGSAADFPRLSVKVRPELVAFGAPERIR
+VDEHGVVGTGEHLPADQLHALVAERAAQGRPVRFLDGRNSVEAAIGRFEDAVIPAAHTTR
+DLLEAVDSGSLDHLKDQPVVTYCTGGVRCEVLSALLKDRGFSEVYQLDGGIVRYGEAHGD
+AGLWHGRLAVFDRRLSLAFTDGAETLGRCVTCGGATSHLANCADPACTTLQVRCPDCVAA
+HPDHVCPRCLERTPA*
+>NZ_CP097650.1_1689
+MSTAALSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYVRGTREHPAFRDLEVKWSDGSAADFPRLSVKLKPELVAFGAPERVTVDADGVVGTGER
+LTPAQVDALVAERAGSANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCEAPTSALRNCADPACTTLEVRCAACAVDDPERRCPVCVHH
+PHPAERTEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001482.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001482.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c6877c7af233dada73f542a47480970b486ce4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001482.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1769
+MRDGRGLARTGLTPYPSDMTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPAH
+MIPGGSGRATVDVPATWEHVVVNPSRAELEDLREAVRDQEQILLTVFGDAGEDPKAMGLK
+AQAEPERFMTMDMDPELQDVEPPLLPEGYEARVDQPMEGSRRLRILAVGASTAPEGEEEL
+AALGWVTEEDGTAVYDRIWTSPNHRRRGLGSLVMRYLTSEVMSEGEISRGLLVASPDGQK
+LYRHLAWTDLGPVSIWGRGLAEDNPTAEHTGTMGA*
+>NZ_CP033200.1_1477
+MTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPACMIPGGSGRATVDVPATWE
+HVVVNPSRGELEDLREAVRDQEQILLTVFGDAGEDPKAMGLKAQAEPERFMTMDMDPELQ
+DVEPPLLPEGYEARVDQPMEGSRRLRILAVGASTVPEGEEELAALGWVTEEGGTAVYDRI
+WTSPNHRRRGLGSLVMRYLTSEVMSEGEISRGLLVASPDGQKLYRHLAWTDLGPVSIWGR
+GLAEDNPAAEHTGTMGA*
+>NZ_CP040019.1_1029
+MSEHLDTALVDTWFAAWSRSRGYRTSPEAGRRAALRTRRPARMIPGGSGRATVDVPATWE
+YVVVDPTREQLEELREALRDEEQILLTVFGDAGADPKAMGLTPQAEPERFMSMDMDPEVQ
+DVEPPLLPDGYEARVDQPMEGSVRVRIMAVGASTAPEGEEELAALGWVTREDGTAVYDRI
+WTSPNHRRRGLGSLVMRYLTSEVMSDGEISLGLLVASPDGRKLYEHLAWTDLGPVSIWGR
+GLAADTPTAEHTGTMGA*
+>NZ_CP083691.1_967
+MTQSIDDTLVGTWFAAWSRSRGYETRIEDGMRSALRKKRSAQRIPGGAGRAAMDIPTTWE
+HVLVSPDADALAPALASLEEQPDRLVTVFGETDQDLTSAGLHSAVLPERFMSMELDREVQ
+DVEPPLLPEGYEAHVDEPRPGSRRVRFYAAGALSGVPEGEEELAALGWVTFEGETAVFDR
+IWTSPDHRRRGLGSLVMRHLTSEALGADDELERGLLVASPDGQKLYGHLGWTDLGPVRIW
+TRADGEAPGAEHTGTMAR*
+>NZ_CP097650.1_1690
+MRDGRGLARTGLTPYPSDMTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPAH
+MIPGGSGRATVDVPATWEHVVVNPSRAELEDLREAVRDQEQILLTVFGDAGEDPKAMGLK
+AQAEPERFMTMDMDPELQDVEPPLLPEGYEARVDQPMEGSRRLRILAVGASTAPEGEEEL
+AALGWVTEEDGTAVYDRIWTSPNHRRRGLGSLVMRYLTSEVMSEGEISRGLLVASPDGQK
+LYRHLAWTDLGPVSIWGRGLAEDNPTAEHTGTMGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001509.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001509.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f4ad1ce73bb97c0800b2f4d42ee6f7c9a41ebd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001509.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1802
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+APPARTTPTERTPEQ*
+>NZ_CP033200.1_1509
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFAALLSMLGTGVLGLIVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+TPPARTTSTERTPEQ*
+>NZ_CP040019.1_991
+MTTGPERSQHQHAYTVRRAPRLAAVLAVALALGLVIALVITTAVHGSPTPPADPYSGIPL
+SFSETFGFAALLSMLGTGVLGLVVWLLLDRRSRATTRTVVLERTDDPAAADIRLDRSAAD
+ALRSRTAPTERTPEQ*
+>NZ_CP083691.1_934
+MTSGPERSTPSAPQQQEYVLRRAPRLSAAVIVSALVGVVLALLGTAAVHAGPQPPADPYS
+GMPLSFASTFGYMVVAAVLACLVLGLLVWLLLDRRSRRTQRTVLLERTDDPAAADVALPR
+PEAVAPAARPAADPSDGRTPEQ*
+>NZ_CP097650.1_1722
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+APPARTTPTERTPEQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001548.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001548.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07300eb111dfc6c8e12df7ed7c8f01f8766c4f82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001548.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1850
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATDAAPASDASPA
+ASTADGQAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVS
+GEDGQMVMQESPDGFTVPAGGSLELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLE
+VTSVVRPFTGANESYHGGQSHESEDHADH*
+>NZ_CP033200.1_1557
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATGASSAASTADG
+QAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVSGEDGQM
+VMQQSPDGFTVPAGGSFELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLEVTSVVR
+PFTGANESYHGGESHESEDHADH*
+>NZ_CP040019.1_937
+MTTPRSARCLSAAAVMAAAALGLTACAGGADDAASSSSSAPTAATSSAPAEGQGAPLTVS
+DPWTKATEDGMTGSFGLLENSSDEDLHVVGVSAEVGAKAGLHVMVADEDGQMVMQQSPDG
+FTVPAGGSFELAPGGAHVMLMGLTEPIEPGEEVAYELELEDGSTVEVVSVARPYTGANES
+YDGGEAEESDEHADH*
+>NZ_CP083691.1_876
+MTMKHPSQTVSRRLSLAALAAAGSLALAACGGASAPASSSSSAAASSATATTPEAAGSAA
+SSSATAADSSAAPLTMTDAWTKATDGAMTGSFGTLENTSDAPVHVVAVTSDRTDRVELHE
+MAADGKGQMTMQQSPDGFTVPAGGTFELVPGGDHVMFMGLTQPVKAGAEVSYTLKTEDGR
+TLEVTSVARPFTGADESYHGGEASSSMSGMGMNSSMPAGSGHADH*
+>NZ_CP097650.1_1770
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATDASPAASTADG
+QAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVSGEDGQM
+VMQQSPDGFTVPAGGSFELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLEVTSVVR
+PFTGANESYHGGDSHESEGHADH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001554.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001554.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0beac9cb82e034f3c5e4e8700fc5bfa4c4fb758e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001554.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1856
+MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID
+VRGIDAVVADLIAKGVKL*
+>NZ_CP033200.1_1563
+MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVMLTLSAKGIKTID
+VRGIDAVVADLIAKGVKL*
+>NZ_CP040019.1_931
+MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID
+VRGIDAVVADLIAKGVKL*
+>NZ_CP083691.1_870
+MAAHCQVTGAGPGFGHSISHSHRRNKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID
+VRGIDAVVADLISKGVKL*
+>NZ_CP097650.1_1776
+MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID
+VRGIDAVVADLIAKGVKL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001566.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001566.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9100ca22be853676850a5570d135dd4f50cfdbec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001566.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1875
+MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM
+VRTGLWDEIRRRGWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD
+VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP
+LPHTWDLDTVRRG*
+>NZ_CP033200.1_1583
+MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM
+VRTGLWDEIRRRGWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD
+VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP
+LPHTWDLDTVRRG*
+>NZ_CP040019.1_911
+MHLIPRTLWVLARARRRPPLSIWDSASLPMRALPTDVDIAGHVNNGQYFGLFDLGRFDLM
+ARSGLMRAVRRRGWLPVVQAEQIAFRRSVTLGTAFTLETRIIGLDERAVWFEQRVVVAGD
+VAVRGYVCTRLRGRDGTPVGNDEVRALAVELGHDPAAEPELPGWLHDWREQVALPSARTP
+LPHAWGR*
+>NZ_CP083691.1_844
+MLHLLPRTALVVVRARRRPRLGIWEASTLPLRALPTDVDFAGHINNGQYFGLFDLGRFDL
+MVRAGVWDGAKRRGWLPVVQAEQIAFRRSVTLGTRFTVESRIIGLDERAVWFEQRAVVDG
+DVAVRAFICTRLRAKDGTPVSNEDVRDLARELGHDLAAEPVLPEWLHGWRSDIALPSART
+PLPHAWGTPAPAGV*
+>NZ_CP097650.1_1795
+MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM
+VRTGLWDEIRRRHWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD
+VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP
+LPHTWDLDTVRRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001601.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001601.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d09931ac0c0545efd9c481425862c3a4f841573
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001601.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1937
+MTEKTSIEARKPAGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHAIADIMETRGNQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG*
+>NZ_CP033200.1_1643
+MTEKTSIEARKPEGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPQGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG*
+>NZ_CP040019.1_848
+MTEINDRKPEGLPDLIRHYIDGQSVDSVDGDTFDVLDPVTNQPYIKAASGKTADVDKAVA
+AAKAAFESGVWSQALPRERSRVLHKIADIMETRGDQLAAMECFDTGLPIKQAKGQAARAA
+ENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAIATG
+NSVVLKPAEFTPLSASLWPGIFEEAGLPKGVFNMVHGFGEEGFAGDPLVKHPDVPLISFT
+GESRTGQIIFGNAAPHLKGLSMELGGKSPAVVFADADLDAAIDATIFGVFSLNGERCTAG
+SRILVAREVYDEFVERYAAQASRVKVGMPNDETTEVGAIVHPEHFEKVMSYVEIGKSEAH
+LVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDSDEEALELANNTK
+YGLAAYIWTNDLKRAHNFAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRSIDF
+YTDQQAVHINLGEVHNPVFGKQEQAAAKIDG*
+>NZ_CP083691.1_785
+MTEKTSIAARTPEGMPDVIRHYIDGEFVDSIDGDTFDVLDPVTNEPYIKAASGKSADVDA
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQAKGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPTGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKA
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNFAQDVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQESKETGDA*
+>NZ_CP097650.1_1864
+MTEKTSIEARKPQGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALELAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001612.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001612.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f9c262f38c782a9513684455e73f05a47be1a06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001612.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1953
+MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV
+PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL*
+>NZ_CP033200.1_1675
+MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV
+PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL*
+>NZ_CP040019.1_817
+MGENTAASNAWPLWEVFVRANRGLSHVHAGSLHAPDASLALRNARDLYTRRNEGTSVWVV
+PAEAIAASDPDSKGGFFESPQGKSYRHATYYQQSEGVPHL*
+>NZ_CP083691.1_753
+MTENTAPSNEWPLWEVFVRANRGLSHVHAGSLHAPDATMALRNARDLYTRRNEGTSVWVV
+PADAVAASDPDSKGGFFESPQGKSYRHATYYQKSEGVPHL*
+>NZ_CP097650.1_1892
+MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV
+PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001616.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001616.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff4f70b859984e9191ef3afee5259accd09b3538
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001616.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1957
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAKDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDRRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG*
+>NZ_CP033200.1_1679
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAEDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDHRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG*
+>NZ_CP040019.1_813
+MTVADGVAEVRLNAPKKMNSLDEAALADLHEAYRRAAAGVESGEVRAVLLHGEGRGFCAG
+RDISAVDPAEDDATAYLRDKVTPVLRAMSEIGVPTFAAVQGACLGVGLGLAIATDVVYVA
+EDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELISGEEAVRAGLFSRSVPA
+DELLEFTRAKAAKAAQGATLAFRASKELVRQIRDERVGLWESLDAENIAQGDLCNTADYA
+EGFKAFQEKRRPEFTGRG*
+>NZ_CP083691.1_749
+MIELAIADRVAVITLNAPQKMNSLDEQALADLADAYAQASAGAESGEVRAILLRGEGRGF
+CAGRDISNVVPADDDATAYLRDKVTPVLKAISEAPVPTFAAVQGACLGVGLGLAIASDVV
+YVAENAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELISGAEAVQAGLFSRA
+VPAEELDGFTREKVAKVADGATLAFRASKELVRQIRDRRVGLWESLDAENVAQGELCDTA
+DYAEGFTAFQEKRKPEFTGRP*
+>NZ_CP097650.1_1896
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAEDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDHRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001640.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001640.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49fb7c2353cb345ee91c7a4e115b9fd435c9d896
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001640.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_2002
+MSTSVPSSHDGHVRPAATTTADRPTDAGRPRRGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFAGPTAG
+FILGWIPSALIVGLIFWALTSRARPGLDAGRVALGAAVAGLIGGVVMVYFFGVLGFVGIA
+GMEFGAAVLSMAPFVPGDLIKLVVSVILIVGLWKAYPRAFR*
+>NZ_CP033200.1_1720
+MSTSVPSSHDGHVRPAATTTADRPTDAGRPRRGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFAGPTAG
+FILGWIPSALIVGLIFWALTSRARPGLGAGRVALGAAVAGLIGGVVMVYFFGVLGFVGIA
+GMEFGAAVLSMAPFVPGDLLKLVVSVILVVGLWKAYPRAFR*
+>NZ_CP040019.1_744
+MPTSDTLASGRPAHSTDDRRPRRSSAGSGLARVAVFAALMAVLGLVPPVPVAGIPAPIVL
+QNLAVTLAGVILGPWRGAAAILLFNVLVALGLPLLTGGRGGLGVFVGPSSGFILGYVVAA
+AAVGLVFWALTGRARPGLRPGRVLAAALVAGLVGMVVLYAAGAVGFIVAAHMEPGAAVLA
+MGAFVPGDTVKVVLAALLVTGLWKAYPRAFR*
+>NZ_CP083691.1_706
+MTSPSAPQTAVVDAPATHRPRRSPGADLARIAVMAALIAVLGAMPGIPVPGIPTPITLQT
+LGVMLAGLVLGAWRGAASVALFHLLVALGLPLLAGGRGGAAVFVGPSAGFLWGWIPGAFV
+VGLLFHLYLRGRRDGRNTGGLVAAALTACVVGGIAVIYLFGIPGMNLFGGVPLDKAAIGS
+LAFIPGDLLKAVVAALLAAGLWKAYPRAFA*
+>NZ_CP097650.1_1939
+MSTSVPSSHDGHVRPAATTTADRPADAGRPRHGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFNALVALGLPLLTGGRGGLGVFVGPSVG
+FILGWIPSAMIVGLIFWALTSRSRPGLSAGRIALAAAVAGLIGGVIMVYVFGAFGFVGVQ
+GMEFGAAMLSMAVFVPGDLTKLVIAVLLCAGLWKAYPRAFR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001644.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001644.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a48d21402516794c1b389220ff7b6fd33d7798d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001644.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_2026
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG*
+>NZ_CP033200.1_1743
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG*
+>NZ_CP040019.1_685
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQRRKRGERRAALSDLVGEASSAGLYGQNAESYREALRQARADLRGERG*
+>NZ_CP083691.1_595
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRAALSDLVAEASSAELYDQKAESYREALRQARADLRGERG*
+>NZ_CP097650.1_1966
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQRRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001647.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001647.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bae70bf9efdd764261e5c6bcf9a030016e524523
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001647.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_2029
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGTDRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAVTSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDNEETR*
+>NZ_CP033200.1_1746
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGTDRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAVTSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDNEETR*
+>NZ_CP040019.1_682
+MSHATLAPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDKHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEASRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLVATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQAHFVGPHRDLLERWAAAHAARDTEETR*
+>NZ_CP083691.1_592
+MSHATLVPSTVPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERETG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDTEETR*
+>NZ_CP097650.1_1969
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQAHFVGPHRDLLERWAAAHAARDTEETR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001667.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001667.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0aafe0b7624dba9cd9bc049fd9a1c4b2cd497719
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001667.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_2062
+MSVRSLLPDLGTSATGTPEAAVPPFARAVLWAHGDDAWRGEGGWTVLLDGPDRLRRLSAL
+WQAAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHVDADALA
+AAVAADRGARLLADGEVPLPADVADLAWDDAGYAAGVRELLTRMADSGGELAKVVISRTM
+TVPADDADLWRAIGELRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMPRGA
+DEEEDAALRERLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHLATS
+VRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQDGD
+GEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED*
+>NZ_CP033200.1_1782
+MGAMSVRSLLPDLGAPATGAPEAAVPPFARAVLWAHGDDAWRGEGGWTVLLDGTDRLRRL
+SALWQTAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHVDAD
+ALAAAVAADRGARLLADGAVPLPAGVADRAWDDAGYAAGVRELLTRMADSGGELAKVVIS
+RTMTVPADDADLWRAIGELRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMP
+RGADEEEDAALRERLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHL
+ATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQ
+DGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED*
+>NZ_CP040019.1_646
+MSVPTLLPELGTAAAEAAVPPFARAVLWAHGDAAWRGDDGWTVLVDGPDRLRRLSALWQA
+AVAGREDPAAPVRGWVSAPFSDDSVEPAVLRVPARLRRSTASGIRETPQHVDAAALADAV
+AADGGGRLLPDGEVPLPADTSESAWDDAGYAAGVRELLARMAASDGALAKVVISRTLTVP
+ADDADLWRAIRALRREYPQTWVFAVGGLLGATPEILATRHAGLVGSRVLAGSLPRGEDEA
+EDAALRARLATDPRLGEEHRWAARSVLDALAPVVDLADPDPAPTVLTLPNVHHLATSVRG
+RLRDGRGTVLDVVAALHPTAAVGGTPTPEAVRVISEVEPVDRGRYAGPVGWLDQDGDGEI
+ALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKLLPMRRALGIDLD*
+>NZ_CP083691.1_563
+MPPVPSVAVAALAARALSPSGSAAGRVPAFARAVVWAREDTVRVGVGGHTVLLDGPDRLR
+RLSALWRAAVAARPEPASPALAWVSSAFDDASPVPSVLRVPARVLQAGPDGVVEVPVAMP
+REALAAAVAACPGARLTEAGEVPLPADDPALAWDDAGYAAGVEEVVARMEASAGALSKVV
+VSRTETVPAGEDRLWAAVDALRAEYPQTWTFAVGGLVGATPEMLATRRDGVVASRVLAGS
+LPRGVDEGDDARLRARLAADPRLLREHHWAARSVLDALAPVVELEDAHPAPFVLTLPNVH
+HLATDVRGRLRPGEGAVLDVVAALHPTAAVGGTPTAEALEVIRAVEPVDRGRYAGPVGWL
+DQDGDGEIALALRCGQQVPGGVRLQAGGGIVPGAAAEEEVVEVGVKLLPMRRALGVA*
+>NZ_CP097650.1_2001
+MGAMSVRSLLPDLGTPATGTPEAAVPPFARTVLWAHGDDAWRGEGGWTVLLDGTGRLRRL
+SALWQAAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHMDAD
+ALAAAVAADRGARLLADGAVPLPADVADRAWDDAGYAAGVRELLTRMADSDGELAKVVIS
+RTMTVPADDADLWRAIGALRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMP
+RGADEEEDAALRDRLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHL
+ATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQ
+DGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001669.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001669.fa
new file mode 100644
index 0000000000000000000000000000000000000000..068cfbe41975ddd1e6227b8fcaf75fc7e42ffbd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001669.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_2064
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR*
+>NZ_CP033200.1_1784
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR*
+>NZ_CP040019.1_644
+MSTLPTTTDAHDGADPCAGAHPPHAAHRDKDAHLTRLRRIEGQVRGIHRMVDEDVYCIDI
+LTQVAAVTKALQAMSLNLTSEHLRHCVAEAAVEAEASGRTELIDEKVAEATAAIGRLLR*
+>NZ_CP083691.1_561
+MEHDRHAGPGYSPQREAYLKRLKRIEGQVRGIHRMVEEDVYCIDVLTQVAAATKALHAVS
+LGLVEDHLRHCVAEAAVQAEAEGRTELIDEKVAEATAALGRLLR*
+>NZ_CP097650.1_2003
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001672.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001672.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd1b056e2b9dc5d9d22092de84b607ce93c6c3dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001672.fa
@@ -0,0 +1,14 @@
+>NZ_CP042169.1_2069
+MSAGQGATTAGPVIESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPARY
+RLLIGWRTLEDHTVAFRESDSFLAWRALVTPHLAQLPAATHWSAV*
+>NZ_CP033200.1_1789
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDKGATSFALSRQVEDPARY
+RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV*
+>NZ_CP040019.1_639
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAAELFRGARATSFALTRQVEDPARY
+RLLIGWRTLEDHTVGFRESEAFGQWRALVTPHLAQPPAATHWESVAAAF*
+>NZ_CP083691.1_556
+MEDPARYRLLIGWRTLEDHTVGFRESDAFLAWRALVTPHLAQPPAATHWSAV*
+>NZ_CP097650.1_2008
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPAHY
+RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001687.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001687.fa
new file mode 100644
index 0000000000000000000000000000000000000000..102622a62d6d08b48370dd61175c9f8c56d1c537
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001687.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_2085
+MPAPAATTTTTPPATPRERQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVD
+PRVGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQI
+LLGVFGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALAIVVLLP
+RLTTAVPATLVAVVVVTALVMAAGLAVPRVGDRGALPDALPVLGLPDVPLTWETLRLILP
+FSVGIAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTM
+MNVKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPA
+TLRAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDDGD
+AVTYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYARHG
+IHAEVTGLNEASAAMHARLTGRLGA*
+>NZ_CP033200.1_1805
+MPALPAAPPPALTPLQRQSVLRTLRSPRLLGTEVLAAVVVALALIPEAIAFSIIAGVDPR
+VGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQILL
+GVFGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALAIVVLLPRL
+TTAVPATLVAVVVVTALVMAAGLAVPRVGDRGALPDALPVLGLPDVPLTWETLRLILPFS
+VGIAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTMMN
+VKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPATL
+RAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDDGDAV
+TYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYARHGIH
+AEVTGLNEASAAMHARLTGRLGA*
+>NZ_CP040019.1_700
+MTPASTASARVAAPPNSREPSPEQLQSVRLTLRSPGRLKTEVLAGLVVALALIPEAIAFA
+LIAGVDPQVGLFAAATMAMTIAFVGGRPAMVSAATAATALVVAPLVASHGLDHLIAAVIL
+AGGLQVVLGLLGVAKLMRFVPRSVMVGFVNALAILIFTSQLPDLMGVPWLVYPLTALGLA
+IILLLPRVTTAVPAPLVAIVVVTVIVLLAGADVPTVGDKGRLPDSLPALLVPDVPFTLET
+LQLLFPYALGMAVVGLLESLMTAKLVDDITDTRSSKTRESWGQGVANVVSGLFGGMGGCA
+MVGQTMINVKASGARTRISTFMAGVFVLILSVTLGDVVALVPMAALVAVMIFVSLATFDW
+HSIRPSTLAFMPKSETAVMLVTVAATVLTHNLAIGVGLGVLAAMVMFAQRVSHLATVTRT
+LEGQGRDAVARYRVQGELFFASSNDLYTQFDYAGDPARVVIDFSQAHLWDASTIAALDAV
+EEKYRRHGATVEITGLNVASRAMRARMSGRLGGGH*
+>NZ_CP083691.1_538
+MPASPAAPPPALTPLQRQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVDPR
+VGLFASFTMAVTTAVVGGRPAMISAATGAVALVVAPLSHAHGLDHLIAAIILGGLIQVAL
+GLLGVARLIRFIPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALGIVLLLPRL
+TTAVPSTLVAIVVVTALVMAAGWSVPRVGDRGELPDALPGLFVPDVPLTWETLRLILPFS
+VGMAVVGLLESLLTAKLVDDVTDTRSDKTRESWGQGVANIVSGLFGGMGGCAVVGQTMMN
+VKANGARTRISTFLAGVLLLVLVVALGDLVGQIPMAALVGVMVFVAGAAFDWHSVRPATL
+RAMPRSETAVMLLTVLATVVTHNLAIGVGVGVLTAMVLFAQRVSRLARVERVVTDDNGGT
+AVYRVHGELFFASSNDLYSQFEYALDPPRVVIDLSAAHVWDASTVAALDAVVTKYAQHGI
+AAEVTGLNEASAAMHARLTGRTGA*
+>NZ_CP097650.1_2024
+MPALPAAPPPALTPPATPRERQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAG
+VDPRVGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVI
+QILLGVLGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALVIVVL
+LPRLTTAVPATLVAVVVVTSLVMAAGLTVPRVGDRGALPDALPALGLPDVPLTWETLWLI
+LPFSIGMAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQ
+TMMNVKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVR
+PATLRAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDD
+GDAVTYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYAR
+HGIHAEVTGLNEASAAMHARLTGRLGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001702.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001702.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c0a1f469163868ec7233973808ddd73044146b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001702.fa
@@ -0,0 +1,14 @@
+>NZ_CP042169.1_2105
+MTGSILDHPAPTTSRASDPAAERAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA
+LTAGAGLLAGAVAWATARPVLEDDAPGD*
+>NZ_CP033200.1_1830
+MTGSILDHPTPTTSRASDPAAEQAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA
+LTAGAGLLAGAVAWATARPVLEDDAPGD*
+>NZ_CP040019.1_580
+MTAAVVILGLSLFTQVEGLPRLLVTAASGLLAGAVTWSVTQPVLEDEVLHG*
+>NZ_CP083691.1_503
+MSAAPAPSPAAPAVPPVTAVPPAAREPEGTSPSDRERERGDAECLAFFLALVTAALVMAG
+LALATDLGPLLRVLLSLGASGLAGALTLAFTRPSLED*
+>NZ_CP097650.1_2050
+MTGSILDHPAPTTSRASDPAAERAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA
+LTAGAGLLAGAVAWATARPVLEDDAPGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001728.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001728.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d04f519acbd697626e450447fd702ee80df2ca3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001728.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_2145
+MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW
+ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV
+RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG*
+>NZ_CP033200.1_1870
+MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW
+ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV
+RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG*
+>NZ_CP040019.1_480
+MPSRLHLRPLTVADAEEMSAVLADPALYAHTGGEPPSEELLTQQFRIQTRGESADGSERW
+QNLIVVLEETGEAVGYVQATTPKDGGPTEVAWVIGVPWQGRGLGGEAAAQLVEHLAGQGV
+RELIADIAPGHAASEAVARHIGLEPSDVVVDGEVRWTGTVADRER*
+>NZ_CP083691.1_1274
+MTPPIHLRPLRPDDADEMVAVLADPALYTFTGGEPPTRGALSGQYAVQARGHSEDRSETW
+LNHLVVLDDTGEAVGYVQATIPVAGGAAEIAWVIGVPWQGRGHATAAARLLLDELARRGV
+SEVVADIHPGHAASAAVARRLGLRPTGHIVDGEQRWEGPVAVVDGAASAPGG*
+>NZ_CP097650.1_2090
+MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW
+ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV
+RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001746.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001746.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63e5f385db24b0895dfddd254dbffe56958944b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Single_Copy_Orthologue_Sequences/OG0001746.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_2226
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGGGGF*
+>NZ_CP033200.1_1929
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGSGGF*
+>NZ_CP040019.1_438
+MTEDYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQTVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLSEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLAIDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLASDAGGGPGGF*
+>NZ_CP083691.1_390
+MTEDYGDSGSYGGDRTPERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELTKVGGPAVLHELIQTVPTAANASFYAEI
+VAEKAVLRRLVSAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGSGGF*
+>NZ_CP097650.1_2167
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLASDAGGAGGF*